diff --git a/pathways/WP3844/WP3844.gpml b/pathways/WP3844/WP3844.gpml index 8b5bc671c..bc7917204 100644 --- a/pathways/WP3844/WP3844.gpml +++ b/pathways/WP3844/WP3844.gpml @@ -1,5 +1,5 @@ - + This pathway is based on figure 1 from Merritt et al. (See Bibliography). The PI3K-AKT-mTOR signaling pathway has been shown to have a significant correlation with the development of castration-resistant prostate cancer. The signaling pathway regulates many cellular processes such as protein synthesis, proliferation, survival, metabolism, and differentiation, all factors that would increase a cancerous cell's ability to survive. Scientists have explored the use of various inhibitors for different parts of the signaling pathway, and have been faced with varying success. @@ -353,16 +353,6 @@ Proteins on this pathway have targeted assays available via the [https://assays. - - prostate cancer - DOID:10283 - Disease - - - phosphatidylinositol 3-kinase-Akt signaling pathway - PW:0000232 - Pathway Ontology - disease pathway PW:0000013 @@ -378,6 +368,11 @@ Proteins on this pathway have targeted assays available via the [https://assays. PW:0000003 Pathway Ontology + + phosphatidylinositol 3-kinase-Akt signaling pathway + PW:0000232 + Pathway Ontology + 24759575 PubMed @@ -387,6 +382,11 @@ Proteins on this pathway have targeted assays available via the [https://assays. Merritt P Edlind Andrew C Hsieh + + prostate cancer + DOID:10283 + Disease + phosphatidylinositol 3-kinase signaling pathway PW:0000595 diff --git a/pathways/WP3844/WP3844.json b/pathways/WP3844/WP3844.json index 05f46b025..96bf0b707 100644 --- a/pathways/WP3844/WP3844.json +++ b/pathways/WP3844/WP3844.json @@ -3778,7 +3778,7 @@ "@base": "WP3844/" } ], - "author": "[AAR&Co, Fehrhart, AlexanderPico, Khanspers, Mkutmon, MaintBot, Liling, DeSl]", + "author": "[AAR&Co, Fehrhart, AlexanderPico, Khanspers, Mkutmon, MaintBot, Liling, DeSl, Eweitz]", "comments": [ { "content": "This pathway is based on figure 1 from Merritt et al. (See Bibliography). The PI3K-AKT-mTOR signaling pathway has been shown to have a significant correlation with the development of castration-resistant prostate cancer. The signaling pathway regulates many cellular processes such as protein synthesis, proliferation, survival, metabolism, and differentiation, all factors that would increase a cancerous cell's ability to survive. Scientists have explored the use of various inhibitors for different parts of the signaling pathway, and have been faced with varying success. \r\n\r\n\r\nProteins on this pathway have targeted assays available via the [https://assays.cancer.gov/available_assays?wp_id=WP3844 CPTAC Assay Portal]", @@ -3832,8 +3832,8 @@ "fa884", "c6e90" ], - "dataSourceVersion": "WP3844_r129324", - "displayName": "PI3K-AKT-mTOR signaling pathway and therapeutic opportunities in prostate cancer", + "dataSourceVersion": "WP3844_r129541", + "displayName": "PI3K-AKT-mTOR signaling and therapeutic opportunities in prostate cancer", "drawAs": "rect", "fill": "white", "fontSize": 12, @@ -3842,22 +3842,22 @@ "height": 771, "id": "WP3844", "kaavioType": "Group", - "lastModified": "20240326135839", - "name": "PI3K-AKT-mTOR signaling pathway and therapeutic opportunities in prostate cancer", + "lastModified": "20240510155153", + "name": "PI3K-AKT-mTOR signaling and therapeutic opportunities in prostate cancer", "organism": "Homo sapiens", "padding": 5, "pathwayVersion": "WP3844", - "standardName": "PI3K-AKT-mTOR signaling pathway and therapeutic opportunities in prostate cancer", + "standardName": "PI3K-AKT-mTOR signaling and therapeutic opportunities in prostate cancer", "stroke": "black", "strokeWidth": 0, "textAlign": "left", - "textContent": "Name: PI3K-AKT-mTOR signaling pathway and therapeutic opportunities in prostate cancer\nLast Modified: 20240326135839\nOrganism: Homo sapiens", + "textContent": "Name: PI3K-AKT-mTOR signaling and therapeutic opportunities in prostate cancer\nLast Modified: 20240510155153\nOrganism: Homo sapiens", "type": [ "Pathway", - "http://identifiers.org/pw/PW:0000232", "http://identifiers.org/pw/PW:0000013", "http://identifiers.org/pw/PW:0000605", "http://identifiers.org/pw/PW:0000003", + "http://identifiers.org/pw/PW:0000232", "http://identifiers.org/pw/PW:0000595" ], "verticalAlign": "top", diff --git a/pathways/WP3844/WP3844.png b/pathways/WP3844/WP3844.png index b20207bc9..1231650d7 100644 Binary files a/pathways/WP3844/WP3844.png and b/pathways/WP3844/WP3844.png differ diff --git a/pathways/WP3844/WP3844.svg b/pathways/WP3844/WP3844.svg index bacb91b6f..f1cfa3f5a 100644 --- a/pathways/WP3844/WP3844.svg +++ b/pathways/WP3844/WP3844.svg @@ -448,7 +448,7 @@ - + @@ -862,8 +862,8 @@ - Name: PI3K-AKT-mTOR signaling pathway and therapeutic opportunities in prostate cancer - Last Modified: 20240326135839 + Name: PI3K-AKT-mTOR signaling and therapeutic opportunities in prostate cancer + Last Modified: 20240510155153 Organism: Homo sapiens diff --git a/pathways/WP3893/WP3893-bibliography.tsv b/pathways/WP3893/WP3893-bibliography.tsv index b046c2ad0..2fb78326f 100644 --- a/pathways/WP3893/WP3893-bibliography.tsv +++ b/pathways/WP3893/WP3893-bibliography.tsv @@ -1,2 +1,2 @@ ID Database Citation -27547445 Pubmed "Lai D-M, Shu Q, Fan J. The origin and role of innate lymphoid cells in the lung. Mil Med Res. 2016 Aug 19;3:25. PubMed Europe PMC Scholia" +27547445 Pubmed "The origin and role of innate lymphoid cells in the lung. Lai DM, Shu Q, Fan J. Mil Med Res. 2016 Aug 19;3:25. PubMed Europe PMC Scholia" diff --git a/pathways/WP3893/WP3893-datanodes.tsv b/pathways/WP3893/WP3893-datanodes.tsv index 3d1d838b9..80bf9400d 100644 --- a/pathways/WP3893/WP3893-datanodes.tsv +++ b/pathways/WP3893/WP3893-datanodes.tsv @@ -1,55 +1,55 @@ Label Type Identifier Comment Ensembl NCBI gene HGNC UniProt Wikidata ChEBI InChI -IL15 GeneProduct ensembl:ENSG00000164136 ensembl:ENSG00000164136 ncbigene:3600 hgnc.symbol:IL15 uniprot:P40933 -IL12A GeneProduct ensembl:ENSG00000168811 ensembl:ENSG00000168811 ncbigene:3592 hgnc.symbol:IL12A uniprot:E9PGR3;uniprot:P29459;uniprot:O60595;uniprot:E7ENE1 -ID2 GeneProduct ensembl:ENSG00000115738 ensembl:ENSG00000115738 ncbigene:3398 hgnc.symbol:ID2 uniprot:Q53T66;uniprot:Q02363 -GATA3 GeneProduct ensembl:ENSG00000107485 ensembl:ENSG00000107485 ncbigene:2625 hgnc.symbol:GATA3 uniprot:P23771;uniprot:A0A2R8Y4T2;uniprot:A0A2R8Y2A9 -TNF GeneProduct ensembl:ENSG00000232810 ensembl:ENSG00000232810 ncbigene:7124 hgnc.symbol:TNF uniprot:Q5STB3;uniprot:P01375 -IL1B GeneProduct ensembl:ENSG00000125538 ensembl:ENSG00000125538 ncbigene:3553 hgnc.symbol:IL1B uniprot:C9JSC2;uniprot:C9JWV2;uniprot:C9JVK0;uniprot:P01584 -T-bet GeneProduct ensembl:ENSG00000073861 ensembl:ENSG00000073861 ncbigene:30009 hgnc.symbol:TBX21 uniprot:Q9UL17 -TNF GeneProduct ensembl:ENSG00000232810 ensembl:ENSG00000232810 ncbigene:7124 hgnc.symbol:TNF uniprot:Q5STB3;uniprot:P01375 -AHR GeneProduct ensembl:ENSG00000106546 ensembl:ENSG00000106546 ncbigene:196 hgnc.symbol:AHR uniprot:A0A2R8Y7G1;uniprot:P35869;uniprot:A0A024R9Z8 -IFNG GeneProduct ensembl:ENSG00000111537 ensembl:ENSG00000111537 ncbigene:3458 hgnc.symbol:IFNG uniprot:P01579 -IL6 GeneProduct ensembl:ENSG00000136244 ensembl:ENSG00000136244 ncbigene:3569 hgnc.symbol:IL6 uniprot:B5MCZ3;uniprot:C9J5B0;uniprot:B5MC21;uniprot:B4DNV3;uniprot:P05231;uniprot:B5MC14;uniprot:Q75MH2 -IL-7 GeneProduct ensembl:ENSG00000104432 ensembl:ENSG00000104432 ncbigene:3574 hgnc.symbol:IL7 uniprot:A0A0A0MTG5;uniprot:Q5FBX5;uniprot:Q5FBY6;uniprot:Q5FBY3;uniprot:P13232 -BCL11B GeneProduct ensembl:ENSG00000127152 ensembl:ENSG00000127152 ncbigene:64919 hgnc.symbol:BCL11B uniprot:L8B7P7;uniprot:Q9C0K0;uniprot:L8B567;uniprot:D3YTK1 -GFI1 GeneProduct ensembl:ENSG00000162676 ensembl:ENSG00000162676 ncbigene:2672 hgnc.symbol:GFI1 uniprot:Q99684 -TCF1 GeneProduct ensembl:ENSG00000135100 ensembl:ENSG00000135100 ncbigene:6927 hgnc.symbol:HNF1A uniprot:H0YND5;uniprot:A0A0A0MQU7;uniprot:A0A0A0MTK8;uniprot:F5H3Z5;uniprot:U3KQS6;uniprot:P20823;uniprot:F5H0K0 -NFIL3 GeneProduct ensembl:ENSG00000165030 ensembl:ENSG00000165030 ncbigene:4783 hgnc.symbol:NFIL3 uniprot:Q16649;uniprot:A0A024R241 -IL13 GeneProduct ensembl:ENSG00000169194 ensembl:ENSG00000169194 ncbigene:3596 hgnc.symbol:IL13 uniprot:P35225 -NFIL3 GeneProduct ensembl:ENSG00000165030 ensembl:ENSG00000165030 ncbigene:4783 hgnc.symbol:NFIL3 uniprot:Q16649;uniprot:A0A024R241 -IL-4 GeneProduct ensembl:ENSG00000113520 ensembl:ENSG00000113520 ncbigene:3565 hgnc.symbol:IL4 uniprot:D4HNR6;uniprot:Q5FC01;uniprot:U3LVN1;uniprot:P05112 -PLZF GeneProduct ensembl:ENSG00000109906 ensembl:ENSG00000109906 ncbigene:7704 hgnc.symbol:ZBTB16 uniprot:A0A024R3C6;uniprot:Q05516;uniprot:H0YGW2;uniprot:A0A0S2Z4J5;uniprot:F5H6C3 -GATA3 GeneProduct ensembl:ENSG00000107485 ensembl:ENSG00000107485 ncbigene:2625 hgnc.symbol:GATA3 uniprot:P23771;uniprot:A0A2R8Y4T2;uniprot:A0A2R8Y2A9 -IL17A GeneProduct ensembl:ENSG00000112115 ensembl:ENSG00000112115 ncbigene:3605 hgnc.symbol:IL17A uniprot:Q16552 -IL18 GeneProduct ensembl:ENSG00000150782 ensembl:ENSG00000150782 ncbigene:3606 hgnc.symbol:IL18 uniprot:A0A024R3E0;uniprot:Q14116 -TOX GeneProduct ensembl:ENSG00000198846 ensembl:ENSG00000198846 ncbigene:9760 hgnc.symbol:TOX uniprot:O94900 -IL-25 GeneProduct ensembl:ENSG00000166090 ensembl:ENSG00000166090 ncbigene:64806 hgnc.symbol:IL25 uniprot:Q9H293 -IL23A GeneProduct ensembl:ENSG00000110944 ensembl:ENSG00000110944 ncbigene:51561 hgnc.symbol:IL23A uniprot:Q9NPF7 -IL22 GeneProduct ensembl:ENSG00000127318 ensembl:ENSG00000127318 ncbigene:50616 hgnc.symbol:IL22 uniprot:Q9GZX6 -AREG GeneProduct ensembl:ENSG00000109321 ensembl:ENSG00000109321 ncbigene:374 hgnc.symbol:AREG uniprot:P15514;uniprot:D6RFX5 -EOMES GeneProduct ensembl:ENSG00000163508 ensembl:ENSG00000163508 ncbigene:8320 hgnc.symbol:EOMES uniprot:O95936 -IL15 GeneProduct ensembl:ENSG00000164136 ensembl:ENSG00000164136 ncbigene:3600 hgnc.symbol:IL15 uniprot:P40933 -IFNG GeneProduct ensembl:ENSG00000111537 ensembl:ENSG00000111537 ncbigene:3458 hgnc.symbol:IFNG uniprot:P01579 -IFNG GeneProduct ensembl:ENSG00000111537 ensembl:ENSG00000111537 ncbigene:3458 hgnc.symbol:IFNG uniprot:P01579 -ID2 GeneProduct ensembl:ENSG00000115738 ensembl:ENSG00000115738 ncbigene:3398 hgnc.symbol:ID2 uniprot:Q53T66;uniprot:Q02363 -TOX GeneProduct ensembl:ENSG00000198846 ensembl:ENSG00000198846 ncbigene:9760 hgnc.symbol:TOX uniprot:O94900 -RORA GeneProduct ensembl:ENSG00000069667 ensembl:ENSG00000069667 ncbigene:6095 hgnc.symbol:RORA uniprot:A0A0C4DFP5;uniprot:H0YLS5;uniprot:P35398;uniprot:H0YII6;uniprot:A0A0C4DG53;uniprot:A0A087X2G0 -IL-33 GeneProduct ensembl:ENSG00000137033 ensembl:ENSG00000137033 ncbigene:90865 hgnc.symbol:IL33 uniprot:O95760 -TSLP GeneProduct ensembl:ENSG00000145777 ensembl:ENSG00000145777 ncbigene:85480 hgnc.symbol:TSLP uniprot:A0A0C4DG43;uniprot:Q969D9 -IL-25 GeneProduct ensembl:ENSG00000166090 ensembl:ENSG00000166090 ncbigene:64806 hgnc.symbol:IL25 uniprot:Q9H293 -IL-5 GeneProduct ensembl:ENSG00000113525 ensembl:ENSG00000113525 ncbigene:3567 hgnc.symbol:IL5 uniprot:C9JQP9;uniprot:P05113 -IL-9 GeneProduct ensembl:ENSG00000145839 ensembl:ENSG00000145839 ncbigene:3578 hgnc.symbol:IL9 uniprot:P15248 -ID2 GeneProduct ensembl:ENSG00000115738 ensembl:ENSG00000115738 ncbigene:3398 hgnc.symbol:ID2 uniprot:Q53T66;uniprot:Q02363 -NFIL3 GeneProduct ensembl:ENSG00000165030 ensembl:ENSG00000165030 ncbigene:4783 hgnc.symbol:NFIL3 uniprot:Q16649;uniprot:A0A024R241 -T-bet GeneProduct ensembl:ENSG00000073861 ensembl:ENSG00000073861 ncbigene:30009 hgnc.symbol:TBX21 uniprot:Q9UL17 -T-bet GeneProduct ensembl:ENSG00000073861 ensembl:ENSG00000073861 ncbigene:30009 hgnc.symbol:TBX21 uniprot:Q9UL17 -IL-7 GeneProduct ensembl:ENSG00000104432 ensembl:ENSG00000104432 ncbigene:3574 hgnc.symbol:IL7 uniprot:A0A0A0MTG5;uniprot:Q5FBX5;uniprot:Q5FBY6;uniprot:Q5FBY3;uniprot:P13232 -IL12B GeneProduct ensembl:ENSG00000113302 ensembl:ENSG00000113302 ncbigene:3593 hgnc.symbol:IL12B uniprot:P29460 -IFNG GeneProduct ensembl:ENSG00000111537 ensembl:ENSG00000111537 ncbigene:3458 hgnc.symbol:IFNG uniprot:P01579 -IL12A GeneProduct ensembl:ENSG00000168811 ensembl:ENSG00000168811 ncbigene:3592 hgnc.symbol:IL12A uniprot:E9PGR3;uniprot:P29459;uniprot:O60595;uniprot:E7ENE1 -IL12B GeneProduct ensembl:ENSG00000113302 ensembl:ENSG00000113302 ncbigene:3593 hgnc.symbol:IL12B uniprot:P29460 -IFNG GeneProduct ensembl:ENSG00000111537 ensembl:ENSG00000111537 ncbigene:3458 hgnc.symbol:IFNG uniprot:P01579 -IL22 GeneProduct ensembl:ENSG00000127318 ensembl:ENSG00000127318 ncbigene:50616 hgnc.symbol:IL22 uniprot:Q9GZX6 -IL17A GeneProduct ensembl:ENSG00000112115 ensembl:ENSG00000112115 ncbigene:3605 hgnc.symbol:IL17A uniprot:Q16552 -IL23A GeneProduct ensembl:ENSG00000110944 ensembl:ENSG00000110944 ncbigene:51561 hgnc.symbol:IL23A uniprot:Q9NPF7 -IL1B GeneProduct ensembl:ENSG00000125538 ensembl:ENSG00000125538 ncbigene:3553 hgnc.symbol:IL1B uniprot:C9JSC2;uniprot:C9JWV2;uniprot:C9JVK0;uniprot:P01584 +IL15 GeneProduct ensembl:ENSG00000164136 "" ensembl:ENSG00000164136 ncbigene:3600 hgnc.symbol:IL15 uniprot:P40933 +IL12A GeneProduct ensembl:ENSG00000168811 "" ensembl:ENSG00000168811 ncbigene:3592 hgnc.symbol:IL12A uniprot:E9PGR3;uniprot:P29459;uniprot:O60595;uniprot:E7ENE1 +ID2 GeneProduct ensembl:ENSG00000115738 "" ensembl:ENSG00000115738 ncbigene:3398 hgnc.symbol:ID2 uniprot:Q53T66;uniprot:Q02363 +GATA3 GeneProduct ensembl:ENSG00000107485 "" ensembl:ENSG00000107485 ncbigene:2625 hgnc.symbol:GATA3 uniprot:P23771;uniprot:A0A2R8Y4T2;uniprot:A0A2R8Y2A9 +TNF GeneProduct ensembl:ENSG00000232810 "" ensembl:ENSG00000232810 ncbigene:7124 hgnc.symbol:TNF uniprot:Q5STB3;uniprot:P01375 +IL1B GeneProduct ensembl:ENSG00000125538 "" ensembl:ENSG00000125538 ncbigene:3553 hgnc.symbol:IL1B uniprot:C9JSC2;uniprot:C9JWV2;uniprot:C9JVK0;uniprot:P01584 +T-bet GeneProduct ensembl:ENSG00000073861 "" ensembl:ENSG00000073861 ncbigene:30009 hgnc.symbol:TBX21 uniprot:Q9UL17 +TNF GeneProduct ensembl:ENSG00000232810 "" ensembl:ENSG00000232810 ncbigene:7124 hgnc.symbol:TNF uniprot:Q5STB3;uniprot:P01375 +AHR GeneProduct ensembl:ENSG00000106546 "" ensembl:ENSG00000106546 ncbigene:196 hgnc.symbol:AHR uniprot:A0A2R8Y7G1;uniprot:P35869;uniprot:A0A024R9Z8 +IFNG GeneProduct ensembl:ENSG00000111537 "" ensembl:ENSG00000111537 ncbigene:3458 hgnc.symbol:IFNG uniprot:A0A7R8GUN6;uniprot:P01579 +IL6 GeneProduct ensembl:ENSG00000136244 "" ensembl:ENSG00000136244 ncbigene:3569 hgnc.symbol:IL6 uniprot:B5MCZ3;uniprot:C9J5B0;uniprot:B5MC21;uniprot:B4DNV3;uniprot:P05231;uniprot:B5MC14;uniprot:Q75MH2 +IL-7 GeneProduct ensembl:ENSG00000104432 "" ensembl:ENSG00000104432 ncbigene:3574 hgnc.symbol:IL7 uniprot:A0A0A0MTG5;uniprot:Q5FBX5;uniprot:Q5FBY6;uniprot:Q5FBY3;uniprot:P13232 +BCL11B GeneProduct ensembl:ENSG00000127152 "" ensembl:ENSG00000127152 ncbigene:64919 hgnc.symbol:BCL11B uniprot:L8B7P7;uniprot:Q9C0K0;uniprot:L8B567;uniprot:D3YTK1 +GFI1 GeneProduct ensembl:ENSG00000162676 "" ensembl:ENSG00000162676 ncbigene:2672 hgnc.symbol:GFI1 uniprot:Q99684 +TCF1 GeneProduct ensembl:ENSG00000135100 "" ensembl:ENSG00000135100 ncbigene:6927 hgnc.symbol:HNF1A uniprot:H0YND5;uniprot:A0A0A0MQU7;uniprot:A0A0A0MTK8;uniprot:F5H3Z5;uniprot:U3KQS6;uniprot:P20823;uniprot:F5H0K0 +NFIL3 GeneProduct ensembl:ENSG00000165030 "" ensembl:ENSG00000165030 ncbigene:4783 hgnc.symbol:NFIL3 uniprot:Q16649;uniprot:A0A024R241 +IL13 GeneProduct ensembl:ENSG00000169194 "" ensembl:ENSG00000169194 ncbigene:3596 hgnc.symbol:IL13 uniprot:P35225 +NFIL3 GeneProduct ensembl:ENSG00000165030 "" ensembl:ENSG00000165030 ncbigene:4783 hgnc.symbol:NFIL3 uniprot:Q16649;uniprot:A0A024R241 +IL-4 GeneProduct ensembl:ENSG00000113520 "" ensembl:ENSG00000113520 ncbigene:3565 hgnc.symbol:IL4 uniprot:D4HNR6;uniprot:Q5FC01;uniprot:U3LVN1;uniprot:P05112 +PLZF GeneProduct ensembl:ENSG00000109906 "" ensembl:ENSG00000109906 ncbigene:7704 hgnc.symbol:ZBTB16 uniprot:A0A804HJ45;uniprot:A0A804HIC1;uniprot:A0A024R3C6;uniprot:Q05516;uniprot:H0YGW2;uniprot:A0A0S2Z4J5;uniprot:F5H6C3 +GATA3 GeneProduct ensembl:ENSG00000107485 "" ensembl:ENSG00000107485 ncbigene:2625 hgnc.symbol:GATA3 uniprot:P23771;uniprot:A0A2R8Y4T2;uniprot:A0A2R8Y2A9 +IL17A GeneProduct ensembl:ENSG00000112115 "" ensembl:ENSG00000112115 ncbigene:3605 hgnc.symbol:IL17A uniprot:Q16552 +IL18 GeneProduct ensembl:ENSG00000150782 "" ensembl:ENSG00000150782 ncbigene:3606 hgnc.symbol:IL18 uniprot:A0A024R3E0;uniprot:Q14116 +TOX GeneProduct ensembl:ENSG00000198846 "" ensembl:ENSG00000198846 ncbigene:9760 hgnc.symbol:TOX uniprot:O94900 +IL-25 GeneProduct ensembl:ENSG00000166090 "" ensembl:ENSG00000166090 ncbigene:64806 hgnc.symbol:IL25 uniprot:Q9H293 +IL23A GeneProduct ensembl:ENSG00000110944 "" ensembl:ENSG00000110944 ncbigene:51561 hgnc.symbol:IL23A uniprot:Q9NPF7 +IL22 GeneProduct ensembl:ENSG00000127318 "" ensembl:ENSG00000127318 ncbigene:50616 hgnc.symbol:IL22 uniprot:Q9GZX6;uniprot:A0A7R8C389 +AREG GeneProduct ensembl:ENSG00000109321 "" ensembl:ENSG00000109321 ncbigene:374 hgnc.symbol:AREG uniprot:P15514;uniprot:D6RFX5 +EOMES GeneProduct ensembl:ENSG00000163508 "" ensembl:ENSG00000163508 ncbigene:8320 hgnc.symbol:EOMES uniprot:O95936 +IL15 GeneProduct ensembl:ENSG00000164136 "" ensembl:ENSG00000164136 ncbigene:3600 hgnc.symbol:IL15 uniprot:P40933 +IFNG GeneProduct ensembl:ENSG00000111537 "" ensembl:ENSG00000111537 ncbigene:3458 hgnc.symbol:IFNG uniprot:A0A7R8GUN6;uniprot:P01579 +IFNG GeneProduct ensembl:ENSG00000111537 "" ensembl:ENSG00000111537 ncbigene:3458 hgnc.symbol:IFNG uniprot:A0A7R8GUN6;uniprot:P01579 +ID2 GeneProduct ensembl:ENSG00000115738 "" ensembl:ENSG00000115738 ncbigene:3398 hgnc.symbol:ID2 uniprot:Q53T66;uniprot:Q02363 +TOX GeneProduct ensembl:ENSG00000198846 "" ensembl:ENSG00000198846 ncbigene:9760 hgnc.symbol:TOX uniprot:O94900 +RORA GeneProduct ensembl:ENSG00000069667 "" ensembl:ENSG00000069667 ncbigene:6095 hgnc.symbol:RORA uniprot:A0A0C4DFP5;uniprot:H0YLS5;uniprot:P35398;uniprot:H0YII6;uniprot:A0A0C4DG53;uniprot:A0A087X2G0 +IL-33 GeneProduct ensembl:ENSG00000137033 "" ensembl:ENSG00000137033 ncbigene:90865 hgnc.symbol:IL33 uniprot:O95760 +TSLP GeneProduct ensembl:ENSG00000145777 "" ensembl:ENSG00000145777 ncbigene:85480 hgnc.symbol:TSLP uniprot:A0A0C4DG43;uniprot:Q969D9 +IL-25 GeneProduct ensembl:ENSG00000166090 "" ensembl:ENSG00000166090 ncbigene:64806 hgnc.symbol:IL25 uniprot:Q9H293 +IL-5 GeneProduct ensembl:ENSG00000113525 "" ensembl:ENSG00000113525 ncbigene:3567 hgnc.symbol:IL5 uniprot:C9JQP9;uniprot:P05113 +IL-9 GeneProduct ensembl:ENSG00000145839 "" ensembl:ENSG00000145839 ncbigene:3578 hgnc.symbol:IL9 uniprot:P15248 +ID2 GeneProduct ensembl:ENSG00000115738 "" ensembl:ENSG00000115738 ncbigene:3398 hgnc.symbol:ID2 uniprot:Q53T66;uniprot:Q02363 +NFIL3 GeneProduct ensembl:ENSG00000165030 "" ensembl:ENSG00000165030 ncbigene:4783 hgnc.symbol:NFIL3 uniprot:Q16649;uniprot:A0A024R241 +T-bet GeneProduct ensembl:ENSG00000073861 "" ensembl:ENSG00000073861 ncbigene:30009 hgnc.symbol:TBX21 uniprot:Q9UL17 +T-bet GeneProduct ensembl:ENSG00000073861 "" ensembl:ENSG00000073861 ncbigene:30009 hgnc.symbol:TBX21 uniprot:Q9UL17 +IL-7 GeneProduct ensembl:ENSG00000104432 "" ensembl:ENSG00000104432 ncbigene:3574 hgnc.symbol:IL7 uniprot:A0A0A0MTG5;uniprot:Q5FBX5;uniprot:Q5FBY6;uniprot:Q5FBY3;uniprot:P13232 +IL12B GeneProduct ensembl:ENSG00000113302 "" ensembl:ENSG00000113302 ncbigene:3593 hgnc.symbol:IL12B uniprot:P29460 +IFNG GeneProduct ensembl:ENSG00000111537 "" ensembl:ENSG00000111537 ncbigene:3458 hgnc.symbol:IFNG uniprot:A0A7R8GUN6;uniprot:P01579 +IL12A GeneProduct ensembl:ENSG00000168811 "" ensembl:ENSG00000168811 ncbigene:3592 hgnc.symbol:IL12A uniprot:E9PGR3;uniprot:P29459;uniprot:O60595;uniprot:E7ENE1 +IL12B GeneProduct ensembl:ENSG00000113302 "" ensembl:ENSG00000113302 ncbigene:3593 hgnc.symbol:IL12B uniprot:P29460 +IFNG GeneProduct ensembl:ENSG00000111537 "" ensembl:ENSG00000111537 ncbigene:3458 hgnc.symbol:IFNG uniprot:A0A7R8GUN6;uniprot:P01579 +IL22 GeneProduct ensembl:ENSG00000127318 "" ensembl:ENSG00000127318 ncbigene:50616 hgnc.symbol:IL22 uniprot:Q9GZX6;uniprot:A0A7R8C389 +IL17A GeneProduct ensembl:ENSG00000112115 "" ensembl:ENSG00000112115 ncbigene:3605 hgnc.symbol:IL17A uniprot:Q16552 +IL23A GeneProduct ensembl:ENSG00000110944 "" ensembl:ENSG00000110944 ncbigene:51561 hgnc.symbol:IL23A uniprot:Q9NPF7 +IL1B GeneProduct ensembl:ENSG00000125538 "" ensembl:ENSG00000125538 ncbigene:3553 hgnc.symbol:IL1B uniprot:C9JSC2;uniprot:C9JWV2;uniprot:C9JVK0;uniprot:P01584 diff --git a/pathways/WP3893/WP3893.gpml b/pathways/WP3893/WP3893.gpml index 44e5b6dfd..13414233d 100644 --- a/pathways/WP3893/WP3893.gpml +++ b/pathways/WP3893/WP3893.gpml @@ -1,5 +1,5 @@ - + Development and heterogeneity of the innate lymphoid cell (ILC) family. ILCs develop from distinct progenitors in the fetal liver or bone marrow and then develop into mature ILCs in the periphery. Different transcription factors and cytokines are involved in the development of the three groups of mature ILCs. All ILCs develop from CLPs, which can differentiate into NKps or CHILPs. CHILPs can further differentiate into LTi cells through α4β7+ populations or into other ILC populations through differentiation into ILCps. ILC1s express T-bet, are responsive to IL-12, and produce IFN-γ and/or TNF. ILC2s highly express GATA3, are responsive to IL-25, IL-33 and TSLP, and produce IL-4, IL-5, IL-9, IL-13 and amphiregulin. ILC3s express ROR-γt, are responsive to IL-1β and IL-23, and produce IL-17 and/or IL-22. Proteins on this pathway have targeted assays available via the [https://assays.cancer.gov/available_assays?wp_id=WP3893 CPTAC Assay Portal] @@ -227,276 +227,276 @@ Proteins on this pathway have targeted assays available via the [https://assays. - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + @@ -560,7 +560,7 @@ Proteins on this pathway have targeted assays available via the [https://assays. - + @@ -575,22 +575,22 @@ Proteins on this pathway have targeted assays available via the [https://assays. - + - + - + - + @@ -607,82 +607,95 @@ Proteins on this pathway have targeted assays available via the [https://assays. - + - + - + - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - common lymphoid progenitor - CL:0000051 - Cell Ontology + innate lymphoid cell + CL:0001065 + Cell Type + + + regulatory pathway + PW:0000004 + Pathway Ontology + + + + CL:0000623 + Cell Type 27547445 @@ -694,5 +707,16 @@ Proteins on this pathway have targeted assays available via the [https://assays. Shu Q Fan J + + common lymphoid progenitor + CL:0000051 + Cell Type + + + + CL:0000825 + Cell Type + + diff --git a/pathways/WP3893/WP3893.json b/pathways/WP3893/WP3893.json index 508878856..d2c09a926 100644 --- a/pathways/WP3893/WP3893.json +++ b/pathways/WP3893/WP3893.json @@ -1,27 +1,5 @@ { "entitiesById": { - "760741": { - "__HighlandStream__": true, - "_can_drain": false, - "_consume_waiting_for_next": false, - "_consumers": [], - "_delegate": null, - "_destructors": [], - "_events": {}, - "_eventsCount": 2, - "_in_consume_cb": false, - "_incoming": [], - "_is_observer": false, - "_nil_pushed": false, - "_observers": [], - "_outgoing": [], - "_repeat_resume": false, - "_send_events": false, - "id": "760741", - "paused": true, - "source": null, - "writable": true - }, "a107c": { "drawAs": "rect", "fill": "#ffffff", @@ -32,7 +10,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "a107c", - "isPartOf": "eab53", + "isPartOf": "df629", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -67,7 +45,7 @@ }, "a173f": { "cellularComponent": "Cell", - "drawAs": "rect", + "drawAs": "Ellipse", "fill": "transparent", "fontFamily": "Arial", "fontSize": 12, @@ -81,8 +59,6 @@ "overflow": "hidden", "padding": 8, "rotation": 0, - "rx": 15, - "ry": 15, "stroke": "#780fe1", "strokeStyle": "double", "strokeWidth": 3, @@ -104,6 +80,36 @@ "y": 220.30672268907574, "zIndex": 16388 }, + "a18b5": { + "contains": [ + "ebbd6", + "ca76f", + "f953a" + ], + "drawAs": "none", + "fill": "transparent", + "fillOpacity": 0.1, + "fontSize": 1, + "fontWeight": "bold", + "gpmlElementName": "Group", + "height": 76, + "id": "a18b5", + "kaavioType": "Group", + "padding": 8, + "stroke": "#808080", + "strokeDasharray": "5,3", + "strokeWidth": 0, + "textAlign": "center", + "type": [ + "Group", + "GroupGroup" + ], + "verticalAlign": "middle", + "width": 58, + "x": 779.4488432638751, + "y": 532.5244735159772, + "zIndex": 32768 + }, "a27ec": { "drawAs": "rect", "fill": "#ffffff", @@ -114,7 +120,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "a27ec", - "isPartOf": "afebf", + "isPartOf": "fcd2a", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -157,7 +163,7 @@ "gpmlElementName": "Label", "height": 20, "id": "a420d", - "isPartOf": "d65c1", + "isPartOf": "eba3e", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -179,6 +185,37 @@ "y": 48.5, "zIndex": 32803 }, + "a52e8": { + "contains": [ + "cabd1", + "cd163", + "e7431", + "db9f9" + ], + "drawAs": "none", + "fill": "transparent", + "fillOpacity": 0.1, + "fontSize": 1, + "fontWeight": "bold", + "gpmlElementName": "Group", + "height": 56, + "id": "a52e8", + "kaavioType": "Group", + "padding": 8, + "stroke": "#808080", + "strokeDasharray": "5,3", + "strokeWidth": 0, + "textAlign": "center", + "type": [ + "Group", + "GroupGroup" + ], + "verticalAlign": "middle", + "width": 110.00000000000051, + "x": 460.2310924369753, + "y": 337.80672268907574, + "zIndex": 32768 + }, "a55b2": { "drawAs": "rect", "fill": "#ffffff", @@ -189,7 +226,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "a55b2", - "isPartOf": "b75fe", + "isPartOf": "fd9dc", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -225,66 +262,6 @@ "y": 8, "zIndex": 32768 }, - "a5acf": { - "contains": [ - "b2b13", - "cb1e6" - ], - "drawAs": "none", - "fill": "transparent", - "fillOpacity": 0.1, - "fontSize": 1, - "fontWeight": "bold", - "gpmlElementName": "Group", - "height": 56, - "id": "a5acf", - "kaavioType": "Group", - "padding": 8, - "stroke": "#808080", - "strokeDasharray": "5,3", - "strokeWidth": 0, - "textAlign": "center", - "type": [ - "Group", - "GroupGroup" - ], - "verticalAlign": "middle", - "width": 57, - "x": 346.7310924369753, - "y": 327.80672268907574, - "zIndex": 32768 - }, - "a77fb": { - "contains": [ - "cabd1", - "cd163", - "e7431", - "db9f9" - ], - "drawAs": "none", - "fill": "transparent", - "fillOpacity": 0.1, - "fontSize": 1, - "fontWeight": "bold", - "gpmlElementName": "Group", - "height": 56, - "id": "a77fb", - "kaavioType": "Group", - "padding": 8, - "stroke": "#808080", - "strokeDasharray": "5,3", - "strokeWidth": 0, - "textAlign": "center", - "type": [ - "Group", - "GroupGroup" - ], - "verticalAlign": "middle", - "width": 110.00000000000051, - "x": 460.2310924369753, - "y": 337.80672268907574, - "zIndex": 32768 - }, "a7dc8": { "drawAs": "Brace", "fill": "transparent", @@ -295,7 +272,7 @@ "gpmlElementName": "Shape", "height": 15, "id": "a7dc8", - "isPartOf": "b5d85", + "isPartOf": "f1c02", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -319,7 +296,7 @@ }, "a8145": { "cellularComponent": "Cell", - "drawAs": "rect", + "drawAs": "Ellipse", "fill": "transparent", "fontFamily": "Arial", "fontSize": 12, @@ -328,14 +305,12 @@ "gpmlElementName": "Shape", "height": 43, "id": "a8145", - "isPartOf": "c9f0d", + "isPartOf": "b9a4d", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", "padding": 8, "rotation": 0, - "rx": 15, - "ry": 15, "stroke": "#ff6600", "strokeStyle": "double", "strokeWidth": 3, @@ -367,7 +342,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "a81e8", - "isPartOf": "e6561", + "isPartOf": "e7c0c", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -403,7 +378,7 @@ }, "a84b3": { "cellularComponent": "Cell", - "drawAs": "rect", + "drawAs": "Ellipse", "fill": "transparent", "fontFamily": "Arial", "fontSize": 12, @@ -412,14 +387,12 @@ "gpmlElementName": "Shape", "height": 43, "id": "a84b3", - "isPartOf": "c9f0d", + "isPartOf": "b9a4d", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", "padding": 8, "rotation": 0, - "rx": 15, - "ry": 15, "stroke": "#ff6600", "strokeStyle": "double", "strokeWidth": 3, @@ -451,7 +424,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "a8780", - "isPartOf": "dddac", + "isPartOf": "d07b9", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -496,7 +469,7 @@ "gpmlElementName": "Label", "height": 20, "id": "aa392", - "isPartOf": "e2ea1", + "isPartOf": "d30e3", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -528,7 +501,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "ab627", - "isPartOf": "d60e6", + "isPartOf": "da628", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -625,7 +598,6 @@ 0.5 ] }, - "id": "d26a0", "isAttachedTo": "f06fd", "orientation": [ 1, @@ -645,7 +617,6 @@ 0.5 ] }, - "id": "a84b0", "isAttachedTo": "f901e", "orientation": [ 1, @@ -678,7 +649,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "afa6c", - "isPartOf": "e2dc8", + "isPartOf": "fd9ba", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -712,11 +683,10 @@ "y": 28, "zIndex": 32768 }, - "afebf": { + "b1929": { "contains": [ - "a27ec", - "ef22b", - "ca28a" + "f3d37", + "db19c" ], "drawAs": "none", "fill": "transparent", @@ -724,8 +694,8 @@ "fontSize": 1, "fontWeight": "bold", "gpmlElementName": "Group", - "height": 75.99999999999955, - "id": "afebf", + "height": 56, + "id": "b1929", "kaavioType": "Group", "padding": 8, "stroke": "#808080", @@ -737,10 +707,10 @@ "GroupGroup" ], "verticalAlign": "middle", - "width": 56, - "x": 371.7310924369753, - "y": 485.80672268907574, - "zIndex": 32787 + "width": 61, + "x": 603.9361641018023, + "y": 602.8067226890753, + "zIndex": 32768 }, "b1c79": { "burrs": [ @@ -752,7 +722,7 @@ "id": "b1c79", "isAttachedTo": [ "e6987", - "f2a8d" + "ebc7e" ], "kaavioType": "Edge", "markerEnd": "Arrow", @@ -768,7 +738,6 @@ 1 ] }, - "id": "eaed0", "isAttachedTo": "e6987", "orientation": [ 0, @@ -788,8 +757,7 @@ 0 ] }, - "id": "e9c79", - "isAttachedTo": "f2a8d", + "isAttachedTo": "ebc7e", "orientation": [ 0, 1 @@ -820,7 +788,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "b1d8a", - "isPartOf": "bc878", + "isPartOf": "e48f6", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -891,7 +859,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "b2b13", - "isPartOf": "a5acf", + "isPartOf": "f7262", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -934,7 +902,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "b39b3", - "isPartOf": "e2dc8", + "isPartOf": "fd9ba", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -955,6 +923,7 @@ "Ensembl:ENSG00000111537", "Entrez Gene:3458", "HGNC:IFNG", + "UniProt:A0A7R8GUN6", "UniProt:P01579" ], "verticalAlign": "middle", @@ -1008,7 +977,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "b41fc", - "isPartOf": "cdb9e", + "isPartOf": "ca7c7", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -1082,7 +1051,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "b5c4d", - "isPartOf": "da975", + "isPartOf": "c8add", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -1116,36 +1085,6 @@ "y": 28, "zIndex": 32768 }, - "b5d85": { - "contains": [ - "a7dc8", - "bcbdf", - "f06fd" - ], - "drawAs": "none", - "fill": "transparent", - "fillOpacity": 0.1, - "fontSize": 1, - "fontWeight": "bold", - "gpmlElementName": "Group", - "height": 91.4598929181534, - "id": "b5d85", - "kaavioType": "Group", - "padding": 8, - "stroke": "#808080", - "strokeDasharray": "5,3", - "strokeWidth": 0, - "textAlign": "center", - "type": [ - "Group", - "GroupGroup" - ], - "verticalAlign": "middle", - "width": 117.8182098869579, - "x": 575.2310924369735, - "y": 443.30672268907574, - "zIndex": 16384 - }, "b5d8a": { "drawAs": "rect", "fill": "#ffffff", @@ -1156,7 +1095,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "b5d8a", - "isPartOf": "f6e8b", + "isPartOf": "c47ee", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -1217,7 +1156,6 @@ 1 ] }, - "id": "adf7f", "isAttachedTo": "dd31c", "orientation": [ 0, @@ -1237,7 +1175,6 @@ 0 ] }, - "id": "dcd7c", "isAttachedTo": "b8f1d", "orientation": [ 0, @@ -1259,35 +1196,6 @@ ], "zIndex": 32780 }, - "b75fe": { - "contains": [ - "a55b2", - "d40f2" - ], - "drawAs": "none", - "fill": "transparent", - "fillOpacity": 0.1, - "fontSize": 1, - "fontWeight": "bold", - "gpmlElementName": "Group", - "height": 55.99999999999977, - "id": "b75fe", - "kaavioType": "Group", - "padding": 8, - "stroke": "#808080", - "strokeDasharray": "5,3", - "strokeWidth": 0, - "textAlign": "center", - "type": [ - "Group", - "GroupGroup" - ], - "verticalAlign": "middle", - "width": 57, - "x": 175.2310924369753, - "y": 514.8067226890755, - "zIndex": 32768 - }, "b8084": { "drawAs": "rect", "fill": "transparent", @@ -1298,7 +1206,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "b8084", - "isPartOf": "fbfc4", + "isPartOf": "ea5f5", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -1361,6 +1269,7 @@ "Ensembl:ENSG00000111537", "Entrez Gene:3458", "HGNC:IFNG", + "UniProt:A0A7R8GUN6", "UniProt:P01579" ], "verticalAlign": "middle", @@ -1400,7 +1309,7 @@ }, "b8c17": { "cellularComponent": "Cell", - "drawAs": "rect", + "drawAs": "Ellipse", "fill": "transparent", "fontFamily": "Arial", "fontSize": 12, @@ -1414,8 +1323,6 @@ "overflow": "hidden", "padding": 8, "rotation": 0, - "rx": 15, - "ry": 15, "stroke": "#780fe1", "strokeStyle": "double", "strokeWidth": 3, @@ -1467,6 +1374,7 @@ "Ensembl:ENSG00000111537", "Entrez Gene:3458", "HGNC:IFNG", + "UniProt:A0A7R8GUN6", "UniProt:P01579" ], "verticalAlign": "middle", @@ -1479,6 +1387,36 @@ "y": 621.8067226890753, "zIndex": 32778 }, + "b9a4d": { + "contains": [ + "c4b57", + "a84b3", + "a8145" + ], + "drawAs": "none", + "fill": "transparent", + "fillOpacity": 0.1, + "fontSize": 1, + "fontWeight": "bold", + "gpmlElementName": "Group", + "height": 87, + "id": "b9a4d", + "kaavioType": "Group", + "padding": 8, + "stroke": "#808080", + "strokeDasharray": "5,3", + "strokeWidth": 0, + "textAlign": "center", + "type": [ + "Group", + "GroupGroup" + ], + "verticalAlign": "middle", + "width": 115, + "x": 819.2310924369732, + "y": 442.30672268907574, + "zIndex": 16384 + }, "bac5b": { "drawAs": "rect", "fill": "#ffffff", @@ -1489,7 +1427,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "bac5b", - "isPartOf": "fb0c5", + "isPartOf": "fb021", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -1528,9 +1466,38 @@ "y": 48, "zIndex": 32768 }, + "bb0b9": { + "contains": [ + "bd9ec", + "f2929" + ], + "drawAs": "none", + "fill": "transparent", + "fillOpacity": 0.1, + "fontSize": 1, + "fontWeight": "bold", + "gpmlElementName": "Group", + "height": 76.5, + "id": "bb0b9", + "kaavioType": "Group", + "padding": 8, + "stroke": "#808080", + "strokeDasharray": "5,3", + "strokeWidth": 0, + "textAlign": "center", + "type": [ + "Group", + "GroupGroup" + ], + "verticalAlign": "middle", + "width": 70, + "x": 126.73109243697502, + "y": 437.30672268907574, + "zIndex": 28672 + }, "bc6db": { "cellularComponent": "Cell", - "drawAs": "rect", + "drawAs": "Ellipse", "fill": "transparent", "fontFamily": "Arial", "fontSize": 12, @@ -1544,8 +1511,6 @@ "overflow": "hidden", "padding": 8, "rotation": 0, - "rx": 15, - "ry": 15, "stroke": "#780fe1", "strokeStyle": "double", "strokeWidth": 3, @@ -1567,38 +1532,9 @@ "y": 64.30672268907563, "zIndex": 16384 }, - "bc878": { - "contains": [ - "b1d8a", - "f1fb2" - ], - "drawAs": "none", - "fill": "transparent", - "fillOpacity": 0.1, - "fontSize": 1, - "fontWeight": "bold", - "gpmlElementName": "Group", - "height": 56, - "id": "bc878", - "kaavioType": "Group", - "padding": 8, - "stroke": "#808080", - "strokeDasharray": "5,3", - "strokeWidth": 0, - "textAlign": "center", - "type": [ - "Group", - "GroupGroup" - ], - "verticalAlign": "middle", - "width": 60, - "x": 649.7310924369732, - "y": 533.114330186319, - "zIndex": 32768 - }, "bcbdf": { "cellularComponent": "Cell", - "drawAs": "rect", + "drawAs": "Ellipse", "fill": "transparent", "fontFamily": "Arial", "fontSize": 12, @@ -1607,14 +1543,12 @@ "gpmlElementName": "Shape", "height": 48.4598929181534, "id": "bcbdf", - "isPartOf": "b5d85", + "isPartOf": "f1c02", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", "padding": 8, "rotation": 0, - "rx": 15, - "ry": 15, "stroke": "#ff6600", "strokeStyle": "double", "strokeWidth": 3, @@ -1671,7 +1605,7 @@ "gpmlElementName": "Label", "height": 20, "id": "bd9ec", - "isPartOf": "e871c", + "isPartOf": "bb0b9", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -1734,7 +1668,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "be7c5", - "isPartOf": "fb0c5", + "isPartOf": "fb021", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -1772,7 +1706,7 @@ }, "beafd": { "cellularComponent": "Cell", - "drawAs": "rect", + "drawAs": "Ellipse", "fill": "transparent", "fontFamily": "Arial", "fontSize": 12, @@ -1786,8 +1720,6 @@ "overflow": "hidden", "padding": 8, "rotation": 0, - "rx": 15, - "ry": 15, "stroke": "#ff6600", "strokeStyle": "double", "strokeWidth": 3, @@ -1835,7 +1767,6 @@ 1 ] }, - "id": "e5eef", "isAttachedTo": "beafd", "orientation": [ 0, @@ -1855,7 +1786,6 @@ 0 ] }, - "id": "c0c4a", "isAttachedTo": "e8be5", "orientation": [ 0, @@ -1912,7 +1842,7 @@ "id": "c12d5", "isAttachedTo": [ "e7a51", - "da975" + "c8add" ], "kaavioType": "Edge", "markerEnd": "Arrow", @@ -1928,7 +1858,6 @@ 1 ] }, - "id": "ee077", "isAttachedTo": "e7a51", "orientation": [ 0, @@ -1948,8 +1877,7 @@ 0 ] }, - "id": "a89f7", - "isAttachedTo": "da975", + "isAttachedTo": "c8add", "orientation": [ 0, 1 @@ -2001,6 +1929,35 @@ "y": 63.94707828004411, "zIndex": 16384 }, + "c47ee": { + "contains": [ + "b5d8a", + "fac23" + ], + "drawAs": "none", + "fill": "transparent", + "fillOpacity": 0.1, + "fontSize": 1, + "fontWeight": "bold", + "gpmlElementName": "Group", + "height": 56, + "id": "c47ee", + "kaavioType": "Group", + "padding": 8, + "stroke": "#808080", + "strokeDasharray": "5,3", + "strokeWidth": 0, + "textAlign": "center", + "type": [ + "Group", + "GroupGroup" + ], + "verticalAlign": "middle", + "width": 54, + "x": 646.7310924369732, + "y": 329.80672268907574, + "zIndex": 32768 + }, "c4b57": { "drawAs": "Brace", "fill": "transparent", @@ -2011,7 +1968,7 @@ "gpmlElementName": "Shape", "height": 15, "id": "c4b57", - "isPartOf": "c9f0d", + "isPartOf": "b9a4d", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -2130,7 +2087,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "c722e", - "isPartOf": "dddac", + "isPartOf": "d07b9", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -2167,6 +2124,35 @@ "y": 8, "zIndex": 32768 }, + "c8add": { + "contains": [ + "b5c4d", + "d01c1" + ], + "drawAs": "none", + "fill": "transparent", + "fillOpacity": 0.1, + "fontSize": 1, + "fontWeight": "bold", + "gpmlElementName": "Group", + "height": 56, + "id": "c8add", + "kaavioType": "Group", + "padding": 8, + "stroke": "#808080", + "strokeDasharray": "5,3", + "strokeWidth": 0, + "textAlign": "center", + "type": [ + "Group", + "GroupGroup" + ], + "verticalAlign": "middle", + "width": 62, + "x": 294.7310924369753, + "y": 603.8067226890753, + "zIndex": 32768 + }, "c947d": { "drawAs": "none", "fill": "transparent", @@ -2198,36 +2184,6 @@ "y": 180.5209481808158, "zIndex": 32814 }, - "c9f0d": { - "contains": [ - "c4b57", - "a84b3", - "a8145" - ], - "drawAs": "none", - "fill": "transparent", - "fillOpacity": 0.1, - "fontSize": 1, - "fontWeight": "bold", - "gpmlElementName": "Group", - "height": 87, - "id": "c9f0d", - "kaavioType": "Group", - "padding": 8, - "stroke": "#808080", - "strokeDasharray": "5,3", - "strokeWidth": 0, - "textAlign": "center", - "type": [ - "Group", - "GroupGroup" - ], - "verticalAlign": "middle", - "width": 115, - "x": 819.2310924369732, - "y": 442.30672268907574, - "zIndex": 16384 - }, "ca28a": { "drawAs": "rect", "fill": "#ffffff", @@ -2238,7 +2194,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "ca28a", - "isPartOf": "afebf", + "isPartOf": "fcd2a", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -2281,7 +2237,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "ca76f", - "isPartOf": "d79a1", + "isPartOf": "a18b5", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -2317,6 +2273,35 @@ "y": 28, "zIndex": 32806 }, + "ca7c7": { + "contains": [ + "d7ed8", + "b41fc" + ], + "drawAs": "none", + "fill": "transparent", + "fillOpacity": 0.1, + "fontSize": 1, + "fontWeight": "bold", + "gpmlElementName": "Group", + "height": 56, + "id": "ca7c7", + "kaavioType": "Group", + "padding": 8, + "stroke": "#808080", + "strokeDasharray": "5,3", + "strokeWidth": 0, + "textAlign": "center", + "type": [ + "Group", + "GroupGroup" + ], + "verticalAlign": "middle", + "width": 61, + "x": 845.7310924369732, + "y": 625.8067226890753, + "zIndex": 32809 + }, "cabd1": { "drawAs": "rect", "fill": "#ffffff", @@ -2327,7 +2312,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "cabd1", - "isPartOf": "a77fb", + "isPartOf": "a52e8", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -2373,7 +2358,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "cb1e6", - "isPartOf": "a5acf", + "isPartOf": "f7262", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -2491,7 +2476,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "cd163", - "isPartOf": "a77fb", + "isPartOf": "a52e8", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -2534,7 +2519,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "cd8fc", - "isPartOf": "dddac", + "isPartOf": "d07b9", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -2573,64 +2558,6 @@ "y": 28.000000000000114, "zIndex": 32768 }, - "cdb9e": { - "contains": [ - "d7ed8", - "b41fc" - ], - "drawAs": "none", - "fill": "transparent", - "fillOpacity": 0.1, - "fontSize": 1, - "fontWeight": "bold", - "gpmlElementName": "Group", - "height": 56, - "id": "cdb9e", - "kaavioType": "Group", - "padding": 8, - "stroke": "#808080", - "strokeDasharray": "5,3", - "strokeWidth": 0, - "textAlign": "center", - "type": [ - "Group", - "GroupGroup" - ], - "verticalAlign": "middle", - "width": 61, - "x": 845.7310924369732, - "y": 625.8067226890753, - "zIndex": 32809 - }, - "cedc7": { - "contains": [ - "f3d37", - "db19c" - ], - "drawAs": "none", - "fill": "transparent", - "fillOpacity": 0.1, - "fontSize": 1, - "fontWeight": "bold", - "gpmlElementName": "Group", - "height": 56, - "id": "cedc7", - "kaavioType": "Group", - "padding": 8, - "stroke": "#808080", - "strokeDasharray": "5,3", - "strokeWidth": 0, - "textAlign": "center", - "type": [ - "Group", - "GroupGroup" - ], - "verticalAlign": "middle", - "width": 61, - "x": 603.9361641018023, - "y": 602.8067226890753, - "zIndex": 32768 - }, "cf197": { "drawAs": "rect", "fill": "#ffffff", @@ -2641,7 +2568,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "cf197", - "isPartOf": "f2a8d", + "isPartOf": "ebc7e", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -2685,7 +2612,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "cf725", - "isPartOf": "dddac", + "isPartOf": "d07b9", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -2729,7 +2656,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "d00c9", - "isPartOf": "dddac", + "isPartOf": "d07b9", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -2773,7 +2700,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "d01c1", - "isPartOf": "da975", + "isPartOf": "c8add", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -2794,6 +2721,7 @@ "Ensembl:ENSG00000111537", "Entrez Gene:3458", "HGNC:IFNG", + "UniProt:A0A7R8GUN6", "UniProt:P01579" ], "verticalAlign": "middle", @@ -2806,6 +2734,39 @@ "y": 8, "zIndex": 32779 }, + "d07b9": { + "contains": [ + "a8780", + "c722e", + "cd8fc", + "d00c9", + "cf725", + "f5cb2" + ], + "drawAs": "none", + "fill": "transparent", + "fillOpacity": 0.1, + "fontSize": 1, + "fontWeight": "bold", + "gpmlElementName": "Group", + "height": 76.00000000000011, + "id": "d07b9", + "kaavioType": "Group", + "padding": 8, + "stroke": "#808080", + "strokeDasharray": "5,3", + "strokeWidth": 0, + "textAlign": "center", + "type": [ + "Group", + "GroupGroup" + ], + "verticalAlign": "middle", + "width": 118.00000000000006, + "x": 467.7310924369753, + "y": 104.80672268907563, + "zIndex": 32768 + }, "d21aa": { "drawAs": "rect", "fill": "#ffffff", @@ -2816,7 +2777,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "d21aa", - "isPartOf": "f2a8d", + "isPartOf": "ebc7e", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -2859,7 +2820,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "d2fc2", - "isPartOf": "d60e6", + "isPartOf": "da628", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -2896,6 +2857,35 @@ "y": 8, "zIndex": 32799 }, + "d30e3": { + "contains": [ + "e7a51", + "aa392" + ], + "drawAs": "none", + "fill": "transparent", + "fillOpacity": 0.1, + "fontSize": 1, + "fontWeight": "bold", + "gpmlElementName": "Group", + "height": 75.5, + "id": "d30e3", + "kaavioType": "Group", + "padding": 8, + "stroke": "#808080", + "strokeDasharray": "5,3", + "strokeWidth": 0, + "textAlign": "center", + "type": [ + "Group", + "GroupGroup" + ], + "verticalAlign": "middle", + "width": 70, + "x": 290.7310924369753, + "y": 439.30672268907574, + "zIndex": 28678 + }, "d3a76": { "drawAs": "none", "fill": "transparent", @@ -2937,7 +2927,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "d40f2", - "isPartOf": "b75fe", + "isPartOf": "fd9dc", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -3001,35 +2991,6 @@ "y": 68.21664829106918, "zIndex": 32817 }, - "d60e6": { - "contains": [ - "ab627", - "d2fc2" - ], - "drawAs": "none", - "fill": "transparent", - "fillOpacity": 0.1, - "fontSize": 1, - "fontWeight": "bold", - "gpmlElementName": "Group", - "height": 56, - "id": "d60e6", - "kaavioType": "Group", - "padding": 8, - "stroke": "#808080", - "strokeDasharray": "5,3", - "strokeWidth": 0, - "textAlign": "center", - "type": [ - "Group", - "GroupGroup" - ], - "verticalAlign": "middle", - "width": 90, - "x": 725.2310924369732, - "y": 341.216866018734, - "zIndex": 32768 - }, "d621a": { "drawAs": "rect", "fill": "#ffffff", @@ -3040,7 +3001,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "d621a", - "isPartOf": "fbfc4", + "isPartOf": "ea5f5", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -3074,35 +3035,6 @@ "y": 28, "zIndex": 32796 }, - "d65c1": { - "contains": [ - "dd31c", - "a420d" - ], - "drawAs": "none", - "fill": "transparent", - "fillOpacity": 0.1, - "fontSize": 1, - "fontWeight": "bold", - "gpmlElementName": "Group", - "height": 76.5, - "id": "d65c1", - "kaavioType": "Group", - "padding": 8, - "stroke": "#808080", - "strokeDasharray": "5,3", - "strokeWidth": 0, - "textAlign": "center", - "type": [ - "Group", - "GroupGroup" - ], - "verticalAlign": "middle", - "width": 70, - "x": 212.7310924369753, - "y": 438.30672268907574, - "zIndex": 28677 - }, "d7054": { "attachmentDisplay": { "offset": [ @@ -3128,36 +3060,6 @@ "width": 0, "zIndex": 12288 }, - "d79a1": { - "contains": [ - "ebbd6", - "ca76f", - "f953a" - ], - "drawAs": "none", - "fill": "transparent", - "fillOpacity": 0.1, - "fontSize": 1, - "fontWeight": "bold", - "gpmlElementName": "Group", - "height": 76, - "id": "d79a1", - "kaavioType": "Group", - "padding": 8, - "stroke": "#808080", - "strokeDasharray": "5,3", - "strokeWidth": 0, - "textAlign": "center", - "type": [ - "Group", - "GroupGroup" - ], - "verticalAlign": "middle", - "width": 58, - "x": 779.4488432638751, - "y": 532.5244735159772, - "zIndex": 32768 - }, "d7ed8": { "drawAs": "rect", "fill": "#ffffff", @@ -3168,7 +3070,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "d7ed8", - "isPartOf": "cdb9e", + "isPartOf": "ca7c7", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -3189,7 +3091,8 @@ "Ensembl:ENSG00000127318", "Entrez Gene:50616", "HGNC:IL22", - "UniProt:Q9GZX6" + "UniProt:Q9GZX6", + "UniProt:A0A7R8C389" ], "verticalAlign": "middle", "whiteSpace": "pre", @@ -3211,7 +3114,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "d9b86", - "isPartOf": "e6561", + "isPartOf": "e7c0c", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -3245,10 +3148,10 @@ "y": 8, "zIndex": 32768 }, - "da975": { + "da628": { "contains": [ - "b5c4d", - "d01c1" + "ab627", + "d2fc2" ], "drawAs": "none", "fill": "transparent", @@ -3257,7 +3160,7 @@ "fontWeight": "bold", "gpmlElementName": "Group", "height": 56, - "id": "da975", + "id": "da628", "kaavioType": "Group", "padding": 8, "stroke": "#808080", @@ -3269,9 +3172,9 @@ "GroupGroup" ], "verticalAlign": "middle", - "width": 62, - "x": 294.7310924369753, - "y": 603.8067226890753, + "width": 90, + "x": 725.2310924369732, + "y": 341.216866018734, "zIndex": 32768 }, "dace9": { @@ -3284,7 +3187,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "dace9", - "isPartOf": "fb0c5", + "isPartOf": "fb021", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -3327,7 +3230,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "db19c", - "isPartOf": "cedc7", + "isPartOf": "b1929", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -3348,6 +3251,7 @@ "Ensembl:ENSG00000111537", "Entrez Gene:3458", "HGNC:IFNG", + "UniProt:A0A7R8GUN6", "UniProt:P01579" ], "verticalAlign": "middle", @@ -3370,7 +3274,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "db9f9", - "isPartOf": "a77fb", + "isPartOf": "a52e8", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -3418,7 +3322,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "dc659", - "isPartOf": "f2a8d", + "isPartOf": "ebc7e", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -3453,7 +3357,7 @@ }, "dd31c": { "cellularComponent": "Cell", - "drawAs": "rect", + "drawAs": "Ellipse", "fill": "transparent", "fontFamily": "Arial", "fontSize": 12, @@ -3462,14 +3366,12 @@ "gpmlElementName": "Shape", "height": 43, "id": "dd31c", - "isPartOf": "d65c1", + "isPartOf": "eba3e", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", "padding": 8, "rotation": 0, - "rx": 15, - "ry": 15, "stroke": "#6666ff", "strokeStyle": "double", "strokeWidth": 3, @@ -3491,39 +3393,6 @@ "y": 8, "zIndex": 28677 }, - "dddac": { - "contains": [ - "a8780", - "c722e", - "cd8fc", - "d00c9", - "cf725", - "f5cb2" - ], - "drawAs": "none", - "fill": "transparent", - "fillOpacity": 0.1, - "fontSize": 1, - "fontWeight": "bold", - "gpmlElementName": "Group", - "height": 76.00000000000011, - "id": "dddac", - "kaavioType": "Group", - "padding": 8, - "stroke": "#808080", - "strokeDasharray": "5,3", - "strokeWidth": 0, - "textAlign": "center", - "type": [ - "Group", - "GroupGroup" - ], - "verticalAlign": "middle", - "width": 118.00000000000006, - "x": 467.7310924369753, - "y": 104.80672268907563, - "zIndex": 32768 - }, "de5a6": { "drawAs": "rect", "fill": "#ffffff", @@ -3534,7 +3403,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "de5a6", - "isPartOf": "f2a8d", + "isPartOf": "ebc7e", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -3570,6 +3439,35 @@ "y": 8, "zIndex": 32768 }, + "df629": { + "contains": [ + "a107c", + "fdbf9" + ], + "drawAs": "none", + "fill": "transparent", + "fillOpacity": 0.1, + "fontSize": 1, + "fontWeight": "bold", + "gpmlElementName": "Group", + "height": 56, + "id": "df629", + "kaavioType": "Group", + "padding": 8, + "stroke": "#808080", + "strokeDasharray": "5,3", + "strokeWidth": 0, + "textAlign": "center", + "type": [ + "Group", + "GroupGroup" + ], + "verticalAlign": "middle", + "width": 61, + "x": 175.7310924369753, + "y": 305.80672268907574, + "zIndex": 32768 + }, "dfce5": { "drawAs": "none", "fill": "transparent", @@ -3687,6 +3585,8 @@ "Ensembl:ENSG00000109906", "Entrez Gene:7704", "HGNC:ZBTB16", + "UniProt:A0A804HJ45", + "UniProt:A0A804HIC1", "UniProt:A0A024R3C6", "UniProt:Q05516", "UniProt:H0YGW2", @@ -3713,7 +3613,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "e1d86", - "isPartOf": "fbfc4", + "isPartOf": "ea5f5", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -3747,10 +3647,10 @@ "y": 8, "zIndex": 32795 }, - "e2dc8": { + "e48f6": { "contains": [ - "afa6c", - "b39b3" + "b1d8a", + "f1fb2" ], "drawAs": "none", "fill": "transparent", @@ -3759,7 +3659,7 @@ "fontWeight": "bold", "gpmlElementName": "Group", "height": 56, - "id": "e2dc8", + "id": "e48f6", "kaavioType": "Group", "padding": 8, "stroke": "#808080", @@ -3771,40 +3671,11 @@ "GroupGroup" ], "verticalAlign": "middle", - "width": 61, - "x": 734.4488432638751, - "y": 600.7041868566607, + "width": 60, + "x": 649.7310924369732, + "y": 533.114330186319, "zIndex": 32768 }, - "e2ea1": { - "contains": [ - "e7a51", - "aa392" - ], - "drawAs": "none", - "fill": "transparent", - "fillOpacity": 0.1, - "fontSize": 1, - "fontWeight": "bold", - "gpmlElementName": "Group", - "height": 75.5, - "id": "e2ea1", - "kaavioType": "Group", - "padding": 8, - "stroke": "#808080", - "strokeDasharray": "5,3", - "strokeWidth": 0, - "textAlign": "center", - "type": [ - "Group", - "GroupGroup" - ], - "verticalAlign": "middle", - "width": 70, - "x": 290.7310924369753, - "y": 439.30672268907574, - "zIndex": 28678 - }, "e6106": { "drawAs": "none", "fill": "transparent", @@ -3873,39 +3744,9 @@ "y": 403.8067226890762, "zIndex": 28674 }, - "e6561": { - "contains": [ - "a81e8", - "d9b86", - "ec6b7" - ], - "drawAs": "none", - "fill": "transparent", - "fillOpacity": 0.1, - "fontSize": 1, - "fontWeight": "bold", - "gpmlElementName": "Group", - "height": 76.00000000000011, - "id": "e6561", - "kaavioType": "Group", - "padding": 8, - "stroke": "#808080", - "strokeDasharray": "5,3", - "strokeWidth": 0, - "textAlign": "center", - "type": [ - "Group", - "GroupGroup" - ], - "verticalAlign": "middle", - "width": 56, - "x": 263.2310924369753, - "y": 112.80672268907563, - "zIndex": 32768 - }, "e6987": { "cellularComponent": "Cell", - "drawAs": "rect", + "drawAs": "Ellipse", "fill": "transparent", "fontFamily": "Arial", "fontSize": 12, @@ -3919,8 +3760,6 @@ "overflow": "hidden", "padding": 8, "rotation": 0, - "rx": 15, - "ry": 15, "stroke": "#0066ff", "strokeStyle": "double", "strokeWidth": 3, @@ -3952,7 +3791,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "e7431", - "isPartOf": "a77fb", + "isPartOf": "a52e8", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -3989,7 +3828,7 @@ }, "e7a51": { "cellularComponent": "Cell", - "drawAs": "rect", + "drawAs": "Ellipse", "fill": "transparent", "fontFamily": "Arial", "fontSize": 12, @@ -3998,14 +3837,12 @@ "gpmlElementName": "Shape", "height": 43, "id": "e7a51", - "isPartOf": "e2ea1", + "isPartOf": "d30e3", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", "padding": 8, "rotation": 0, - "rx": 15, - "ry": 15, "stroke": "#6666ff", "strokeStyle": "double", "strokeWidth": 3, @@ -4027,10 +3864,11 @@ "y": 8, "zIndex": 28678 }, - "e871c": { + "e7c0c": { "contains": [ - "bd9ec", - "f2929" + "a81e8", + "d9b86", + "ec6b7" ], "drawAs": "none", "fill": "transparent", @@ -4038,8 +3876,8 @@ "fontSize": 1, "fontWeight": "bold", "gpmlElementName": "Group", - "height": 76.5, - "id": "e871c", + "height": 76.00000000000011, + "id": "e7c0c", "kaavioType": "Group", "padding": 8, "stroke": "#808080", @@ -4051,10 +3889,10 @@ "GroupGroup" ], "verticalAlign": "middle", - "width": 70, - "x": 126.73109243697502, - "y": 437.30672268907574, - "zIndex": 28672 + "width": 56, + "x": 263.2310924369753, + "y": 112.80672268907563, + "zIndex": 32768 }, "e8be5": { "drawAs": "rect", @@ -4100,7 +3938,7 @@ }, "e8f96": { "cellularComponent": "Cell", - "drawAs": "rect", + "drawAs": "Ellipse", "fill": "transparent", "fontFamily": "Arial", "fontSize": 12, @@ -4114,8 +3952,6 @@ "overflow": "hidden", "padding": 8, "rotation": 0, - "rx": 15, - "ry": 15, "stroke": "#780fe1", "strokeStyle": "double", "strokeWidth": 3, @@ -4137,10 +3973,11 @@ "y": 271.2041868566612, "zIndex": 16387 }, - "eab53": { + "ea5f5": { "contains": [ - "a107c", - "fdbf9" + "e1d86", + "d621a", + "b8084" ], "drawAs": "none", "fill": "transparent", @@ -4148,8 +3985,8 @@ "fontSize": 1, "fontWeight": "bold", "gpmlElementName": "Group", - "height": 56, - "id": "eab53", + "height": 76, + "id": "ea5f5", "kaavioType": "Group", "padding": 8, "stroke": "#808080", @@ -4161,10 +3998,39 @@ "GroupGroup" ], "verticalAlign": "middle", - "width": 61, - "x": 175.7310924369753, - "y": 305.80672268907574, - "zIndex": 32768 + "width": 53, + "x": 263.2310924369753, + "y": 303.80672268907574, + "zIndex": 32795 + }, + "eba3e": { + "contains": [ + "dd31c", + "a420d" + ], + "drawAs": "none", + "fill": "transparent", + "fillOpacity": 0.1, + "fontSize": 1, + "fontWeight": "bold", + "gpmlElementName": "Group", + "height": 76.5, + "id": "eba3e", + "kaavioType": "Group", + "padding": 8, + "stroke": "#808080", + "strokeDasharray": "5,3", + "strokeWidth": 0, + "textAlign": "center", + "type": [ + "Group", + "GroupGroup" + ], + "verticalAlign": "middle", + "width": 70, + "x": 212.7310924369753, + "y": 438.30672268907574, + "zIndex": 28677 }, "ebbd6": { "drawAs": "rect", @@ -4176,7 +4042,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "ebbd6", - "isPartOf": "d79a1", + "isPartOf": "a18b5", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -4210,6 +4076,38 @@ "y": 8, "zIndex": 32768 }, + "ebc7e": { + "contains": [ + "d21aa", + "de5a6", + "fad3f", + "cf197", + "dc659" + ], + "drawAs": "none", + "fill": "transparent", + "fillOpacity": 0.1, + "fontSize": 1, + "fontWeight": "bold", + "gpmlElementName": "Group", + "height": 76, + "id": "ebc7e", + "kaavioType": "Group", + "padding": 8, + "stroke": "#808080", + "strokeDasharray": "5,3", + "strokeWidth": 0, + "textAlign": "center", + "type": [ + "Group", + "GroupGroup" + ], + "verticalAlign": "middle", + "width": 102, + "x": 387.7310924369753, + "y": 584.8067226890753, + "zIndex": 32768 + }, "ec6b7": { "drawAs": "rect", "fill": "#ffffff", @@ -4220,7 +4118,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "ec6b7", - "isPartOf": "e6561", + "isPartOf": "e7c0c", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -4336,7 +4234,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "ef22b", - "isPartOf": "afebf", + "isPartOf": "fcd2a", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -4372,7 +4270,7 @@ }, "f06fd": { "cellularComponent": "Cell", - "drawAs": "rect", + "drawAs": "Ellipse", "fill": "transparent", "fontFamily": "Arial", "fontSize": 12, @@ -4381,14 +4279,12 @@ "gpmlElementName": "Shape", "height": 45.81817566574273, "id": "f06fd", - "isPartOf": "b5d85", + "isPartOf": "f1c02", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", "padding": 8, "rotation": 0, - "rx": 15, - "ry": 15, "stroke": "#ff6600", "strokeStyle": "double", "strokeWidth": 3, @@ -4410,6 +4306,36 @@ "y": 35, "zIndex": 32770 }, + "f1c02": { + "contains": [ + "a7dc8", + "bcbdf", + "f06fd" + ], + "drawAs": "none", + "fill": "transparent", + "fillOpacity": 0.1, + "fontSize": 1, + "fontWeight": "bold", + "gpmlElementName": "Group", + "height": 91.4598929181534, + "id": "f1c02", + "kaavioType": "Group", + "padding": 8, + "stroke": "#808080", + "strokeDasharray": "5,3", + "strokeWidth": 0, + "textAlign": "center", + "type": [ + "Group", + "GroupGroup" + ], + "verticalAlign": "middle", + "width": 117.8182098869579, + "x": 575.2310924369735, + "y": 443.30672268907574, + "zIndex": 16384 + }, "f1fb2": { "drawAs": "rect", "fill": "#ffffff", @@ -4420,7 +4346,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "f1fb2", - "isPartOf": "bc878", + "isPartOf": "e48f6", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -4486,7 +4412,7 @@ }, "f2929": { "cellularComponent": "Cell", - "drawAs": "rect", + "drawAs": "Ellipse", "fill": "transparent", "fontFamily": "Arial", "fontSize": 12, @@ -4495,14 +4421,12 @@ "gpmlElementName": "Shape", "height": 43, "id": "f2929", - "isPartOf": "e871c", + "isPartOf": "bb0b9", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", "padding": 8, "rotation": 0, - "rx": 15, - "ry": 15, "stroke": "#6666ff", "strokeStyle": "double", "strokeWidth": 3, @@ -4524,38 +4448,6 @@ "y": 8, "zIndex": 28676 }, - "f2a8d": { - "contains": [ - "d21aa", - "de5a6", - "fad3f", - "cf197", - "dc659" - ], - "drawAs": "none", - "fill": "transparent", - "fillOpacity": 0.1, - "fontSize": 1, - "fontWeight": "bold", - "gpmlElementName": "Group", - "height": 76, - "id": "f2a8d", - "kaavioType": "Group", - "padding": 8, - "stroke": "#808080", - "strokeDasharray": "5,3", - "strokeWidth": 0, - "textAlign": "center", - "type": [ - "Group", - "GroupGroup" - ], - "verticalAlign": "middle", - "width": 102, - "x": 387.7310924369753, - "y": 584.8067226890753, - "zIndex": 32768 - }, "f3d37": { "drawAs": "rect", "fill": "#ffffff", @@ -4566,7 +4458,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "f3d37", - "isPartOf": "cedc7", + "isPartOf": "b1929", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -4587,7 +4479,8 @@ "Ensembl:ENSG00000127318", "Entrez Gene:50616", "HGNC:IL22", - "UniProt:Q9GZX6" + "UniProt:Q9GZX6", + "UniProt:A0A7R8C389" ], "verticalAlign": "middle", "whiteSpace": "pre", @@ -4634,7 +4527,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "f5cb2", - "isPartOf": "dddac", + "isPartOf": "d07b9", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -4698,10 +4591,10 @@ "y": 409.80672268907574, "zIndex": 32793 }, - "f6e8b": { + "f7262": { "contains": [ - "b5d8a", - "fac23" + "b2b13", + "cb1e6" ], "drawAs": "none", "fill": "transparent", @@ -4710,7 +4603,7 @@ "fontWeight": "bold", "gpmlElementName": "Group", "height": 56, - "id": "f6e8b", + "id": "f7262", "kaavioType": "Group", "padding": 8, "stroke": "#808080", @@ -4722,14 +4615,14 @@ "GroupGroup" ], "verticalAlign": "middle", - "width": 54, - "x": 646.7310924369732, - "y": 329.80672268907574, + "width": 57, + "x": 346.7310924369753, + "y": 327.80672268907574, "zIndex": 32768 }, "f86c3": { "cellularComponent": "Cell", - "drawAs": "rect", + "drawAs": "Ellipse", "fill": "transparent", "fontFamily": "Arial", "fontSize": 12, @@ -4743,8 +4636,6 @@ "overflow": "hidden", "padding": 8, "rotation": 0, - "rx": 15, - "ry": 15, "stroke": "#780fe1", "strokeStyle": "double", "strokeWidth": 3, @@ -4824,7 +4715,7 @@ }, "f901e": { "cellularComponent": "Cell", - "drawAs": "rect", + "drawAs": "Ellipse", "fill": "transparent", "fontFamily": "Arial", "fontSize": 12, @@ -4838,8 +4729,6 @@ "overflow": "hidden", "padding": 8, "rotation": 0, - "rx": 15, - "ry": 15, "stroke": "#6666ff", "strokeStyle": "double", "strokeWidth": 3, @@ -4871,7 +4760,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "f953a", - "isPartOf": "d79a1", + "isPartOf": "a18b5", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -4951,7 +4840,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "fac23", - "isPartOf": "f6e8b", + "isPartOf": "c47ee", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -5019,7 +4908,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "fad3f", - "isPartOf": "f2a8d", + "isPartOf": "ebc7e", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -5053,7 +4942,7 @@ "y": 48, "zIndex": 32768 }, - "fb0c5": { + "fb021": { "contains": [ "bac5b", "dace9", @@ -5066,7 +4955,7 @@ "fontWeight": "bold", "gpmlElementName": "Group", "height": 76, - "id": "fb0c5", + "id": "fb021", "kaavioType": "Group", "padding": 8, "stroke": "#808080", @@ -5151,11 +5040,11 @@ "y": 666.8067226890753, "zIndex": 32775 }, - "fbfc4": { + "fcd2a": { "contains": [ - "e1d86", - "d621a", - "b8084" + "a27ec", + "ef22b", + "ca28a" ], "drawAs": "none", "fill": "transparent", @@ -5163,8 +5052,8 @@ "fontSize": 1, "fontWeight": "bold", "gpmlElementName": "Group", - "height": 76, - "id": "fbfc4", + "height": 75.99999999999955, + "id": "fcd2a", "kaavioType": "Group", "padding": 8, "stroke": "#808080", @@ -5176,10 +5065,68 @@ "GroupGroup" ], "verticalAlign": "middle", - "width": 53, - "x": 263.2310924369753, - "y": 303.80672268907574, - "zIndex": 32795 + "width": 56, + "x": 371.7310924369753, + "y": 485.80672268907574, + "zIndex": 32787 + }, + "fd9ba": { + "contains": [ + "afa6c", + "b39b3" + ], + "drawAs": "none", + "fill": "transparent", + "fillOpacity": 0.1, + "fontSize": 1, + "fontWeight": "bold", + "gpmlElementName": "Group", + "height": 56, + "id": "fd9ba", + "kaavioType": "Group", + "padding": 8, + "stroke": "#808080", + "strokeDasharray": "5,3", + "strokeWidth": 0, + "textAlign": "center", + "type": [ + "Group", + "GroupGroup" + ], + "verticalAlign": "middle", + "width": 61, + "x": 734.4488432638751, + "y": 600.7041868566607, + "zIndex": 32768 + }, + "fd9dc": { + "contains": [ + "a55b2", + "d40f2" + ], + "drawAs": "none", + "fill": "transparent", + "fillOpacity": 0.1, + "fontSize": 1, + "fontWeight": "bold", + "gpmlElementName": "Group", + "height": 55.99999999999977, + "id": "fd9dc", + "kaavioType": "Group", + "padding": 8, + "stroke": "#808080", + "strokeDasharray": "5,3", + "strokeWidth": 0, + "textAlign": "center", + "type": [ + "Group", + "GroupGroup" + ], + "verticalAlign": "middle", + "width": 57, + "x": 175.2310924369753, + "y": 514.8067226890755, + "zIndex": 32768 }, "fdbf9": { "drawAs": "rect", @@ -5191,7 +5138,7 @@ "gpmlElementName": "DataNode", "height": 20, "id": "fdbf9", - "isPartOf": "eab53", + "isPartOf": "df629", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -5280,6 +5227,54 @@ "width": 0, "zIndex": 12288 }, + "http://identifiers.org/cl/CL:0000051": { + "gpmlElementName": "openControlledVocabulary", + "id": "http://identifiers.org/cl/CL:0000051", + "ontology": "Cell Type", + "term": "common lymphoid progenitor", + "type": [ + "openControlledVocabulary" + ], + "xrefIdentifier": "CL:0000051" + }, + "http://identifiers.org/cl/CL:0000623": { + "gpmlElementName": "openControlledVocabulary", + "id": "http://identifiers.org/cl/CL:0000623", + "ontology": "Cell Type", + "type": [ + "openControlledVocabulary" + ], + "xrefIdentifier": "CL:0000623" + }, + "http://identifiers.org/cl/CL:0000825": { + "gpmlElementName": "openControlledVocabulary", + "id": "http://identifiers.org/cl/CL:0000825", + "ontology": "Cell Type", + "type": [ + "openControlledVocabulary" + ], + "xrefIdentifier": "CL:0000825" + }, + "http://identifiers.org/cl/CL:0001065": { + "gpmlElementName": "openControlledVocabulary", + "id": "http://identifiers.org/cl/CL:0001065", + "ontology": "Cell Type", + "term": "innate lymphoid cell", + "type": [ + "openControlledVocabulary" + ], + "xrefIdentifier": "CL:0001065" + }, + "http://identifiers.org/pw/PW:0000004": { + "gpmlElementName": "openControlledVocabulary", + "id": "http://identifiers.org/pw/PW:0000004", + "ontology": "Pathway Ontology", + "term": "regulatory pathway", + "type": [ + "openControlledVocabulary" + ], + "xrefIdentifier": "PW:0000004" + }, "id15e16bf8": { "burrs": [ "f441e" @@ -5290,7 +5285,7 @@ "id": "id15e16bf8", "isAttachedTo": [ "e8f96", - "c9f0d" + "b9a4d" ], "kaavioType": "Edge", "markerEnd": "Arrow", @@ -5306,7 +5301,6 @@ 1 ] }, - "id": "bb431", "isAttachedTo": "e8f96", "orientation": [ 0, @@ -5326,8 +5320,7 @@ 0 ] }, - "id": "f4b20", - "isAttachedTo": "c9f0d", + "isAttachedTo": "b9a4d", "orientation": [ 0, 1 @@ -5358,7 +5351,7 @@ "id": "id166907e3", "isAttachedTo": [ "f86c3", - "b5d85" + "f1c02" ], "kaavioType": "Edge", "markerEnd": "Arrow", @@ -5374,7 +5367,6 @@ 0.5 ] }, - "id": "a17b9", "isAttachedTo": "f86c3", "orientation": [ 1, @@ -5394,8 +5386,7 @@ 0 ] }, - "id": "b6632", - "isAttachedTo": "b5d85", + "isAttachedTo": "f1c02", "orientation": [ 0, 1 @@ -5422,7 +5413,7 @@ "gpmlElementName": "Interaction", "id": "id190209d", "isAttachedTo": [ - "b75fe", + "fd9dc", "b6886" ], "kaavioType": "Edge", @@ -5439,8 +5430,7 @@ 0.5 ] }, - "id": "c7770", - "isAttachedTo": "b75fe", + "isAttachedTo": "fd9dc", "orientation": [ 1, 0 @@ -5460,7 +5450,6 @@ 0 ] }, - "id": "b2eac", "isAttachedTo": "b2815", "orientation": [], "x": 248.30579867966617, @@ -5485,7 +5474,7 @@ "gpmlElementName": "Interaction", "id": "id1e462864", "isAttachedTo": [ - "eab53", + "df629", "id6a9f982c" ], "kaavioType": "Edge", @@ -5502,8 +5491,7 @@ 0.5 ] }, - "id": "ac1b1", - "isAttachedTo": "eab53", + "isAttachedTo": "df629", "orientation": [ -1, 0 @@ -5523,7 +5511,6 @@ 0 ] }, - "id": "cd32b", "isAttachedTo": "ff721", "orientation": [], "x": 160.53109243697497, @@ -5548,7 +5535,7 @@ "gpmlElementName": "Interaction", "id": "id27c68564", "isAttachedTo": [ - "afebf", + "fcd2a", "b1c79" ], "kaavioType": "Edge", @@ -5565,8 +5552,7 @@ 0.5 ] }, - "id": "c2901", - "isAttachedTo": "afebf", + "isAttachedTo": "fcd2a", "orientation": [ 1, 0 @@ -5586,7 +5572,6 @@ 0 ] }, - "id": "b2a2b", "isAttachedTo": "f8a2b", "orientation": [], "x": 438.7310924369753, @@ -5615,7 +5600,7 @@ "id": "id36021de8", "isAttachedTo": [ "f901e", - "e2dc8" + "fd9ba" ], "kaavioType": "Edge", "markerEnd": "Arrow", @@ -5631,7 +5616,6 @@ 1 ] }, - "id": "b168d", "isAttachedTo": "f901e", "orientation": [ 0, @@ -5651,8 +5635,7 @@ 0 ] }, - "id": "d30ca", - "isAttachedTo": "e2dc8", + "isAttachedTo": "fd9ba", "orientation": [ 0, 1 @@ -5679,7 +5662,7 @@ "gpmlElementName": "Interaction", "id": "id39f359de", "isAttachedTo": [ - "fb0c5", + "fb021", "idf3f3bc65" ], "kaavioType": "Edge", @@ -5696,8 +5679,7 @@ 0.5 ] }, - "id": "b71d2", - "isAttachedTo": "fb0c5", + "isAttachedTo": "fb021", "orientation": [ -1, 0 @@ -5717,7 +5699,6 @@ 0 ] }, - "id": "ef912", "isAttachedTo": "d7054", "orientation": [], "x": 876.5310924369732, @@ -5759,7 +5740,6 @@ 0.5 ] }, - "id": "e516c", "isAttachedTo": "b8c17", "orientation": [ 1, @@ -5779,7 +5759,6 @@ 0 ] }, - "id": "d7fbb", "isAttachedTo": "e8f96", "orientation": [ 0, @@ -5807,7 +5786,7 @@ "gpmlElementName": "Interaction", "id": "id62c0514c", "isAttachedTo": [ - "d60e6", + "da628", "id15e16bf8" ], "kaavioType": "Edge", @@ -5824,8 +5803,7 @@ 0.5 ] }, - "id": "eb458", - "isAttachedTo": "d60e6", + "isAttachedTo": "da628", "orientation": [ 1, 0 @@ -5845,7 +5823,6 @@ 0 ] }, - "id": "a9904", "isAttachedTo": "f441e", "orientation": [], "x": 876.7658441565272, @@ -5870,7 +5847,7 @@ "gpmlElementName": "Interaction", "id": "id68e7105b", "isAttachedTo": [ - "a5acf", + "f7262", "ide2f1feb1" ], "kaavioType": "Edge", @@ -5887,8 +5864,7 @@ 0.5 ] }, - "id": "e64e6", - "isAttachedTo": "a5acf", + "isAttachedTo": "f7262", "orientation": [ -1, 0 @@ -5908,7 +5884,6 @@ 0 ] }, - "id": "e95ac", "isAttachedTo": "c1079", "orientation": [], "x": 325.7310924369753, @@ -5950,7 +5925,6 @@ 0.5 ] }, - "id": "fb1dd", "isAttachedTo": "e0c25", "orientation": [ -1, @@ -5971,7 +5945,6 @@ 0 ] }, - "id": "d1743", "isAttachedTo": "bd8f3", "orientation": [], "x": 444.73109243697536, @@ -6000,7 +5973,7 @@ "id": "id6a9f982c", "isAttachedTo": [ "a173f", - "e871c" + "bb0b9" ], "kaavioType": "Edge", "markerEnd": "Arrow", @@ -6016,7 +5989,6 @@ 1 ] }, - "id": "b2705", "isAttachedTo": "a173f", "orientation": [ 0, @@ -6036,8 +6008,7 @@ 0 ] }, - "id": "da79b", - "isAttachedTo": "e871c", + "isAttachedTo": "bb0b9", "orientation": [ 0, 1 @@ -6064,7 +6035,7 @@ "gpmlElementName": "Interaction", "id": "id711ea204", "isAttachedTo": [ - "fbfc4", + "ea5f5", "id91bf8e04" ], "kaavioType": "Edge", @@ -6081,8 +6052,7 @@ 0.5 ] }, - "id": "ba418", - "isAttachedTo": "fbfc4", + "isAttachedTo": "ea5f5", "orientation": [ -1, 0 @@ -6102,7 +6072,6 @@ 0 ] }, - "id": "f1d2d", "isAttachedTo": "e0584", "orientation": [], "x": 247.1310924369753, @@ -6127,7 +6096,7 @@ "gpmlElementName": "Interaction", "id": "id7201ee5f", "isAttachedTo": [ - "b75fe", + "fd9dc", "idf8e7b9cd" ], "kaavioType": "Edge", @@ -6144,8 +6113,7 @@ 0.5 ] }, - "id": "f93e0", - "isAttachedTo": "b75fe", + "isAttachedTo": "fd9dc", "orientation": [ -1, 0 @@ -6165,7 +6133,6 @@ 0 ] }, - "id": "bcd79", "isAttachedTo": "c5fdb", "orientation": [], "x": 160.73109243697496, @@ -6190,7 +6157,7 @@ "gpmlElementName": "Interaction", "id": "id7ac77e26", "isAttachedTo": [ - "f6e8b", + "c47ee", "id166907e3" ], "kaavioType": "Edge", @@ -6207,8 +6174,7 @@ 0.5 ] }, - "id": "d130c", - "isAttachedTo": "f6e8b", + "isAttachedTo": "c47ee", "orientation": [ -1, 0 @@ -6228,7 +6194,6 @@ 0 ] }, - "id": "e54a9", "isAttachedTo": "cca0f", "orientation": [], "x": 634.1401973804525, @@ -6256,8 +6221,8 @@ "gpmlElementName": "Interaction", "id": "id7b7d372d", "isAttachedTo": [ - "b5d85", - "cedc7" + "f1c02", + "b1929" ], "kaavioType": "Edge", "markerEnd": "Arrow", @@ -6273,8 +6238,7 @@ 1 ] }, - "id": "ea985", - "isAttachedTo": "b5d85", + "isAttachedTo": "f1c02", "orientation": [ 0, 1 @@ -6293,8 +6257,7 @@ 0 ] }, - "id": "ea4a7", - "isAttachedTo": "cedc7", + "isAttachedTo": "b1929", "orientation": [ 0, 1 @@ -6321,7 +6284,7 @@ "gpmlElementName": "Interaction", "id": "id82aa627b", "isAttachedTo": [ - "e6561", + "e7c0c", "idcbcbee08" ], "kaavioType": "Edge", @@ -6338,8 +6301,7 @@ 0 ] }, - "id": "f58d9", - "isAttachedTo": "e6561", + "isAttachedTo": "e7c0c", "orientation": [ 0, -1 @@ -6359,7 +6321,6 @@ 0 ] }, - "id": "daf29", "isAttachedTo": "fac71", "orientation": [], "x": 290.35906077470605, @@ -6387,13 +6348,12 @@ "gpmlElementName": "GraphicalLine", "id": "id91bf8e04", "isAttachedTo": [ - "d65c1" + "eba3e" ], "kaavioType": "Edge", "markerEnd": "Arrow", "points": [ { - "id": "cfafa", "x": 246.7310924369753, "y": 276.80672268907574 }, @@ -6408,8 +6368,7 @@ 0 ] }, - "id": "e9780", - "isAttachedTo": "d65c1", + "isAttachedTo": "eba3e", "orientation": [ 0, 1 @@ -6437,7 +6396,7 @@ "gpmlElementName": "Interaction", "id": "id9a6c98f0", "isAttachedTo": [ - "d79a1", + "a18b5", "id36021de8" ], "kaavioType": "Edge", @@ -6454,8 +6413,7 @@ 0.5 ] }, - "id": "b62af", - "isAttachedTo": "d79a1", + "isAttachedTo": "a18b5", "orientation": [ -1, 0 @@ -6475,7 +6433,6 @@ 0 ] }, - "id": "d14cc", "isAttachedTo": "abc9b", "orientation": [], "x": 764.6866729860697, @@ -6500,7 +6457,7 @@ "gpmlElementName": "Interaction", "id": "ida2b8a28e", "isAttachedTo": [ - "b75fe", + "fd9dc", "c12d5" ], "kaavioType": "Edge", @@ -6517,8 +6474,7 @@ 0.25 ] }, - "id": "c2ab1", - "isAttachedTo": "b75fe", + "isAttachedTo": "fd9dc", "orientation": [ 1, 0 @@ -6538,7 +6494,6 @@ 0 ] }, - "id": "df029", "isAttachedTo": "cbf94", "orientation": [], "x": 325.3222008597789, @@ -6563,7 +6518,7 @@ "gpmlElementName": "Interaction", "id": "idaeb2c8cf", "isAttachedTo": [ - "bc878", + "e48f6", "id7b7d372d" ], "kaavioType": "Edge", @@ -6580,8 +6535,7 @@ 0.5 ] }, - "id": "ac6d5", - "isAttachedTo": "bc878", + "isAttachedTo": "e48f6", "orientation": [ -1, 0 @@ -6601,7 +6555,6 @@ 0 ] }, - "id": "db2ef", "isAttachedTo": "abd94", "orientation": [], "x": 634.2585840689924, @@ -6626,7 +6579,7 @@ "gpmlElementName": "Interaction", "id": "idb6b9d9", "isAttachedTo": [ - "dddac", + "d07b9", "ide5efa553" ], "kaavioType": "Edge", @@ -6643,8 +6596,7 @@ 0.5 ] }, - "id": "d7c89", - "isAttachedTo": "dddac", + "isAttachedTo": "d07b9", "orientation": [ -1, 0 @@ -6664,7 +6616,6 @@ 0 ] }, - "id": "d237e", "isAttachedTo": "c5e50", "orientation": [], "x": 444.7310924369753, @@ -6706,7 +6657,6 @@ 0.5 ] }, - "id": "cc8c0", "isAttachedTo": "e6987", "orientation": [ 1, @@ -6726,7 +6676,6 @@ 0.5 ] }, - "id": "dc74c", "isAttachedTo": "beafd", "orientation": [ 1, @@ -6755,7 +6704,7 @@ "gpmlElementName": "Interaction", "id": "idbbf4e535", "isAttachedTo": [ - "a77fb", + "a52e8", "idfd8514c2" ], "kaavioType": "Edge", @@ -6772,8 +6721,7 @@ 0.5 ] }, - "id": "f0530", - "isAttachedTo": "a77fb", + "isAttachedTo": "a52e8", "orientation": [ -1, 0 @@ -6793,7 +6741,6 @@ 0 ] }, - "id": "c0382", "isAttachedTo": "b8602", "orientation": [], "x": 442.3310924369753, @@ -6838,7 +6785,6 @@ 0.5 ] }, - "id": "c3d85", "isAttachedTo": "bc6db", "orientation": [ -1, @@ -6858,7 +6804,6 @@ 0 ] }, - "id": "ade05", "isAttachedTo": "a173f", "orientation": [ 0, @@ -6906,7 +6851,6 @@ 1 ] }, - "id": "d4672", "isAttachedTo": "b8c17", "orientation": [ 0, @@ -6926,7 +6870,6 @@ 0 ] }, - "id": "a7e99", "isAttachedTo": "f86c3", "orientation": [ 0, @@ -6958,7 +6901,7 @@ "id": "ide2f1feb1", "isAttachedTo": [ "f86c3", - "e2ea1" + "d30e3" ], "kaavioType": "Edge", "markerEnd": "Arrow", @@ -6974,7 +6917,6 @@ 0.5 ] }, - "id": "baf6a", "isAttachedTo": "f86c3", "orientation": [ -1, @@ -6994,8 +6936,7 @@ 0 ] }, - "id": "b799a", - "isAttachedTo": "e2ea1", + "isAttachedTo": "d30e3", "orientation": [ 0, 1 @@ -7042,7 +6983,6 @@ 1 ] }, - "id": "f7f8b", "isAttachedTo": "bc6db", "orientation": [ 0, @@ -7062,7 +7002,6 @@ 0 ] }, - "id": "acca9", "isAttachedTo": "b8c17", "orientation": [ 0, @@ -7107,7 +7046,6 @@ 0.5 ] }, - "id": "c62e9", "isAttachedTo": "ecb1c", "orientation": [ 1, @@ -7128,7 +7066,6 @@ 0 ] }, - "id": "f0168", "isAttachedTo": "cbe00", "orientation": [], "x": 533.5310924369758, @@ -7156,8 +7093,8 @@ "gpmlElementName": "Interaction", "id": "idf3f3bc65", "isAttachedTo": [ - "c9f0d", - "cdb9e" + "b9a4d", + "ca7c7" ], "kaavioType": "Edge", "markerEnd": "Arrow", @@ -7173,8 +7110,7 @@ 1 ] }, - "id": "cba26", - "isAttachedTo": "c9f0d", + "isAttachedTo": "b9a4d", "orientation": [ 0, 1 @@ -7193,8 +7129,7 @@ 0 ] }, - "id": "ed7d0", - "isAttachedTo": "cdb9e", + "isAttachedTo": "ca7c7", "orientation": [ 0, 1 @@ -7241,7 +7176,6 @@ 1 ] }, - "id": "e5de0", "isAttachedTo": "f2929", "orientation": [ 0, @@ -7261,7 +7195,6 @@ 0 ] }, - "id": "b01c1", "isAttachedTo": "b8129", "orientation": [ 0, @@ -7309,7 +7242,6 @@ 1 ] }, - "id": "f4054", "isAttachedTo": "f86c3", "orientation": [ 0, @@ -7329,7 +7261,6 @@ 0 ] }, - "id": "bc00a", "isAttachedTo": "e6987", "orientation": [ 0, @@ -7375,10 +7306,10 @@ "@context": [ "https://cdn.rawgit.com/wikipathways/WpVocabularies/7a46a05/contexts/pvjs.jsonld", { - "@base": "http://identifiers.org/wikipathways/WP3893/" + "@base": "WP3893/" } ], - "author": "[Khanspers, Eweitz]", + "author": "[Khanspers, Eweitz, Mkutmon]", "comments": [ { "content": "Development and heterogeneity of the innate lymphoid cell (ILC) family. ILCs develop from distinct progenitors in the fetal liver or bone marrow and then develop into mature ILCs in the periphery. Different transcription factors and cytokines are involved in the development of the three groups of mature ILCs. All ILCs develop from CLPs, which can differentiate into NKps or CHILPs. CHILPs can further differentiate into LTi cells through α4β7+ populations or into other ILC populations through differentiation into ILCps. ILC1s express T-bet, are responsive to IL-12, and produce IFN-γ and/or TNF. ILC2s highly express GATA3, are responsive to IL-25, IL-33 and TSLP, and produce IL-4, IL-5, IL-9, IL-13 and amphiregulin. ILC3s express ROR-γt, are responsive to IL-1β and IL-23, and produce IL-17 and/or IL-22.\r\n\r\nProteins on this pathway have targeted assays available via the [https://assays.cancer.gov/available_assays?wp_id=WP3893 CPTAC Assay Portal]", @@ -7421,8 +7352,8 @@ "bc6db", "c3f95", "fa062", - "c9f0d", - "b5d85", + "b9a4d", + "f1c02", "b8c17", "f86c3", "e8f96", @@ -7433,33 +7364,33 @@ "f2484", "f8c81", "fdf95", - "e871c", + "bb0b9", "c6c79", "e61f2", "fb3eb", - "d65c1", - "e2ea1", + "eba3e", + "d30e3", "e6987", "beafd", "b8129", "e0c25", "e8be5", "ecb1c", - "d79a1", - "a77fb", - "cedc7", - "f6e8b", - "da975", - "dddac", - "d60e6", - "eab53", - "bc878", - "e6561", - "f2a8d", - "a5acf", - "fb0c5", - "e2dc8", - "b75fe", + "a18b5", + "a52e8", + "b1929", + "c47ee", + "c8add", + "d07b9", + "da628", + "df629", + "e48f6", + "e7c0c", + "ebc7e", + "f7262", + "fb021", + "fd9ba", + "fd9dc", "f901e", "fb5a4", "b3b6e", @@ -7469,18 +7400,18 @@ "c12d5", "b1c79", "bfad3", - "afebf", + "fcd2a", "ae02c", "f620b", "ee416", - "fbfc4", - "cdb9e", + "ea5f5", + "ca7c7", "c947d", "dfce5", "be026", "d5d6d" ], - "dataSourceVersion": "WP3893_r118859", + "dataSourceVersion": "WP3893_r129544", "displayName": "Development and heterogeneity of the ILC family", "drawAs": "rect", "fill": "white", @@ -7488,9 +7419,9 @@ "fontWeight": "bold", "gpmlElementName": "Pathway", "height": 722.8067226890762, - "id": "http://identifiers.org/wikipathways/WP3893", + "id": "WP3893", "kaavioType": "Group", - "lastModified": "20210602211943", + "lastModified": "20240510160121", "name": "Development and heterogeneity of the ILC family", "organism": "Homo sapiens", "padding": 5, @@ -7499,9 +7430,10 @@ "stroke": "black", "strokeWidth": 0, "textAlign": "left", - "textContent": "Name: Development and heterogeneity of the ILC family\nLast Modified: 20210602211943\nOrganism: Homo sapiens", + "textContent": "Name: Development and heterogeneity of the ILC family\nLast Modified: 20240510160121\nOrganism: Homo sapiens", "type": [ - "Pathway" + "Pathway", + "http://identifiers.org/pw/PW:0000004" ], "verticalAlign": "top", "width": 1410.374862183021, diff --git a/pathways/WP3893/WP3893.png b/pathways/WP3893/WP3893.png index 982c03559..d725bd61b 100644 Binary files a/pathways/WP3893/WP3893.png and b/pathways/WP3893/WP3893.png differ diff --git a/pathways/WP3893/WP3893.svg b/pathways/WP3893/WP3893.svg index 4b621516b..a76d360f1 100644 --- a/pathways/WP3893/WP3893.svg +++ b/pathways/WP3893/WP3893.svg @@ -1,5 +1,5 @@ - + @@ -472,8 +472,8 @@ - - + + @@ -675,7 +675,7 @@ - + CLPs @@ -687,14 +687,14 @@ - - + + - + CD4- @@ -702,21 +702,21 @@ - + CD4+ - - + + - + NCR- @@ -724,7 +724,7 @@ - + NCR+ @@ -733,7 +733,7 @@ - + CHILP @@ -741,7 +741,7 @@ - + ILCp @@ -749,7 +749,7 @@ - + a4b7+ @@ -757,7 +757,7 @@ - + NKp @@ -801,8 +801,8 @@ CLP: Common lymphoid progenitor - - + + @@ -811,7 +811,7 @@ - + NK @@ -827,11 +827,11 @@ - - + + - + ILC1 @@ -844,11 +844,11 @@ - - + + - + ILC1 @@ -863,7 +863,7 @@ - + ILC2 @@ -871,19 +871,19 @@ - + ILC3 - + IFNG - + PLZF @@ -901,8 +901,8 @@ IL-25 - - + + @@ -922,8 +922,8 @@ - - + + @@ -949,23 +949,23 @@ - - - + + + IL22 - + IFNG - - + + @@ -979,23 +979,23 @@ - - + + TNF - + IFNG - - + + @@ -1033,8 +1033,8 @@ - - + + @@ -1048,8 +1048,8 @@ - - + + @@ -1063,8 +1063,8 @@ - - + + @@ -1078,8 +1078,8 @@ - - + + @@ -1099,8 +1099,8 @@ - - + + @@ -1132,8 +1132,8 @@ - - + + @@ -1147,8 +1147,8 @@ - - + + @@ -1168,23 +1168,23 @@ - - + + TNF - + IFNG - - + + @@ -1200,7 +1200,7 @@ - + exILC3 @@ -1224,7 +1224,7 @@ ROR-gammat+ ILC3s - + IFNG @@ -1262,8 +1262,8 @@ - - + + @@ -1302,8 +1302,8 @@ LTi cells - - + + @@ -1323,9 +1323,9 @@ - - - + + + IL22 @@ -1362,9 +1362,9 @@ Legend - + Name: Development and heterogeneity of the ILC family - Last Modified: 20210602211943 + Last Modified: 20240510160121 Organism: Homo sapiens diff --git a/pathways/WP3969/WP3969-bibliography.tsv b/pathways/WP3969/WP3969-bibliography.tsv index 421b3b2ed..10cf71a33 100644 --- a/pathways/WP3969/WP3969-bibliography.tsv +++ b/pathways/WP3969/WP3969-bibliography.tsv @@ -1,2 +1,2 @@ ID Database Citation -27789274 Pubmed "Ohtsuka M, Ling H, Ivan C, Pichler M, Matsushita D, Goblirsch M, et al. H19 Noncoding RNA, an Independent Prognostic Factor, Regulates Essential Rb-E2F and CDK8-β-Catenin Signaling in Colorectal Cancer. EBioMedicine. 2016 Nov;13:113–24. PubMed Europe PMC Scholia" +27789274 Pubmed "H19 Noncoding RNA, an Independent Prognostic Factor, Regulates Essential Rb-E2F and CDK8-β-Catenin Signaling in Colorectal Cancer. Ohtsuka M, Ling H, Ivan C, Pichler M, Matsushita D, Goblirsch M, et al. EBioMedicine. 2016 Nov;13:113–24. PubMed Europe PMC Scholia" diff --git a/pathways/WP3969/WP3969-datanodes.tsv b/pathways/WP3969/WP3969-datanodes.tsv index 3fa005c1a..7c8510319 100644 --- a/pathways/WP3969/WP3969-datanodes.tsv +++ b/pathways/WP3969/WP3969-datanodes.tsv @@ -1,18 +1,18 @@ Label Type Identifier Comment Ensembl NCBI gene HGNC UniProt Wikidata ChEBI InChI -macroH2A GeneProduct ensembl:ENSG00000113648 ensembl:ENSG00000113648 ncbigene:9555 hgnc.symbol:MACROH2A1 uniprot:D6RCF2;uniprot:O75367;uniprot:B4DJC3 -CDK4 GeneProduct ensembl:ENSG00000135446 ensembl:ENSG00000135446 ncbigene:1019 hgnc.symbol:CDK4 uniprot:F8VTV8;uniprot:F8VWX7;uniprot:F8VXD2;uniprot:F8VZ51;uniprot:F8VZ13;uniprot:F8W1L8;uniprot:F8VYH9;uniprot:F8VZZ0;uniprot:P11802;uniprot:A0A024RBB6;uniprot:F8VYY1;uniprot:Q96BE9 -CTNNB1 GeneProduct ensembl:ENSG00000168036 ensembl:ENSG00000168036 ncbigene:1499 hgnc.symbol:CTNNB1 uniprot:A0A2R8Y6G0;uniprot:A0A2R8Y804;uniprot:A0A2R8Y815;uniprot:A0A2R8Y5A3;uniprot:C9IZ65;uniprot:A0A2R8Y5C3;uniprot:P35222;uniprot:A0A2R8Y7Z0;uniprot:A0A2R8YG06;uniprot:A0A2R8Y5Z1;uniprot:A0A2R8Y750;uniprot:A0A2R8YCH5;uniprot:A0A024R2Q3;uniprot:A0A2R8Y543;uniprot:B4DGU4 -CCND1 GeneProduct ensembl:ENSG00000110092 ensembl:ENSG00000110092 ncbigene:595 hgnc.symbol:CCND1 uniprot:P24385;uniprot:Q6FI00;uniprot:F5H437 -E2F1 GeneProduct ensembl:ENSG00000101412 ensembl:ENSG00000101412 ncbigene:1869 hgnc.symbol:E2F1 uniprot:Q01094 -CDK8 GeneProduct ensembl:ENSG00000132964 ensembl:ENSG00000132964 ncbigene:1024 hgnc.symbol:CDK8 uniprot:A0A0D9SEP3;uniprot:A0A0D9SFZ2;uniprot:F5H6D4;uniprot:P49336 -CDK8 GeneProduct ensembl:ENSG00000132964 ensembl:ENSG00000132964 ncbigene:1024 hgnc.symbol:CDK8 uniprot:A0A0D9SEP3;uniprot:A0A0D9SFZ2;uniprot:F5H6D4;uniprot:P49336 -MED1 GeneProduct ensembl:ENSG00000125686 ensembl:ENSG00000125686 ncbigene:5469 hgnc.symbol:MED1 uniprot:J3QKZ7;uniprot:Q15648;uniprot:J3KSD7 -CSRP2 GeneProduct ensembl:ENSG00000175183 ensembl:ENSG00000175183 ncbigene:1466 hgnc.symbol:CSRP2 uniprot:F8VQR7;uniprot:Q16527;uniprot:A0A024RBB5;uniprot:F8VW96 -JAG1 GeneProduct ensembl:ENSG00000101384 ensembl:ENSG00000101384 ncbigene:182 hgnc.symbol:JAG1 uniprot:P78504;uniprot:A0A087WXH5;uniprot:A0A087X1E8 -SOX4 GeneProduct ensembl:ENSG00000124766 ensembl:ENSG00000124766 ncbigene:6659 hgnc.symbol:SOX4 uniprot:Q06945 -CDH1 GeneProduct ensembl:ENSG00000039068 ensembl:ENSG00000039068 ncbigene:999 hgnc.symbol:CDH1 uniprot:H3BVI7;uniprot:P12830;uniprot:H3BNC6;uniprot:A0A0U2ZQU7;uniprot:J3QKP1 -TULP3 GeneProduct ensembl:ENSG00000078246 ensembl:ENSG00000078246 ncbigene:7289 hgnc.symbol:TULP3 uniprot:O75386;uniprot:F5GWL5;uniprot:F5H7B9;uniprot:H0YFU8;uniprot:H0YG12 -PMAIP1 GeneProduct ensembl:ENSG00000141682 ensembl:ENSG00000141682 ncbigene:5366 hgnc.symbol:PMAIP1 uniprot:A0A0S2Z490;uniprot:Q13794;uniprot:A0A0S2Z4V2 -RB1 GeneProduct ensembl:ENSG00000139687 ensembl:ENSG00000139687 ncbigene:5925 hgnc.symbol:RB1 uniprot:A0A3B3IS71;uniprot:Q92728;uniprot:A0A024RDV3;uniprot:A0A2R8YFL6;uniprot:A0A2R8Y743;uniprot:P06400 -E2F1 GeneProduct ensembl:ENSG00000101412 ensembl:ENSG00000101412 ncbigene:1869 hgnc.symbol:E2F1 uniprot:Q01094 -RB1 GeneProduct ensembl:ENSG00000139687 ensembl:ENSG00000139687 ncbigene:5925 hgnc.symbol:RB1 uniprot:A0A3B3IS71;uniprot:Q92728;uniprot:A0A024RDV3;uniprot:A0A2R8YFL6;uniprot:A0A2R8Y743;uniprot:P06400 +macroH2A GeneProduct ensembl:ENSG00000113648 "" ensembl:ENSG00000113648 ncbigene:9555 hgnc.symbol:MACROH2A1 uniprot:D6RCF2;uniprot:O75367;uniprot:B4DJC3 +CDK4 GeneProduct ensembl:ENSG00000135446 "" ensembl:ENSG00000135446 ncbigene:1019 hgnc.symbol:CDK4 uniprot:F8VTV8;uniprot:F8VWX7;uniprot:F8VXD2;uniprot:F8VZ51;uniprot:F8VZ13;uniprot:F8W1L8;uniprot:F8VYH9;uniprot:F8VZZ0;uniprot:P11802;uniprot:A0A024RBB6;uniprot:F8VYY1;uniprot:Q96BE9 +CTNNB1 GeneProduct ensembl:ENSG00000168036 "" ensembl:ENSG00000168036 ncbigene:1499 hgnc.symbol:CTNNB1 uniprot:A0A2R8Y6G0;uniprot:A0A2R8Y804;uniprot:A0A2R8Y815;uniprot:A0A2R8Y5A3;uniprot:C9IZ65;uniprot:A0A2R8Y5C3;uniprot:P35222;uniprot:A0A2R8Y7Z0;uniprot:A0A2R8YG06;uniprot:A0A2R8Y5Z1;uniprot:A0A2R8Y750;uniprot:A0A2R8YCH5;uniprot:A0A024R2Q3;uniprot:A0A2R8Y543;uniprot:B4DGU4 +CCND1 GeneProduct ensembl:ENSG00000110092 "" ensembl:ENSG00000110092 ncbigene:595 hgnc.symbol:CCND1 uniprot:P24385;uniprot:Q6FI00;uniprot:F5H437 +E2F1 GeneProduct ensembl:ENSG00000101412 "" ensembl:ENSG00000101412 ncbigene:1869 hgnc.symbol:E2F1 uniprot:Q01094 +CDK8 GeneProduct ensembl:ENSG00000132964 "" ensembl:ENSG00000132964 ncbigene:1024 hgnc.symbol:CDK8 uniprot:A0A0D9SEP3;uniprot:A0A0D9SFZ2;uniprot:F5H6D4;uniprot:P49336 +CDK8 GeneProduct ensembl:ENSG00000132964 "" ensembl:ENSG00000132964 ncbigene:1024 hgnc.symbol:CDK8 uniprot:A0A0D9SEP3;uniprot:A0A0D9SFZ2;uniprot:F5H6D4;uniprot:P49336 +MED1 GeneProduct ensembl:ENSG00000125686 "" ensembl:ENSG00000125686 ncbigene:5469 hgnc.symbol:MED1 uniprot:J3QKZ7;uniprot:Q15648;uniprot:J3KSD7 +CSRP2 GeneProduct ensembl:ENSG00000175183 "" ensembl:ENSG00000175183 ncbigene:1466 hgnc.symbol:CSRP2 uniprot:F8VQR7;uniprot:Q16527;uniprot:A0A024RBB5;uniprot:F8VW96 +JAG1 GeneProduct ensembl:ENSG00000101384 "" ensembl:ENSG00000101384 ncbigene:182 hgnc.symbol:JAG1 uniprot:P78504;uniprot:A0A087WXH5;uniprot:A0A087X1E8 +SOX4 GeneProduct ensembl:ENSG00000124766 "" ensembl:ENSG00000124766 ncbigene:6659 hgnc.symbol:SOX4 uniprot:Q06945 +CDH1 GeneProduct ensembl:ENSG00000039068 "" ensembl:ENSG00000039068 ncbigene:999 hgnc.symbol:CDH1 uniprot:H3BVI7;uniprot:P12830;uniprot:H3BNC6;uniprot:A0A0U2ZQU7;uniprot:J3QKP1 +TULP3 GeneProduct ensembl:ENSG00000078246 "" ensembl:ENSG00000078246 ncbigene:7289 hgnc.symbol:TULP3 uniprot:O75386;uniprot:F5GWL5;uniprot:F5H7B9;uniprot:H0YFU8;uniprot:H0YG12 +PMAIP1 GeneProduct ensembl:ENSG00000141682 "" ensembl:ENSG00000141682 ncbigene:5366 hgnc.symbol:PMAIP1 uniprot:A0A0S2Z490;uniprot:Q13794;uniprot:A0A0S2Z4V2 +RB1 GeneProduct ensembl:ENSG00000139687 "" ensembl:ENSG00000139687 ncbigene:5925 hgnc.symbol:RB1 uniprot:A0A3B3IS71;uniprot:Q92728;uniprot:A0A024RDV3;uniprot:A0A2R8YFL6;uniprot:A0A2R8Y743;uniprot:P06400 +E2F1 GeneProduct ensembl:ENSG00000101412 "" ensembl:ENSG00000101412 ncbigene:1869 hgnc.symbol:E2F1 uniprot:Q01094 +RB1 GeneProduct ensembl:ENSG00000139687 "" ensembl:ENSG00000139687 ncbigene:5925 hgnc.symbol:RB1 uniprot:A0A3B3IS71;uniprot:Q92728;uniprot:A0A024RDV3;uniprot:A0A2R8YFL6;uniprot:A0A2R8Y743;uniprot:P06400 diff --git a/pathways/WP3969/WP3969.gpml b/pathways/WP3969/WP3969.gpml index d691627b2..6636a0a88 100644 --- a/pathways/WP3969/WP3969.gpml +++ b/pathways/WP3969/WP3969.gpml @@ -1,6 +1,6 @@ - - In this proposed model, H19 interacts with macroH2A, and this may consequently lead to de-repression of genes including CDK8, CDK4, and CCND1. Increased CDK4-cyclin D1 complex phosphorylates Rb to disrupt Rb-E2F1 interaction, leading to E2F1 activation. The increase of CDK8 expression enhances the function of mediator complex including MED1, and facilitates the gene regulation by β-catenin. These downstream targets could work in a synergistic way of promoting cell proliferation and increasing cell motility in CRC. + + In this proposed model, H19 interacts with macroH2A, and this may consequently lead to de-repression of genes including CDK8, CDK4, and CCND1. Increased CDK4-cyclin D1 complex phosphorylates Rb to disrupt Rb-E2F1 interaction, leading to E2F1 activation. The increase of CDK8 expression enhances the function of mediator complex including MED1, and facilitates the gene regulation by beta-catenin. These downstream targets could work in a synergistic way of promoting cell proliferation and increasing cell motility in colorectal cancer. Reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5264449/ Proteins on this pathway have targeted assays available via the [https://assays.cancer.gov/available_assays?wp_id=WP3969 CPTAC Assay Portal] @@ -14,7 +14,7 @@ Proteins on this pathway have targeted assays available via the [https://assays. - + @@ -86,123 +86,123 @@ Proteins on this pathway have targeted assays available via the [https://assays. - - - - - - - - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + + + + + + + + - - + + - - + + - - + + - - + + @@ -212,19 +212,14 @@ Proteins on this pathway have targeted assays available via the [https://assays. - - - - - - + + + + + + - - colorectal cancer - DOID:9256 - Human Disease Ontology - 27789274 PubMed @@ -256,5 +251,16 @@ Proteins on this pathway have targeted assays available via the [https://assays. Radovich M Calin GA + + signaling pathway + PW:0000003 + Pathway Ontology + + + colorectal cancer + DOID:9256 + Disease + + diff --git a/pathways/WP3969/WP3969.json b/pathways/WP3969/WP3969.json index 9b500930c..592708cbf 100644 --- a/pathways/WP3969/WP3969.json +++ b/pathways/WP3969/WP3969.json @@ -1,26 +1,33 @@ { "entitiesById": { - "582409": { - "__HighlandStream__": true, - "_can_drain": false, - "_consume_waiting_for_next": false, - "_consumers": [], - "_delegate": null, - "_destructors": [], - "_events": {}, - "_eventsCount": 2, - "_in_consume_cb": false, - "_incoming": [], - "_is_observer": false, - "_nil_pushed": false, - "_observers": [], - "_outgoing": [], - "_repeat_resume": false, - "_send_events": false, - "id": "582409", - "paused": true, - "source": null, - "writable": true + "a00f8": { + "contains": [ + "c32fb", + "c9bb7" + ], + "drawAs": "none", + "fill": "transparent", + "fillOpacity": 0.1, + "fontSize": 1, + "fontWeight": "bold", + "gpmlElementName": "Group", + "height": 66.00000000000006, + "id": "a00f8", + "kaavioType": "Group", + "padding": 8, + "stroke": "#808080", + "strokeDasharray": "5,3", + "strokeWidth": 0, + "textAlign": "center", + "type": [ + "Group", + "GroupGroup" + ], + "verticalAlign": "middle", + "width": 77, + "x": 6.577284339671735, + "y": 218.19323379583574, + "zIndex": 32786 }, "a1939": { "drawAs": "StraightLine", @@ -28,7 +35,7 @@ "gpmlElementName": "Interaction", "id": "a1939", "isAttachedTo": [ - "fbbec", + "d643c", "f61a0" ], "kaavioType": "Edge", @@ -45,8 +52,7 @@ 1 ] }, - "id": "a7e7c", - "isAttachedTo": "fbbec", + "isAttachedTo": "d643c", "orientation": [ 0, 1 @@ -65,7 +71,6 @@ 0.25 ] }, - "id": "e8365", "isAttachedTo": "f61a0", "orientation": [ -1, @@ -97,7 +102,7 @@ "gpmlElementName": "DataNode", "height": 25, "id": "a545e", - "isPartOf": "bdebf", + "isPartOf": "d955e", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -142,7 +147,7 @@ "gpmlElementName": "DataNode", "height": 25, "id": "a66fd", - "isPartOf": "ac7c0", + "isPartOf": "f558b", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -187,7 +192,7 @@ "gpmlElementName": "DataNode", "height": 25, "id": "aacb8", - "isPartOf": "d524f", + "isPartOf": "f11cd", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -232,7 +237,7 @@ "gpmlElementName": "DataNode", "height": 25, "id": "ab405", - "isPartOf": "bdebf", + "isPartOf": "d955e", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -286,7 +291,7 @@ "gpmlElementName": "DataNode", "height": 25, "id": "ab411", - "isPartOf": "d524f", + "isPartOf": "f11cd", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -301,48 +306,18 @@ "DataNode", "SingleFreeNode", "Ensembl:ENSG00000130600", - "RNA" + "Rna" ], "verticalAlign": "middle", "whiteSpace": "pre", "width": 58, - "wpType": "RNA", + "wpType": "Rna", "x": 8, "xrefDataSource": "Ensembl", "xrefIdentifier": "ENSG00000130600", "y": 32.99999999999997, "zIndex": 32768 }, - "ac7c0": { - "contains": [ - "e5f2c", - "a66fd", - "f279d" - ], - "drawAs": "none", - "fill": "transparent", - "fillOpacity": 0.1, - "fontSize": 1, - "fontWeight": "bold", - "gpmlElementName": "Group", - "height": 91, - "id": "ac7c0", - "kaavioType": "Group", - "padding": 8, - "stroke": "#808080", - "strokeDasharray": "5,3", - "strokeWidth": 0, - "textAlign": "center", - "type": [ - "Group", - "GroupGroup" - ], - "verticalAlign": "middle", - "width": 77, - "x": 440, - "y": 302.5, - "zIndex": 32774 - }, "ad1bc": { "burrs": [ "f7e81" @@ -403,7 +378,7 @@ "gpmlElementName": "DataNode", "height": 25, "id": "b3438", - "isPartOf": "fbbec", + "isPartOf": "d643c", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -440,39 +415,10 @@ "y": 33, "zIndex": 32778 }, - "b99fc": { + "b827a": { "contains": [ - "c32fb", - "c9bb7" - ], - "drawAs": "none", - "fill": "transparent", - "fillOpacity": 0.1, - "fontSize": 1, - "fontWeight": "bold", - "gpmlElementName": "Group", - "height": 66.00000000000006, - "id": "b99fc", - "kaavioType": "Group", - "padding": 8, - "stroke": "#808080", - "strokeDasharray": "5,3", - "strokeWidth": 0, - "textAlign": "center", - "type": [ - "Group", - "GroupGroup" - ], - "verticalAlign": "middle", - "width": 77, - "x": 6.577284339671735, - "y": 218.19323379583574, - "zIndex": 32786 - }, - "bdebf": { - "contains": [ - "ab405", - "a545e" + "e3a0e", + "d5a02" ], "drawAs": "none", "fill": "transparent", @@ -481,7 +427,7 @@ "fontWeight": "bold", "gpmlElementName": "Group", "height": 66, - "id": "bdebf", + "id": "b827a", "kaavioType": "Group", "padding": 8, "stroke": "#808080", @@ -493,75 +439,10 @@ "GroupGroup" ], "verticalAlign": "middle", - "width": 77, - "x": 175.58015267175583, - "y": 111.54580152671755, - "zIndex": 32768 - }, - "c032c": { - "drawAs": "StraightLine", - "fill": "none", - "gpmlElementName": "Interaction", - "id": "c032c", - "isAttachedTo": [ - "b99fc", - "df2bb" - ], - "kaavioType": "Edge", - "markerEnd": "Arrow", - "points": [ - { - "attachmentDisplay": { - "offset": [ - 0, - 0 - ], - "position": [ - 1, - 0.5 - ] - }, - "id": "d5a36", - "isAttachedTo": "b99fc", - "orientation": [ - 1, - 0 - ], - "x": 83.57728433967173, - "y": 251.19323379583577 - }, - { - "attachmentDisplay": { - "offset": [ - 0, - 0 - ], - "position": [ - 0, - 0.25 - ] - }, - "id": "a71a1", - "isAttachedTo": "df2bb", - "orientation": [ - 1, - 0 - ], - "x": 129.93980327066325, - "y": 275.6120141045448 - } - ], - "stroke": "#000000", - "strokeWidth": 1, - "type": [ - "Interaction", - "Edge", - "SBO:0000167", - "SBO:0000393", - "SBO:0000394", - "DirectedInteraction" - ], - "zIndex": 12288 + "width": 111, + "x": 261, + "y": 326.5, + "zIndex": 32772 }, "c32fb": { "drawAs": "rect", @@ -573,7 +454,7 @@ "gpmlElementName": "DataNode", "height": 25, "id": "c32fb", - "isPartOf": "b99fc", + "isPartOf": "a00f8", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -606,35 +487,6 @@ "y": 33.00000000000006, "zIndex": 32786 }, - "c8040": { - "contains": [ - "e3a0e", - "d5a02" - ], - "drawAs": "none", - "fill": "transparent", - "fillOpacity": 0.1, - "fontSize": 1, - "fontWeight": "bold", - "gpmlElementName": "Group", - "height": 66, - "id": "c8040", - "kaavioType": "Group", - "padding": 8, - "stroke": "#808080", - "strokeDasharray": "5,3", - "strokeWidth": 0, - "textAlign": "center", - "type": [ - "Group", - "GroupGroup" - ], - "verticalAlign": "middle", - "width": 111, - "x": 261, - "y": 326.5, - "zIndex": 32772 - }, "c888f": { "drawAs": "none", "fill": "transparent", @@ -676,7 +528,7 @@ "gpmlElementName": "DataNode", "height": 25, "id": "c9bb7", - "isPartOf": "b99fc", + "isPartOf": "a00f8", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -765,8 +617,8 @@ "gpmlElementName": "Interaction", "id": "d2ad6", "isAttachedTo": [ - "d524f", - "bdebf" + "f11cd", + "d955e" ], "kaavioType": "Edge", "markerEnd": "MimTranscriptionTranslation", @@ -782,8 +634,7 @@ 0.5 ] }, - "id": "a90a9", - "isAttachedTo": "d524f", + "isAttachedTo": "f11cd", "orientation": [ -1, 0 @@ -802,8 +653,7 @@ 0.5 ] }, - "id": "e4f5a", - "isAttachedTo": "bdebf", + "isAttachedTo": "d955e", "orientation": [ -1, 0 @@ -827,7 +677,7 @@ "gpmlElementName": "Interaction", "id": "d2dee", "isAttachedTo": [ - "ac7c0", + "f558b", "c888f" ], "kaavioType": "Edge", @@ -844,8 +694,7 @@ 1 ] }, - "id": "eb7db", - "isAttachedTo": "ac7c0", + "isAttachedTo": "f558b", "orientation": [ 0, 1 @@ -864,7 +713,6 @@ 0 ] }, - "id": "fed65", "isAttachedTo": "c888f", "orientation": [ 0, @@ -886,35 +734,6 @@ ], "zIndex": 32789 }, - "d524f": { - "contains": [ - "aacb8", - "ab411" - ], - "drawAs": "none", - "fill": "transparent", - "fillOpacity": 0.1, - "fontSize": 1, - "fontWeight": "bold", - "gpmlElementName": "Group", - "height": 65.99999999999997, - "id": "d524f", - "kaavioType": "Group", - "padding": 8, - "stroke": "#808080", - "strokeDasharray": "5,3", - "strokeWidth": 0, - "textAlign": "center", - "type": [ - "Group", - "GroupGroup" - ], - "verticalAlign": "middle", - "width": 112, - "x": 378.8091603053435, - "y": 111.92547690801453, - "zIndex": 32768 - }, "d5a02": { "drawAs": "rect", "fill": "#ffffff", @@ -925,7 +744,7 @@ "gpmlElementName": "DataNode", "height": 25, "id": "d5a02", - "isPartOf": "c8040", + "isPartOf": "b827a", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -960,6 +779,36 @@ "y": 33, "zIndex": 32773 }, + "d643c": { + "contains": [ + "e95b1", + "b3438", + "f8b16" + ], + "drawAs": "none", + "fill": "transparent", + "fillOpacity": 0.1, + "fontSize": 1, + "fontWeight": "bold", + "gpmlElementName": "Group", + "height": 91, + "id": "d643c", + "kaavioType": "Group", + "padding": 8, + "stroke": "#808080", + "strokeDasharray": "5,3", + "strokeWidth": 0, + "textAlign": "center", + "type": [ + "Group", + "GroupGroup" + ], + "verticalAlign": "middle", + "width": 77, + "x": 536, + "y": 303.5, + "zIndex": 32777 + }, "d8d56": { "attachmentDisplay": { "offset": [ @@ -985,6 +834,35 @@ "width": 0, "zIndex": 12288 }, + "d955e": { + "contains": [ + "ab405", + "a545e" + ], + "drawAs": "none", + "fill": "transparent", + "fillOpacity": 0.1, + "fontSize": 1, + "fontWeight": "bold", + "gpmlElementName": "Group", + "height": 66, + "id": "d955e", + "kaavioType": "Group", + "padding": 8, + "stroke": "#808080", + "strokeDasharray": "5,3", + "strokeWidth": 0, + "textAlign": "center", + "type": [ + "Group", + "GroupGroup" + ], + "verticalAlign": "middle", + "width": 77, + "x": 175.58015267175583, + "y": 111.54580152671755, + "zIndex": 32768 + }, "dea00": { "drawAs": "rect", "fill": "#ffffff", @@ -1075,7 +953,7 @@ "gpmlElementName": "DataNode", "height": 25, "id": "e3a0e", - "isPartOf": "c8040", + "isPartOf": "b827a", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -1121,7 +999,7 @@ "gpmlElementName": "DataNode", "height": 25, "id": "e5f2c", - "isPartOf": "ac7c0", + "isPartOf": "f558b", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -1167,7 +1045,7 @@ "gpmlElementName": "DataNode", "height": 25, "id": "e95b1", - "isPartOf": "fbbec", + "isPartOf": "d643c", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -1204,6 +1082,35 @@ "y": 8, "zIndex": 32777 }, + "f11cd": { + "contains": [ + "aacb8", + "ab411" + ], + "drawAs": "none", + "fill": "transparent", + "fillOpacity": 0.1, + "fontSize": 1, + "fontWeight": "bold", + "gpmlElementName": "Group", + "height": 65.99999999999997, + "id": "f11cd", + "kaavioType": "Group", + "padding": 8, + "stroke": "#808080", + "strokeDasharray": "5,3", + "strokeWidth": 0, + "textAlign": "center", + "type": [ + "Group", + "GroupGroup" + ], + "verticalAlign": "middle", + "width": 112, + "x": 378.8091603053435, + "y": 111.92547690801453, + "zIndex": 32768 + }, "f279d": { "drawAs": "rect", "fill": "#ffffff", @@ -1214,7 +1121,7 @@ "gpmlElementName": "DataNode", "height": 25, "id": "f279d", - "isPartOf": "ac7c0", + "isPartOf": "f558b", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -1270,7 +1177,6 @@ 1 ] }, - "id": "a81ee", "isAttachedTo": "ca5ca", "orientation": [ 0, @@ -1290,7 +1196,6 @@ 0 ] }, - "id": "f9426", "isAttachedTo": "dea00", "orientation": [ 0, @@ -1312,6 +1217,36 @@ ], "zIndex": 32790 }, + "f558b": { + "contains": [ + "e5f2c", + "a66fd", + "f279d" + ], + "drawAs": "none", + "fill": "transparent", + "fillOpacity": 0.1, + "fontSize": 1, + "fontWeight": "bold", + "gpmlElementName": "Group", + "height": 91, + "id": "f558b", + "kaavioType": "Group", + "padding": 8, + "stroke": "#808080", + "strokeDasharray": "5,3", + "strokeWidth": 0, + "textAlign": "center", + "type": [ + "Group", + "GroupGroup" + ], + "verticalAlign": "middle", + "width": 77, + "x": 440, + "y": 302.5, + "zIndex": 32774 + }, "f61a0": { "drawAs": "none", "fill": "transparent", @@ -1385,7 +1320,7 @@ "gpmlElementName": "DataNode", "height": 25, "id": "f8b16", - "isPartOf": "fbbec", + "isPartOf": "d643c", "kaavioType": "SingleFreeNode", "lineHeight": 1.1, "overflow": "hidden", @@ -1420,36 +1355,6 @@ "y": 58, "zIndex": 32779 }, - "fbbec": { - "contains": [ - "e95b1", - "b3438", - "f8b16" - ], - "drawAs": "none", - "fill": "transparent", - "fillOpacity": 0.1, - "fontSize": 1, - "fontWeight": "bold", - "gpmlElementName": "Group", - "height": 91, - "id": "fbbec", - "kaavioType": "Group", - "padding": 8, - "stroke": "#808080", - "strokeDasharray": "5,3", - "strokeWidth": 0, - "textAlign": "center", - "type": [ - "Group", - "GroupGroup" - ], - "verticalAlign": "middle", - "width": 77, - "x": 536, - "y": 303.5, - "zIndex": 32777 - }, "fe54e": { "drawAs": "rect", "fill": "#ffffff", @@ -1506,13 +1411,33 @@ "y": 241.5, "zIndex": 32768 }, + "http://identifiers.org/doid/DOID:9256": { + "gpmlElementName": "openControlledVocabulary", + "id": "http://identifiers.org/doid/DOID:9256", + "ontology": "Disease", + "term": "colorectal cancer", + "type": [ + "openControlledVocabulary" + ], + "xrefIdentifier": "DOID:9256" + }, + "http://identifiers.org/pw/PW:0000003": { + "gpmlElementName": "openControlledVocabulary", + "id": "http://identifiers.org/pw/PW:0000003", + "ontology": "Pathway Ontology", + "term": "signaling pathway", + "type": [ + "openControlledVocabulary" + ], + "xrefIdentifier": "PW:0000003" + }, "id2e7e9608": { "drawAs": "StraightLine", "fill": "none", "gpmlElementName": "Interaction", "id": "id2e7e9608", "isAttachedTo": [ - "fbbec", + "d643c", "c888f" ], "kaavioType": "Edge", @@ -1529,8 +1454,7 @@ 1 ] }, - "id": "d2b14", - "isAttachedTo": "fbbec", + "isAttachedTo": "d643c", "orientation": [ 0, 1 @@ -1549,7 +1473,6 @@ 0 ] }, - "id": "d7f4a", "isAttachedTo": "c888f", "orientation": [ 0, @@ -1578,7 +1501,7 @@ "id": "id67204f6c", "isAttachedTo": [ "fe54e", - "ac7c0" + "f558b" ], "kaavioType": "Edge", "markerEnd": "Arrow", @@ -1594,7 +1517,6 @@ 1 ] }, - "id": "d3e95", "isAttachedTo": "fe54e", "orientation": [ 0, @@ -1614,8 +1536,7 @@ 0 ] }, - "id": "ffd0b", - "isAttachedTo": "ac7c0", + "isAttachedTo": "f558b", "orientation": [ 0, 1 @@ -1659,7 +1580,6 @@ 1 ] }, - "id": "e1cd7", "isAttachedTo": "df2bb", "orientation": [ 0, @@ -1679,7 +1599,6 @@ 0 ] }, - "id": "ee62b", "isAttachedTo": "dea00", "orientation": [ 0, @@ -1724,7 +1643,6 @@ 0.5 ] }, - "id": "c44a7", "isAttachedTo": "ca5ca", "orientation": [ 1, @@ -1744,7 +1662,6 @@ 0.5 ] }, - "id": "a138e", "isAttachedTo": "fe54e", "orientation": [ 1, @@ -1772,7 +1689,7 @@ "gpmlElementName": "Interaction", "id": "id99c9121f", "isAttachedTo": [ - "d524f", + "f11cd", "ca5ca" ], "kaavioType": "Edge", @@ -1789,8 +1706,7 @@ 0.5 ] }, - "id": "ed1c5", - "isAttachedTo": "d524f", + "isAttachedTo": "f11cd", "orientation": [ -1, 0 @@ -1809,7 +1725,6 @@ 0 ] }, - "id": "c94c4", "isAttachedTo": "ca5ca", "orientation": [ 0, @@ -1851,7 +1766,6 @@ 1 ] }, - "id": "e48ef", "isAttachedTo": "dea00", "orientation": [ 0, @@ -1871,7 +1785,6 @@ 0.25 ] }, - "id": "ce538", "isAttachedTo": "f61a0", "orientation": [ 1, @@ -1899,7 +1812,7 @@ "gpmlElementName": "Interaction", "id": "idd2f7294d", "isAttachedTo": [ - "bdebf", + "d955e", "idd54b8361" ], "kaavioType": "Edge", @@ -1916,8 +1829,7 @@ 0.5 ] }, - "id": "ca144", - "isAttachedTo": "bdebf", + "isAttachedTo": "d955e", "orientation": [ -1, 0 @@ -1937,7 +1849,6 @@ 0 ] }, - "id": "ba797", "isAttachedTo": "d8d56", "orientation": [ 0, @@ -1964,7 +1875,7 @@ "gpmlElementName": "Interaction", "id": "idd54b8361", "isAttachedTo": [ - "b99fc", + "a00f8", "ad1bc" ], "kaavioType": "Edge", @@ -1981,8 +1892,7 @@ 0.5 ] }, - "id": "a0d9c", - "isAttachedTo": "b99fc", + "isAttachedTo": "a00f8", "orientation": [ 1, 0 @@ -2001,7 +1911,6 @@ 0.5 ] }, - "id": "ab7c1", "isAttachedTo": "ad1bc", "orientation": [ 1, @@ -2029,7 +1938,7 @@ "gpmlElementName": "Interaction", "id": "idd975a653", "isAttachedTo": [ - "c8040", + "b827a", "f61a0" ], "kaavioType": "Edge", @@ -2046,8 +1955,7 @@ 1 ] }, - "id": "e5847", - "isAttachedTo": "c8040", + "isAttachedTo": "b827a", "orientation": [ 0, 1 @@ -2066,7 +1974,6 @@ 0 ] }, - "id": "eb31c", "isAttachedTo": "f61a0", "orientation": [ 0, @@ -2095,7 +2002,7 @@ "id": "iddeb3a82e", "isAttachedTo": [ "ca5ca", - "c8040" + "b827a" ], "kaavioType": "Edge", "markerEnd": "Arrow", @@ -2111,7 +2018,6 @@ 1 ] }, - "id": "aa229", "isAttachedTo": "ca5ca", "orientation": [ 0, @@ -2131,8 +2037,7 @@ 0 ] }, - "id": "f297d", - "isAttachedTo": "c8040", + "isAttachedTo": "b827a", "orientation": [ 0, 1 @@ -2160,7 +2065,7 @@ "id": "idedaf9dc2", "isAttachedTo": [ "fe54e", - "fbbec" + "d643c" ], "kaavioType": "Edge", "markerEnd": "MimInhibition", @@ -2176,7 +2081,6 @@ 1 ] }, - "id": "d4292", "isAttachedTo": "fe54e", "orientation": [ 0, @@ -2196,8 +2100,7 @@ 0 ] }, - "id": "daa4c", - "isAttachedTo": "fbbec", + "isAttachedTo": "d643c", "orientation": [ 0, 1 @@ -2220,7 +2123,7 @@ "gpmlElementName": "Interaction", "id": "idef46713c", "isAttachedTo": [ - "ac7c0", + "f558b", "f61a0" ], "kaavioType": "Edge", @@ -2237,8 +2140,7 @@ 1 ] }, - "id": "f6651", - "isAttachedTo": "ac7c0", + "isAttachedTo": "f558b", "orientation": [ 0, 1 @@ -2257,7 +2159,6 @@ 0.25 ] }, - "id": "a1165", "isAttachedTo": "f61a0", "orientation": [ -1, @@ -2279,6 +2180,69 @@ ], "zIndex": 12288 }, + "idf1452b33": { + "drawAs": "StraightLine", + "fill": "none", + "gpmlElementName": "Interaction", + "id": "idf1452b33", + "isAttachedTo": [ + "a00f8", + "df2bb" + ], + "kaavioType": "Edge", + "markerEnd": "Arrow", + "points": [ + { + "attachmentDisplay": { + "offset": [ + 0, + 0 + ], + "position": [ + 1, + 0.5 + ] + }, + "isAttachedTo": "a00f8", + "orientation": [ + 1, + 0 + ], + "x": 83.57728433967173, + "y": 251.19323379583577 + }, + { + "attachmentDisplay": { + "offset": [ + 0, + 0 + ], + "position": [ + 0, + 0.25 + ] + }, + "isAttachedTo": "df2bb", + "orientation": [ + 1, + 0 + ], + "x": 129.93980327066325, + "y": 275.6120141045448 + } + ], + "stroke": "#000000", + "strokeWidth": 1, + "type": [ + "Interaction", + "Edge", + "SBO:0000167", + "SBO:0000393", + "SBO:0000394", + "DirectedInteraction" + ], + "zIndex": 12288 + }, "publicationXrefcdc": { "authors": [ "Ohtsuka M", @@ -2324,13 +2288,13 @@ "@context": [ "https://cdn.rawgit.com/wikipathways/WpVocabularies/7a46a05/contexts/pvjs.jsonld", { - "@base": "http://identifiers.org/wikipathways/WP3969/" + "@base": "WP3969/" } ], - "author": "[Khanspers, AlexanderPico, Egonw]", + "author": "[Khanspers, AlexanderPico, Egonw, Mkutmon, Eweitz]", "comments": [ { - "content": "In this proposed model, H19 interacts with macroH2A, and this may consequently lead to de-repression of genes including CDK8, CDK4, and CCND1. Increased CDK4-cyclin D1 complex phosphorylates Rb to disrupt Rb-E2F1 interaction, leading to E2F1 activation. The increase of CDK8 expression enhances the function of mediator complex including MED1, and facilitates the gene regulation by β-catenin. These downstream targets could work in a synergistic way of promoting cell proliferation and increasing cell motility in CRC.\r\nReference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5264449/\r\n\r\nProteins on this pathway have targeted assays available via the [https://assays.cancer.gov/available_assays?wp_id=WP3969 CPTAC Assay Portal]", + "content": "In this proposed model, H19 interacts with macroH2A, and this may consequently lead to de-repression of genes including CDK8, CDK4, and CCND1. Increased CDK4-cyclin D1 complex phosphorylates Rb to disrupt Rb-E2F1 interaction, leading to E2F1 activation. The increase of CDK8 expression enhances the function of mediator complex including MED1, and facilitates the gene regulation by beta-catenin. These downstream targets could work in a synergistic way of promoting cell proliferation and increasing cell motility in colorectal cancer.\r\nReference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5264449/\r\n\r\nProteins on this pathway have targeted assays available via the [https://assays.cancer.gov/available_assays?wp_id=WP3969 CPTAC Assay Portal]", "source": "WikiPathways-description" } ], @@ -2338,8 +2302,8 @@ "id8f30766f", "id947172ed", "idc02d1cf8", - "c032c", "idd54b8361", + "idf1452b33", "idd975a653", "iddeb3a82e", "id2e7e9608", @@ -2351,43 +2315,44 @@ "f61a0", "dea00", "fe54e", - "bdebf", - "d524f", + "d955e", + "f11cd", "df2bb", "ca5ca", - "c8040", - "ac7c0", - "fbbec", + "b827a", + "f558b", + "d643c", "ad1bc", "c888f", "d2ad6", - "b99fc", + "a00f8", "a1939", "d2dee", "f3447" ], - "dataSourceVersion": "WP3969_r123402", - "displayName": "H19 action Rb-E2F1 signaling and CDK-Beta-catenin activity", + "dataSourceVersion": "WP3969_r129540", + "displayName": "H19, Rb-E2F1, and CDK-beta-catenin in colorectal cancer", "drawAs": "rect", "fill": "white", "fontSize": 12, "fontWeight": "bold", "gpmlElementName": "Pathway", "height": 527.5420841683372, - "id": "http://identifiers.org/wikipathways/WP3969", + "id": "WP3969", "kaavioType": "Group", - "lastModified": "20220723062748", - "name": "H19 action Rb-E2F1 signaling and CDK-Beta-catenin activity", + "lastModified": "20240510154947", + "name": "H19, Rb-E2F1, and CDK-beta-catenin in colorectal cancer", "organism": "Homo sapiens", "padding": 5, "pathwayVersion": "WP3969", - "standardName": "H19 action Rb-E2F1 signaling and CDK-Beta-catenin activity", + "standardName": "H19, Rb-E2F1, and CDK-beta-catenin in colorectal cancer", "stroke": "black", "strokeWidth": 0, "textAlign": "left", - "textContent": "Name: H19 action Rb-E2F1 signaling and CDK-Beta-catenin activity\nLast Modified: 20220723062748\nOrganism: Homo sapiens", + "textContent": "Name: H19, Rb-E2F1, and CDK-beta-catenin in colorectal cancer\nLast Modified: 20240510154947\nOrganism: Homo sapiens", "type": [ - "Pathway" + "Pathway", + "http://identifiers.org/pw/PW:0000003" ], "verticalAlign": "top", "width": 650.002004008016, diff --git a/pathways/WP3969/WP3969.png b/pathways/WP3969/WP3969.png index e92e2be18..67df45c00 100644 Binary files a/pathways/WP3969/WP3969.png and b/pathways/WP3969/WP3969.png differ diff --git a/pathways/WP3969/WP3969.svg b/pathways/WP3969/WP3969.svg index 412e62d62..87b7ade1a 100644 --- a/pathways/WP3969/WP3969.svg +++ b/pathways/WP3969/WP3969.svg @@ -1,5 +1,5 @@ - + @@ -448,8 +448,8 @@ - - + + @@ -465,11 +465,6 @@ - - - - - @@ -478,6 +473,11 @@ + + + + + @@ -536,8 +536,8 @@ CTNNB1 - - + + @@ -551,15 +551,15 @@ - - + + macroH2A - + H19 @@ -578,8 +578,8 @@ CDK8 - - + + @@ -593,8 +593,8 @@ - - + + @@ -614,8 +614,8 @@ - - + + @@ -658,8 +658,8 @@ - - + + @@ -688,9 +688,9 @@ - - Name: H19 action Rb-E2F1 signaling and CDK-Beta-catenin activity - Last Modified: 20220723062748 + + Name: H19, Rb-E2F1, and CDK-beta-catenin in colorectal cancer + Last Modified: 20240510154947 Organism: Homo sapiens diff --git a/pathways/WP4666/WP4666.gpml b/pathways/WP4666/WP4666.gpml index 3d673c4e2..8b9f0d277 100644 --- a/pathways/WP4666/WP4666.gpml +++ b/pathways/WP4666/WP4666.gpml @@ -1,6 +1,6 @@ - - The Hepatitis B virus (HBV) is a virus in the Hepadnaviridae family which infects hepatocytes in the liver. It causes both acute and chronic infections, and prolonged chronic infection can lead to complications such as cirrhosis and an increased risk of hepatocellular carcinoma (HCC). + + The bepatitis B virus (HBV) is a virus in the Hepadnaviridae family which infects hepatocytes in the liver. It causes both acute and chronic infections, and prolonged chronic infection can lead to complications such as cirrhosis and an increased risk of hepatocellular carcinoma (HCC). The left side of the pathway describes the pathogenesis of HBV. The virus binds NTCP (SLC10A1) and is subsequently endocytosed. It is transported to the nucleus where viral polymerase creates covalently closed circular DNA (cccDNA). Using the host RNA polymerase, this is transcribed into viral mRNAs. Viral DNA polymerase then synthesizes viral DNA via its reverse transcriptase activity. Assembled viral particles exit the cell via the ESCRT pathway. The HBV regulatory protein HBx interferes with many cellular processes including transcription, signal transduction, cell cycle progress, protein degradation, apoptosis and chromosomal stability. @@ -2342,6 +2342,16 @@ This pathway was developed based on https://www.kegg.jp/dbget-bin/www_bget?pathw Latham V Skrzypek E + + disease pathway + PW:0000013 + Pathway Ontology + + + infectious disease pathway + PW:0001028 + Pathway Ontology + hepatocyte CL:0000182 diff --git a/pathways/WP4666/WP4666.json b/pathways/WP4666/WP4666.json index 2ff767027..e006a9f14 100644 --- a/pathways/WP4666/WP4666.json +++ b/pathways/WP4666/WP4666.json @@ -17675,6 +17675,26 @@ ], "xrefIdentifier": "DOID:2043" }, + "http://identifiers.org/pw/PW:0000013": { + "gpmlElementName": "openControlledVocabulary", + "id": "http://identifiers.org/pw/PW:0000013", + "ontology": "Pathway Ontology", + "term": "disease pathway", + "type": [ + "openControlledVocabulary" + ], + "xrefIdentifier": "PW:0000013" + }, + "http://identifiers.org/pw/PW:0001028": { + "gpmlElementName": "openControlledVocabulary", + "id": "http://identifiers.org/pw/PW:0001028", + "ontology": "Pathway Ontology", + "term": "infectious disease pathway", + "type": [ + "openControlledVocabulary" + ], + "xrefIdentifier": "PW:0001028" + }, "id12414a79": { "drawAs": "StraightLine", "fill": "none", @@ -24448,13 +24468,13 @@ "@context": [ "https://cdn.rawgit.com/wikipathways/WpVocabularies/7a46a05/contexts/pvjs.jsonld", { - "@base": "http://identifiers.org/wikipathways/WP4666/" + "@base": "WP4666/" } ], - "author": "[Khanspers, Finterly, Egonw]", + "author": "[Khanspers, Finterly, Egonw, Mkutmon, Eweitz]", "comments": [ { - "content": "The Hepatitis B virus (HBV) is a virus in the Hepadnaviridae family which infects hepatocytes in the liver. It causes both acute and chronic infections, and prolonged chronic infection can lead to complications such as cirrhosis and an increased risk of hepatocellular carcinoma (HCC). \r\nThe left side of the pathway describes the pathogenesis of HBV. The virus binds NTCP (SLC10A1) and is subsequently endocytosed. It is transported to the nucleus where viral polymerase creates covalently closed circular DNA (cccDNA). Using the host RNA polymerase, this is transcribed into viral mRNAs. Viral DNA polymerase then synthesizes viral DNA via its reverse transcriptase activity. Assembled viral particles exit the cell via the ESCRT pathway.\r\n\r\nThe HBV regulatory protein HBx interferes with many cellular processes including transcription, signal transduction, cell cycle progress, protein degradation, apoptosis and chromosomal stability. \r\nThis pathway was developed based on https://www.kegg.jp/dbget-bin/www_bget?pathway+hsa05161. Protein phosphorylation sites were added based on information from PhosphoSitePlus (R), www.phosphosite.org", + "content": "The bepatitis B virus (HBV) is a virus in the Hepadnaviridae family which infects hepatocytes in the liver. It causes both acute and chronic infections, and prolonged chronic infection can lead to complications such as cirrhosis and an increased risk of hepatocellular carcinoma (HCC). \r\nThe left side of the pathway describes the pathogenesis of HBV. The virus binds NTCP (SLC10A1) and is subsequently endocytosed. It is transported to the nucleus where viral polymerase creates covalently closed circular DNA (cccDNA). Using the host RNA polymerase, this is transcribed into viral mRNAs. Viral DNA polymerase then synthesizes viral DNA via its reverse transcriptase activity. Assembled viral particles exit the cell via the ESCRT pathway.\r\n\r\nThe HBV regulatory protein HBx interferes with many cellular processes including transcription, signal transduction, cell cycle progress, protein degradation, apoptosis and chromosomal stability. \r\nThis pathway was developed based on https://www.kegg.jp/dbget-bin/www_bget?pathway+hsa05161. Protein phosphorylation sites were added based on information from PhosphoSitePlus (R), www.phosphosite.org", "source": "WikiPathways-description" } ], @@ -24748,7 +24768,7 @@ "e60d7", "b19d7" ], - "dataSourceVersion": "WP4666_r127759", + "dataSourceVersion": "WP4666_r129538", "displayName": "Hepatitis B infection", "drawAs": "rect", "fill": "white", @@ -24756,9 +24776,9 @@ "fontWeight": "bold", "gpmlElementName": "Pathway", "height": 1670.3129231284072, - "id": "http://identifiers.org/wikipathways/WP4666", + "id": "WP4666", "kaavioType": "Group", - "lastModified": "20231203092514", + "lastModified": "20240510154504", "name": "Hepatitis B infection", "organism": "Homo sapiens", "padding": 5, @@ -24767,9 +24787,11 @@ "stroke": "black", "strokeWidth": 0, "textAlign": "left", - "textContent": "Name: Hepatitis B infection\nLast Modified: 20231203092514\nOrganism: Homo sapiens", + "textContent": "Name: Hepatitis B infection\nLast Modified: 20240510154504\nOrganism: Homo sapiens", "type": [ - "Pathway" + "Pathway", + "http://identifiers.org/pw/PW:0000013", + "http://identifiers.org/pw/PW:0001028" ], "verticalAlign": "top", "width": 3138, diff --git a/pathways/WP4666/WP4666.png b/pathways/WP4666/WP4666.png index a2c0a7749..bd24b5e29 100644 Binary files a/pathways/WP4666/WP4666.png and b/pathways/WP4666/WP4666.png differ diff --git a/pathways/WP4666/WP4666.svg b/pathways/WP4666/WP4666.svg index 09592dad6..0d3cb0da6 100644 --- a/pathways/WP4666/WP4666.svg +++ b/pathways/WP4666/WP4666.svg @@ -1,5 +1,5 @@ - + @@ -478,8 +478,8 @@ - - + + @@ -3231,9 +3231,9 @@ - + Name: Hepatitis B infection - Last Modified: 20231203092514 + Last Modified: 20240510154504 Organism: Homo sapiens