diff --git a/_data/drafts/WP010-bibliography.tsv b/_data/drafts/WP010-bibliography.tsv deleted file mode 100644 index 19b0dd46..00000000 --- a/_data/drafts/WP010-bibliography.tsv +++ /dev/null @@ -1,4 +0,0 @@ -ID Database Citation -10.1002/cmdc.201600105 DOI "An Endogenous Mammalian Retinoid X Receptor Ligand, At Last! de Lera ÁR, Krezel W, Rühl R. ChemMedChem [Internet]. 2016 May 6;11(10):1027–37. Available from: http://dx.doi.org/10.1002/cmdc.201600105 DOI" -26030625 Pubmed "9-cis-13,14-Dihydroretinoic Acid Is an Endogenous Retinoid Acting as RXR Ligand in Mice. Rühl R, Krzyżosiak A, Niewiadomska-Cimicka A, Rochel N, Szeles L, Vaz B, et al. PLoS Genet. 2015 Jun 1;11(6):e1005213. PubMed Europe PMC Scholia" -33809241 Pubmed "Vitamin A5/X, a New Food to Lipid Hormone Concept for a Nutritional Ligand to Control RXR-Mediated Signaling. Krężel W, Rivas A, Szklenar M, Ciancia M, Alvarez R, de Lera AR, et al. Nutrients. 2021 Mar 12;13(3):925. PubMed Europe PMC Scholia" diff --git a/_data/drafts/WP010-datanodes.tsv b/_data/drafts/WP010-datanodes.tsv deleted file mode 100644 index 5fc7fda0..00000000 --- a/_data/drafts/WP010-datanodes.tsv +++ /dev/null @@ -1,18 +0,0 @@ -Label Type Identifier Comment Ensembl NCBI gene HGNC UniProt Wikidata ChEBI InChI -ATBC Metabolite wikidata:Q306135 "provitamin A1" wikidata:Q306135 chebi:17579;chebi:17579 inchikey:OENHQHLEOONYIE-JLTXGRSLSA-N -9CDHROL-ES Metabolite wikidata:Q120868159 "" -9CDHROL Metabolite wikidata:Q120868469 "" -9CBC Metabolite wikidata:Q27135678 "" wikidata:Q27135678 chebi:67188;chebi:67188 inchikey:OENHQHLEOONYIE-BVZAMQQESA-N -9CDHBC Metabolite wikidata:Q120868409 "" -9CDHRA Metabolite wikidata:Q120868444 "vitamin A5/X acid
Both R and S forms bind, but R better. The R stereoisomer is patented" -9CDHRA-ES Metabolite wikidata:Q120868227 "" -ATRA Metabolite pubchem.compound:444795 "vitamin A1 acid" wikidata:Q29417 chebi:15367;chebi:15367 inchikey:SHGAZHPCJJPHSC-YCNIQYBTSA-N -ATRAL Metabolite pubchem.compound:638015 "vitamin A1 aldehyde" wikidata:Q28529715 chebi:17898;chebi:17898 inchikey:NCYCYZXNIZJOKI-OVSJKPMPSA-N -ATROL Metabolite pubchem.compound:445354 "vitamin A1" wikidata:Q424976 chebi:17336;chebi:17336 inchikey:FPIPGXGPPPQFEQ-OVSJKPMPSA-N -ATROL-ES Metabolite wikidata:Q120868257 "vitamin A1" -RXRa Protein ncbigene:6256 "" ensembl:ENSG00000186350 ncbigene:6256 hgnc.symbol:RXRA uniprot:A0A5F9ZHH6;uniprot:F1D8Q5;uniprot:P19793;uniprot:A0A3B3IS44 -RXRb Protein ncbigene:6257 "" ensembl:ENSG00000204231 ncbigene:6257 hgnc.symbol:RXRB uniprot:Q5STP9;uniprot:P28702;uniprot:E9PK75;uniprot:A0A0S2Z570 -RXRc Protein ncbigene:6258 "" ensembl:ENSG00000143171 ncbigene:6258 hgnc.symbol:RXRG uniprot:P48443;uniprot:F1D8Q7;uniprot:A0A087WZ88 -RARa Protein ncbigene:5914 "" ensembl:ENSG00000131759 ncbigene:5914 hgnc.symbol:RARA uniprot:J3QRM2;uniprot:A8MUP8;uniprot:F1D8N9;uniprot:J3KSJ4;uniprot:P10276;uniprot:Q6I9R7 -RARb Protein ncbigene:5915 "" ensembl:ENSG00000077092 ncbigene:5915 hgnc.symbol:RARB uniprot:D6RBI3;uniprot:P10826;uniprot:F1D8S6;uniprot:Q5QHG3 -RARg Protein ncbigene:5916 "" ensembl:ENSG00000172819 ncbigene:5916 hgnc.symbol:RARG uniprot:P13631;uniprot:H3BMK1;uniprot:F1D8P1;uniprot:A8K3H3;uniprot:H3BMH6;uniprot:H3BMY6 diff --git a/_data/drafts/WP554-bibliography.tsv b/_data/drafts/WP554-bibliography.tsv deleted file mode 100644 index 5f732c2a..00000000 --- a/_data/drafts/WP554-bibliography.tsv +++ /dev/null @@ -1,8 +0,0 @@ -ID Database Citation -15134803 Pubmed "The regulation of aldosterone synthase expression. Bassett MH, White PC, Rainey WE. Mol Cell Endocrinol. 2004 Mar 31;217(1–2):67–74. PubMed Europe PMC Scholia" -15174896 Pubmed "Pharmacogenetics of antihypertensive drug responses. Schwartz GL, Turner ST. Am J Pharmacogenomics. 2004;4(3):151–60. PubMed Europe PMC Scholia" -16374430 Pubmed "Renin increases mesangial cell transforming growth factor-beta1 and matrix proteins through receptor-mediated, angiotensin II-independent mechanisms. Huang Y, Wongamorntham S, Kasting J, McQuillan D, Owens RT, Yu L, et al. Kidney Int. 2006 Jan;69(1):105–13. PubMed Europe PMC Scholia" -17464936 Pubmed "The emerging role of ACE2 in physiology and disease. Hamming I, Cooper ME, Haagmans BL, Hooper NM, Korstanje R, Osterhaus ADME, et al. J Pathol. 2007 May;212(1):1–11. PubMed Europe PMC Scholia" -18035185 Pubmed "Effects of renin-angiotensin system inhibition on end-organ protection: can we do better? Weir MR. Clin Ther. 2007 Sep;29(9):1803–24. PubMed Europe PMC Scholia" -18417113 Pubmed "The (pro)renin receptor: a new addition to the renin-angiotensin system? Batenburg WW, Jan Danser AH. Eur J Pharmacol. 2008 May 13;585(2–3):320–4. PubMed Europe PMC Scholia" -18449520 Pubmed "Are we poised to target ACE2 for the next generation of antihypertensives? Ferreira AJ, Raizada MK. J Mol Med (Berl). 2008 Jun;86(6):685–90. PubMed Europe PMC Scholia" diff --git a/_data/drafts/WP554-datanodes.tsv b/_data/drafts/WP554-datanodes.tsv deleted file mode 100644 index b712cc67..00000000 --- a/_data/drafts/WP554-datanodes.tsv +++ /dev/null @@ -1,32 +0,0 @@ -Label Type Identifier Comment Ensembl NCBI gene HGNC UniProt Wikidata ChEBI InChI -Bradykinin Metabolite hmdb:HMDB0004246 "" chebi:3165;chebi:3165 inchikey:QXZGBUJJYSLZLT-FDISYFBBSA-N -Ang 1-9 Metabolite kegg.compound:C15851 "" wikidata:Q58310864 chebi:80128;chebi:80128 inchikey:LJXGOQOPNPFXFT-JWRYNVNRSA-N -Ang 1-7 Metabolite chemspider:110354 "" wikidata:Q27074464 chebi:55438;chebi:55438 inchikey:PVHLMTREZMEJCG-GDTLVBQBSA-N -Angiotensin II Metabolite hmdb:HMDB0001035 "" chebi:2719;chebi:2719 inchikey:CZGUSIXMZVURDU-JZXHSEFVSA-N -ACE Inhibitor Metabolite chebi:35457 "" wikidata:Q288280 chebi:35457;chebi:35457 -Deoxycorticosterone Metabolite hmdb:HMDB0000016 "" chebi:16973;chebi:16973 inchikey:ZESRJSPZRDMNHY-YFWFAHHUSA-N -Aldosterone Metabolite hmdb:HMDB0000037 "" chebi:27584;chebi:27584 inchikey:PQSUYGKTWSAVDQ-ZVIOFETBSA-N -Angiotensin I Metabolite pubchem.compound:3081372 "" wikidata:Q539799 chebi:2718;chebi:2718 inchikey:ORWYRWWVDCYOMK-HBZPZAIKSA-N -Ca++ Metabolite hmdb:HMDB0000464 "" chebi:29108;chebi:29108 inchikey:BHPQYMZQTOCNFJ-UHFFFAOYSA-N -Prostacyclin Metabolite pubchem.compound:114805 "" wikidata:Q26998032 inchikey:KAQKFAOMNZTLHT-IJCBKZNRSA-N -Ang 1-5 Metabolite kegg.compound:C15852 "" wikidata:Q58310855 chebi:80129;chebi:80129 inchikey:UVPBVMCAVNABKX-GXYVSGTKSA-N -CYP11B2 GeneProduct ncbigene:1585 "" ensembl:ENSG00000179142 ncbigene:1585 hgnc.symbol:CYP11B2 uniprot:P19099 -ACE2 GeneProduct ncbigene:59272 "" ensembl:ENSG00000130234 ncbigene:59272 hgnc.symbol:ACE2 uniprot:A0A7I2V3X6;uniprot:A0A7I2V5W5;uniprot:A0A7I2V2E9;uniprot:Q9BYF1;uniprot:A0A7I2V3N4;uniprot:A0A7I2V4H0 -TGFB1 GeneProduct ncbigene:7040 "" ensembl:ENSG00000105329 ncbigene:7040 hgnc.symbol:TGFB1 uniprot:A0A7I2V5Z9;uniprot:A0A499FJK2;uniprot:A0A7I2YQL8 -NEW ACE! GeneProduct ncbigene:1636 "" ensembl:ENSG00000159640 ncbigene:1636 hgnc.symbol:ACE uniprot:J3QSC7;uniprot:P12821;uniprot:J3KRH5;uniprot:J3KTH9;uniprot:J3QLR4;uniprot:J3KTB8;uniprot:J3KS28;uniprot:A0A0A0MSN4;uniprot:J3KSQ5 -NOS3 GeneProduct ncbigene:4846 "" ensembl:ENSG00000164867 ncbigene:4846 hgnc.symbol:NOS3 uniprot:P29474;uniprot:H7C4V4;uniprot:E7ESA7 -AGTR2 GeneProduct ncbigene:186 "" ensembl:ENSG00000180772 ncbigene:186 hgnc.symbol:AGTR2 uniprot:P50052 -NR3C2 GeneProduct ncbigene:4306 "" ensembl:ENSG00000151623 ncbigene:4306 hgnc.symbol:NR3C2 uniprot:B0ZBF6;uniprot:B0ZBF8;uniprot:P08235 -KNG1 GeneProduct ncbigene:3827 "" ensembl:ENSG00000113889 ncbigene:3827 hgnc.symbol:KNG1 uniprot:P01042 -MAS1 GeneProduct ncbigene:4142 "" ensembl:ENSG00000130368 ncbigene:4142 hgnc.symbol:MAS1 uniprot:W8W3P4;uniprot:P04201 -REN GeneProduct ncbigene:5972 "" ensembl:ENSG00000143839 ncbigene:5972 hgnc.symbol:REN uniprot:P00797;uniprot:A0A1B0GUZ2 -BDKRB2 GeneProduct ncbigene:624 "" ensembl:ENSG00000168398 ncbigene:624 hgnc.symbol:BDKRB2 uniprot:P30411 -CMA1 GeneProduct ncbigene:1215 "" ensembl:ENSG00000092009 ncbigene:1215 hgnc.symbol:CMA1 uniprot:P23946 -ACE GeneProduct ncbigene:1636 "" ensembl:ENSG00000159640 ncbigene:1636 hgnc.symbol:ACE uniprot:J3QSC7;uniprot:P12821;uniprot:J3KRH5;uniprot:J3KTH9;uniprot:J3QLR4;uniprot:J3KTB8;uniprot:J3KS28;uniprot:A0A0A0MSN4;uniprot:J3KSQ5 -CTSG GeneProduct ncbigene:1511 "" ensembl:ENSG00000100448 ncbigene:1511 hgnc.symbol:CTSG uniprot:P08311 -BDKRB1 GeneProduct ncbigene:623 "" ensembl:ENSG00000100739 ncbigene:623 hgnc.symbol:BDKRB1 uniprot:G3V4Y2;uniprot:P46663 -AGT GeneProduct ncbigene:183 "" ensembl:ENSG00000135744 ncbigene:183 hgnc.symbol:AGT uniprot:A0A7P0TA52;uniprot:A0A7P0T9S6;uniprot:P01019;uniprot:A0A7P0TBH1;uniprot:A0A7P0T8D1;uniprot:A0A7P0TAP4;uniprot:A0A7P0Z441 -AGTR1 GeneProduct ncbigene:185 "" ensembl:ENSG00000144891 ncbigene:185 hgnc.symbol:AGTR1 uniprot:D3DNG8;uniprot:P30556;uniprot:A0A0A0MSE3;uniprot:Q53YY0 -ATP6AP2 GeneProduct ncbigene:10159 "" ensembl:ENSG00000182220 ncbigene:10159 hgnc.symbol:ATP6AP2 uniprot:A0A1B0GW13;uniprot:A0A1B0GUT7;uniprot:A0A1B0GV24;uniprot:A0A1B0GTU8;uniprot:B7Z413;uniprot:A0A1B0GU12;uniprot:A0A1B0GTB0;uniprot:O75787;uniprot:H7C240;uniprot:A0A1B0GVC7;uniprot:A0A1B0GWD6;uniprot:A0A1C7CYW4;uniprot:A0A1B0GTD6;uniprot:A0A1B0GVI9;uniprot:A0A1B0GWJ8;uniprot:A0A1B0GUV3;uniprot:B7Z1I9;uniprot:A0A1B0GV60;uniprot:A0A1B0GVW0;uniprot:H7C3E1;uniprot:A0A1B0GVB9;uniprot:A0A1B0GVZ1 -ACE GeneProduct ncbigene:1636 "" ensembl:ENSG00000159640 ncbigene:1636 hgnc.symbol:ACE uniprot:J3QSC7;uniprot:P12821;uniprot:J3KRH5;uniprot:J3KTH9;uniprot:J3QLR4;uniprot:J3KTB8;uniprot:J3KS28;uniprot:A0A0A0MSN4;uniprot:J3KSQ5 -ACE2 GeneProduct ncbigene:59272 "" ensembl:ENSG00000130234 ncbigene:59272 hgnc.symbol:ACE2 uniprot:A0A7I2V3X6;uniprot:A0A7I2V5W5;uniprot:A0A7I2V2E9;uniprot:Q9BYF1;uniprot:A0A7I2V3N4;uniprot:A0A7I2V4H0 diff --git a/_drafts/WP010.md b/_drafts/WP010.md deleted file mode 100644 index d8a073f5..00000000 --- a/_drafts/WP010.md +++ /dev/null @@ -1,65 +0,0 @@ ---- -annotations: -- id: PW:0000135 - parent: classic metabolic pathway - type: Pathway Ontology - value: metabolic pathway of cofactors, vitamins, nutrients -- id: PW:0000141 - parent: classic metabolic pathway - type: Pathway Ontology - value: retinol metabolic pathway -- id: PW:0001116 - parent: signaling pathway - type: Pathway Ontology - value: vitamin A and metabolites signaling pathway -authors: -- Egonw -- AlexanderPico -citedin: '' -communities: [] -description: Vitamin A5/X pathway which shows how our food results in precursors from - which Vitamin A5/X (9CBC, 9CDHBC, 9CDHROL-ES and 9CDKHROL) is metabolized which - is converted into Vitamin A5/X acid (9CDHRA) which binds to RXR. -last-edited: 2023-12-13 -ndex: null -organisms: -- Homo sapiens -redirect_from: -- /index.php/Pathway:WP010 -- /instance/WP010 -- /instance/WP010_20231104 -revision: '20231104' -schema-jsonld: -- '@context': https://schema.org/ - '@id': https://wikipathways.github.io/pathways/WP010.html - '@type': Dataset - creator: - '@type': Organization - name: WikiPathways - description: Vitamin A5/X pathway which shows how our food results in precursors - from which Vitamin A5/X (9CBC, 9CDHBC, 9CDHROL-ES and 9CDKHROL) is metabolized - which is converted into Vitamin A5/X acid (9CDHRA) which binds to RXR. - keywords: - - 9CBC - - 9CDHBC - - 9CDHRA - - 9CDHRA-ES - - 9CDHROL - - 9CDHROL-ES - - ATBC - - ATRA - - ATRAL - - ATROL - - ATROL-ES - - RARa - - RARb - - RARg - - RXRa - - RXRb - - RXRc - license: CC0 - name: Vitamin A1 and A5/X pathways -seo: CreativeWork -title: Vitamin A1 and A5/X pathways -wpid: WP010 ---- \ No newline at end of file diff --git a/_drafts/WP554.md b/_drafts/WP554.md deleted file mode 100644 index 91b2ef16..00000000 --- a/_drafts/WP554.md +++ /dev/null @@ -1,112 +0,0 @@ ---- -annotations: -- id: PW:0001228 - parent: drug pathway - type: Pathway Ontology - value: ACE inhibitor drug pathway -- id: CL:0000650 - parent: native cell - type: Cell Type Ontology - value: mesangial cell -- id: DOID:10763 - parent: cardiovascular system disease - type: Disease Ontology - value: hypertension -- id: PW:0000003 - parent: signaling pathway - type: Pathway Ontology - value: signaling pathway -- id: PW:0000245 - parent: regulatory pathway - type: Pathway Ontology - value: angiotensin signaling pathway -authors: -- C.F.Thorn -- MaintBot -- Jinwook -- Khanspers -- AlexanderPico -- Thomas -- MartijnVanIersel -- Egonw -- Christine Chichester -- Nuno -- DeSl -- Mkutmon -- Eweitz -citedin: -- link: PMC7982796 - title: 'ACE2 correlates with immune infiltrates in colon adenocarcinoma: Implication - for COVID-19 (2021)' -- link: PMC7360763 - title: Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing - (2020) -- link: PMC4338111 - title: 'PathVisio 3: An Extendable Pathway Analysis Toolbox (2015)' -communities: -- Renal_Genomics -description: 'The core of this pathway was elucidated over a century ago and involves - the conversion of angiotensinogen to angiotensin I (Ang I) by renin, its subsequent - conversion to angiotensin II (Ang II) by angiotensin converting enzyme. Ang II activates - the angiotensin II receptor type 1 to induce aldosterone synthesis, increasing water - and salt resorption and potassium excretion in the kidney and increasing blood pressure. Proteins - on this pathway have targeted assays available via the ' -last-edited: 2024-01-11 -ndex: 427c38c3-da09-11eb-b666-0ac135e8bacf -organisms: -- Homo sapiens -redirect_from: -- /index.php/Pathway:WP554 -- /instance/WP554 -- /instance/WP554_r126205 -revision: r126205 -schema-jsonld: -- '@context': https://schema.org/ - '@id': https://wikipathways.github.io/pathways/WP554.html - '@type': Dataset - creator: - '@type': Organization - name: WikiPathways - description: 'The core of this pathway was elucidated over a century ago and involves - the conversion of angiotensinogen to angiotensin I (Ang I) by renin, its subsequent - conversion to angiotensin II (Ang II) by angiotensin converting enzyme. Ang II - activates the angiotensin II receptor type 1 to induce aldosterone synthesis, - increasing water and salt resorption and potassium excretion in the kidney and - increasing blood pressure. Proteins on this pathway have targeted assays available - via the ' - keywords: - - ACE - - ACE Inhibitor - - ACE2 - - AGT - - AGTR1 - - AGTR2 - - ATP6AP2 - - Aldosterone - - Ang 1-5 - - Ang 1-7 - - Ang 1-9 - - Angiotensin I - - Angiotensin II - - BDKRB1 - - BDKRB2 - - Bradykinin - - CMA1 - - CTSG - - CYP11B2 - - Ca++ - - Deoxycorticosterone - - KNG1 - - MAS1 - - NEW ACE! - - NOS3 - - NR3C2 - - Prostacyclin - - REN - - TGFB1 - license: CC0 - name: ACE inhibitor pathway -seo: CreativeWork -title: ACE inhibitor pathway -wpid: WP554 ---- \ No newline at end of file diff --git a/draft_assets/WP010/WP010-bibliography.tsv b/draft_assets/WP010/WP010-bibliography.tsv deleted file mode 100644 index 19b0dd46..00000000 --- a/draft_assets/WP010/WP010-bibliography.tsv +++ /dev/null @@ -1,4 +0,0 @@ -ID Database Citation -10.1002/cmdc.201600105 DOI "An Endogenous Mammalian Retinoid X Receptor Ligand, At Last! de Lera ÁR, Krezel W, Rühl R. ChemMedChem [Internet]. 2016 May 6;11(10):1027–37. Available from: http://dx.doi.org/10.1002/cmdc.201600105 DOI" -26030625 Pubmed "9-cis-13,14-Dihydroretinoic Acid Is an Endogenous Retinoid Acting as RXR Ligand in Mice. Rühl R, Krzyżosiak A, Niewiadomska-Cimicka A, Rochel N, Szeles L, Vaz B, et al. PLoS Genet. 2015 Jun 1;11(6):e1005213. PubMed Europe PMC Scholia" -33809241 Pubmed "Vitamin A5/X, a New Food to Lipid Hormone Concept for a Nutritional Ligand to Control RXR-Mediated Signaling. Krężel W, Rivas A, Szklenar M, Ciancia M, Alvarez R, de Lera AR, et al. Nutrients. 2021 Mar 12;13(3):925. PubMed Europe PMC Scholia" diff --git a/draft_assets/WP010/WP010-datanodes.tsv b/draft_assets/WP010/WP010-datanodes.tsv deleted file mode 100644 index 5fc7fda0..00000000 --- a/draft_assets/WP010/WP010-datanodes.tsv +++ /dev/null @@ -1,18 +0,0 @@ -Label Type Identifier Comment Ensembl NCBI gene HGNC UniProt Wikidata ChEBI InChI -ATBC Metabolite wikidata:Q306135 "provitamin A1" wikidata:Q306135 chebi:17579;chebi:17579 inchikey:OENHQHLEOONYIE-JLTXGRSLSA-N -9CDHROL-ES Metabolite wikidata:Q120868159 "" -9CDHROL Metabolite wikidata:Q120868469 "" -9CBC Metabolite wikidata:Q27135678 "" wikidata:Q27135678 chebi:67188;chebi:67188 inchikey:OENHQHLEOONYIE-BVZAMQQESA-N -9CDHBC Metabolite wikidata:Q120868409 "" -9CDHRA Metabolite wikidata:Q120868444 "vitamin A5/X acid
Both R and S forms bind, but R better. The R stereoisomer is patented" -9CDHRA-ES Metabolite wikidata:Q120868227 "" -ATRA Metabolite pubchem.compound:444795 "vitamin A1 acid" wikidata:Q29417 chebi:15367;chebi:15367 inchikey:SHGAZHPCJJPHSC-YCNIQYBTSA-N -ATRAL Metabolite pubchem.compound:638015 "vitamin A1 aldehyde" wikidata:Q28529715 chebi:17898;chebi:17898 inchikey:NCYCYZXNIZJOKI-OVSJKPMPSA-N -ATROL Metabolite pubchem.compound:445354 "vitamin A1" wikidata:Q424976 chebi:17336;chebi:17336 inchikey:FPIPGXGPPPQFEQ-OVSJKPMPSA-N -ATROL-ES Metabolite wikidata:Q120868257 "vitamin A1" -RXRa Protein ncbigene:6256 "" ensembl:ENSG00000186350 ncbigene:6256 hgnc.symbol:RXRA uniprot:A0A5F9ZHH6;uniprot:F1D8Q5;uniprot:P19793;uniprot:A0A3B3IS44 -RXRb Protein ncbigene:6257 "" ensembl:ENSG00000204231 ncbigene:6257 hgnc.symbol:RXRB uniprot:Q5STP9;uniprot:P28702;uniprot:E9PK75;uniprot:A0A0S2Z570 -RXRc Protein ncbigene:6258 "" ensembl:ENSG00000143171 ncbigene:6258 hgnc.symbol:RXRG uniprot:P48443;uniprot:F1D8Q7;uniprot:A0A087WZ88 -RARa Protein ncbigene:5914 "" ensembl:ENSG00000131759 ncbigene:5914 hgnc.symbol:RARA uniprot:J3QRM2;uniprot:A8MUP8;uniprot:F1D8N9;uniprot:J3KSJ4;uniprot:P10276;uniprot:Q6I9R7 -RARb Protein ncbigene:5915 "" ensembl:ENSG00000077092 ncbigene:5915 hgnc.symbol:RARB uniprot:D6RBI3;uniprot:P10826;uniprot:F1D8S6;uniprot:Q5QHG3 -RARg Protein ncbigene:5916 "" ensembl:ENSG00000172819 ncbigene:5916 hgnc.symbol:RARG uniprot:P13631;uniprot:H3BMK1;uniprot:F1D8P1;uniprot:A8K3H3;uniprot:H3BMH6;uniprot:H3BMY6 diff --git a/draft_assets/WP010/WP010-info.json b/draft_assets/WP010/WP010-info.json deleted file mode 100644 index 937ba8f5..00000000 --- a/draft_assets/WP010/WP010-info.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "wpid": "WP010", - "organisms": ["Homo sapiens"], - "description": "Vitamin A5/X pathway which shows how our food results in precursors from which Vitamin A5/X (9CBC, 9CDHBC, 9CDHROL-ES and 9CDKHROL) is metabolized which is converted into Vitamin A5/X acid (9CDHRA) which binds to RXR.", - "ontology-ids": [ - "PW:0000135", - "PW:0000141", - "PW:0001116" - ], - "last-edited": "2023-12-13", - "title": "Vitamin A1 and A5/X pathways", - "authors": [ - "Egonw", - "AlexanderPico" - ], - "revision": "20231104" -} \ No newline at end of file diff --git a/draft_assets/WP010/WP010-refs.tsv b/draft_assets/WP010/WP010-refs.tsv deleted file mode 100644 index 8ce223fc..00000000 --- a/draft_assets/WP010/WP010-refs.tsv +++ /dev/null @@ -1,4 +0,0 @@ -ID Database -33809241 Pubmed -26030625 Pubmed -10.1002/cmdc.201600105 DOI diff --git a/draft_assets/WP010/WP010-thumb.png b/draft_assets/WP010/WP010-thumb.png deleted file mode 100644 index 69ca3ad3..00000000 Binary files a/draft_assets/WP010/WP010-thumb.png and /dev/null differ diff --git a/draft_assets/WP010/WP010.gpml b/draft_assets/WP010/WP010.gpml deleted file mode 100644 index 11d2e888..00000000 --- a/draft_assets/WP010/WP010.gpml +++ /dev/null @@ -1,363 +0,0 @@ - - - Vitamin A5/X pathway which shows how our food results in precursors from which Vitamin A5/X (9CBC, 9CDHBC, 9CDHROL-ES and 9CDKHROL) is metabolized which is converted into Vitamin A5/X acid (9CDHRA) which binds to RXR. - cc4 - - - provitamin A1 - - - - - - - - - - - - - cc4 - - - - - - - - - - - - - - - - - - - - - - - - - vitamin A5/X acid - Both R and S forms bind, but R better. The R stereoisomer is patented - aab - - - - - - - - - - - - - vitamin A1 acid - - - - - vitamin A1 aldehyde - - - - - vitamin A1 - - - - - vitamin A1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cc4 - aab - ac9 - - - - - - - - - - - - - - - Multistep - cc4 - - - - - - - - - - - - - - - multistep - - - - - - - - - - - - - - - Multistep - cc4 - - - - - - - - - - - - - - - cc4 - - - - - - - - Multistep - cc4 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - multistep - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aab - - - - - - - metabolic pathway of cofactors, vitamins, nutrients - PW:0000135 - Pathway Ontology - - - 10.1002/cmdc.201600105 - DOI - An Endogenous Mammalian Retinoid X Receptor Ligand, At Last! - ChemMedChem - 2016 - de Lera, A.R. - Krezel, W. - Ruehl, R. - - - 26030625 - PubMed - 9-cis-13,14-Dihydroretinoic Acid Is an Endogenous Retinoid Acting as RXR Ligand in Mice. - 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Bassett MH, White PC, Rainey WE. Mol Cell Endocrinol. 2004 Mar 31;217(1–2):67–74. PubMed Europe PMC Scholia" -15174896 Pubmed "Pharmacogenetics of antihypertensive drug responses. Schwartz GL, Turner ST. Am J Pharmacogenomics. 2004;4(3):151–60. PubMed Europe PMC Scholia" -16374430 Pubmed "Renin increases mesangial cell transforming growth factor-beta1 and matrix proteins through receptor-mediated, angiotensin II-independent mechanisms. Huang Y, Wongamorntham S, Kasting J, McQuillan D, Owens RT, Yu L, et al. Kidney Int. 2006 Jan;69(1):105–13. PubMed Europe PMC Scholia" -17464936 Pubmed "The emerging role of ACE2 in physiology and disease. Hamming I, Cooper ME, Haagmans BL, Hooper NM, Korstanje R, Osterhaus ADME, et al. J Pathol. 2007 May;212(1):1–11. PubMed Europe PMC Scholia" -18035185 Pubmed "Effects of renin-angiotensin system inhibition on end-organ protection: can we do better? Weir MR. Clin Ther. 2007 Sep;29(9):1803–24. PubMed Europe PMC Scholia" -18417113 Pubmed "The (pro)renin receptor: a new addition to the renin-angiotensin system? Batenburg WW, Jan Danser AH. Eur J Pharmacol. 2008 May 13;585(2–3):320–4. PubMed Europe PMC Scholia" -18449520 Pubmed "Are we poised to target ACE2 for the next generation of antihypertensives? Ferreira AJ, Raizada MK. J Mol Med (Berl). 2008 Jun;86(6):685–90. PubMed Europe PMC Scholia" diff --git a/draft_assets/WP554/WP554-datanodes.tsv b/draft_assets/WP554/WP554-datanodes.tsv deleted file mode 100644 index b712cc67..00000000 --- a/draft_assets/WP554/WP554-datanodes.tsv +++ /dev/null @@ -1,32 +0,0 @@ -Label Type Identifier Comment Ensembl NCBI gene HGNC UniProt Wikidata ChEBI InChI -Bradykinin Metabolite hmdb:HMDB0004246 "" chebi:3165;chebi:3165 inchikey:QXZGBUJJYSLZLT-FDISYFBBSA-N -Ang 1-9 Metabolite kegg.compound:C15851 "" wikidata:Q58310864 chebi:80128;chebi:80128 inchikey:LJXGOQOPNPFXFT-JWRYNVNRSA-N -Ang 1-7 Metabolite chemspider:110354 "" wikidata:Q27074464 chebi:55438;chebi:55438 inchikey:PVHLMTREZMEJCG-GDTLVBQBSA-N -Angiotensin II Metabolite hmdb:HMDB0001035 "" chebi:2719;chebi:2719 inchikey:CZGUSIXMZVURDU-JZXHSEFVSA-N -ACE Inhibitor Metabolite chebi:35457 "" wikidata:Q288280 chebi:35457;chebi:35457 -Deoxycorticosterone Metabolite hmdb:HMDB0000016 "" chebi:16973;chebi:16973 inchikey:ZESRJSPZRDMNHY-YFWFAHHUSA-N -Aldosterone Metabolite hmdb:HMDB0000037 "" chebi:27584;chebi:27584 inchikey:PQSUYGKTWSAVDQ-ZVIOFETBSA-N -Angiotensin I Metabolite pubchem.compound:3081372 "" wikidata:Q539799 chebi:2718;chebi:2718 inchikey:ORWYRWWVDCYOMK-HBZPZAIKSA-N -Ca++ Metabolite hmdb:HMDB0000464 "" chebi:29108;chebi:29108 inchikey:BHPQYMZQTOCNFJ-UHFFFAOYSA-N -Prostacyclin Metabolite pubchem.compound:114805 "" wikidata:Q26998032 inchikey:KAQKFAOMNZTLHT-IJCBKZNRSA-N -Ang 1-5 Metabolite kegg.compound:C15852 "" wikidata:Q58310855 chebi:80129;chebi:80129 inchikey:UVPBVMCAVNABKX-GXYVSGTKSA-N -CYP11B2 GeneProduct ncbigene:1585 "" ensembl:ENSG00000179142 ncbigene:1585 hgnc.symbol:CYP11B2 uniprot:P19099 -ACE2 GeneProduct ncbigene:59272 "" ensembl:ENSG00000130234 ncbigene:59272 hgnc.symbol:ACE2 uniprot:A0A7I2V3X6;uniprot:A0A7I2V5W5;uniprot:A0A7I2V2E9;uniprot:Q9BYF1;uniprot:A0A7I2V3N4;uniprot:A0A7I2V4H0 -TGFB1 GeneProduct ncbigene:7040 "" ensembl:ENSG00000105329 ncbigene:7040 hgnc.symbol:TGFB1 uniprot:A0A7I2V5Z9;uniprot:A0A499FJK2;uniprot:A0A7I2YQL8 -NEW ACE! GeneProduct ncbigene:1636 "" ensembl:ENSG00000159640 ncbigene:1636 hgnc.symbol:ACE uniprot:J3QSC7;uniprot:P12821;uniprot:J3KRH5;uniprot:J3KTH9;uniprot:J3QLR4;uniprot:J3KTB8;uniprot:J3KS28;uniprot:A0A0A0MSN4;uniprot:J3KSQ5 -NOS3 GeneProduct ncbigene:4846 "" ensembl:ENSG00000164867 ncbigene:4846 hgnc.symbol:NOS3 uniprot:P29474;uniprot:H7C4V4;uniprot:E7ESA7 -AGTR2 GeneProduct ncbigene:186 "" ensembl:ENSG00000180772 ncbigene:186 hgnc.symbol:AGTR2 uniprot:P50052 -NR3C2 GeneProduct ncbigene:4306 "" ensembl:ENSG00000151623 ncbigene:4306 hgnc.symbol:NR3C2 uniprot:B0ZBF6;uniprot:B0ZBF8;uniprot:P08235 -KNG1 GeneProduct ncbigene:3827 "" ensembl:ENSG00000113889 ncbigene:3827 hgnc.symbol:KNG1 uniprot:P01042 -MAS1 GeneProduct ncbigene:4142 "" ensembl:ENSG00000130368 ncbigene:4142 hgnc.symbol:MAS1 uniprot:W8W3P4;uniprot:P04201 -REN GeneProduct ncbigene:5972 "" ensembl:ENSG00000143839 ncbigene:5972 hgnc.symbol:REN uniprot:P00797;uniprot:A0A1B0GUZ2 -BDKRB2 GeneProduct ncbigene:624 "" ensembl:ENSG00000168398 ncbigene:624 hgnc.symbol:BDKRB2 uniprot:P30411 -CMA1 GeneProduct ncbigene:1215 "" ensembl:ENSG00000092009 ncbigene:1215 hgnc.symbol:CMA1 uniprot:P23946 -ACE GeneProduct ncbigene:1636 "" ensembl:ENSG00000159640 ncbigene:1636 hgnc.symbol:ACE uniprot:J3QSC7;uniprot:P12821;uniprot:J3KRH5;uniprot:J3KTH9;uniprot:J3QLR4;uniprot:J3KTB8;uniprot:J3KS28;uniprot:A0A0A0MSN4;uniprot:J3KSQ5 -CTSG GeneProduct ncbigene:1511 "" ensembl:ENSG00000100448 ncbigene:1511 hgnc.symbol:CTSG uniprot:P08311 -BDKRB1 GeneProduct ncbigene:623 "" ensembl:ENSG00000100739 ncbigene:623 hgnc.symbol:BDKRB1 uniprot:G3V4Y2;uniprot:P46663 -AGT GeneProduct ncbigene:183 "" ensembl:ENSG00000135744 ncbigene:183 hgnc.symbol:AGT uniprot:A0A7P0TA52;uniprot:A0A7P0T9S6;uniprot:P01019;uniprot:A0A7P0TBH1;uniprot:A0A7P0T8D1;uniprot:A0A7P0TAP4;uniprot:A0A7P0Z441 -AGTR1 GeneProduct ncbigene:185 "" ensembl:ENSG00000144891 ncbigene:185 hgnc.symbol:AGTR1 uniprot:D3DNG8;uniprot:P30556;uniprot:A0A0A0MSE3;uniprot:Q53YY0 -ATP6AP2 GeneProduct ncbigene:10159 "" ensembl:ENSG00000182220 ncbigene:10159 hgnc.symbol:ATP6AP2 uniprot:A0A1B0GW13;uniprot:A0A1B0GUT7;uniprot:A0A1B0GV24;uniprot:A0A1B0GTU8;uniprot:B7Z413;uniprot:A0A1B0GU12;uniprot:A0A1B0GTB0;uniprot:O75787;uniprot:H7C240;uniprot:A0A1B0GVC7;uniprot:A0A1B0GWD6;uniprot:A0A1C7CYW4;uniprot:A0A1B0GTD6;uniprot:A0A1B0GVI9;uniprot:A0A1B0GWJ8;uniprot:A0A1B0GUV3;uniprot:B7Z1I9;uniprot:A0A1B0GV60;uniprot:A0A1B0GVW0;uniprot:H7C3E1;uniprot:A0A1B0GVB9;uniprot:A0A1B0GVZ1 -ACE GeneProduct ncbigene:1636 "" ensembl:ENSG00000159640 ncbigene:1636 hgnc.symbol:ACE uniprot:J3QSC7;uniprot:P12821;uniprot:J3KRH5;uniprot:J3KTH9;uniprot:J3QLR4;uniprot:J3KTB8;uniprot:J3KS28;uniprot:A0A0A0MSN4;uniprot:J3KSQ5 -ACE2 GeneProduct ncbigene:59272 "" ensembl:ENSG00000130234 ncbigene:59272 hgnc.symbol:ACE2 uniprot:A0A7I2V3X6;uniprot:A0A7I2V5W5;uniprot:A0A7I2V2E9;uniprot:Q9BYF1;uniprot:A0A7I2V3N4;uniprot:A0A7I2V4H0 diff --git a/draft_assets/WP554/WP554-info.json b/draft_assets/WP554/WP554-info.json deleted file mode 100644 index c5b44def..00000000 --- a/draft_assets/WP554/WP554-info.json +++ /dev/null @@ -1,30 +0,0 @@ -{ - "wpid": "WP554", - "organisms": ["Homo sapiens"], - "description": "The core of this pathway was elucidated over a century ago and involves the conversion of angiotensinogen to angiotensin I (Ang I) by renin, its subsequent conversion to angiotensin II (Ang II) by angiotensin converting enzyme. 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Kidney Int - 2006 - Huang Y - Wongamorntham S - Kasting J - McQuillan D - Owens RT - Yu L - Noble NA - Border W - - - 17376010 - PubMed - Angiotensin II reactivation and aldosterone escape phenomena in renin-angiotensin-aldosterone system blockade: is oral renin inhibition the solution? - Expert Opin Pharmacother - 2007 - Athyros VG - Mikhailidis DP - Kakafika AI - Tziomalos K - Karagiannis A - - - 18729003 - PubMed - Mineralocorticoid receptor antagonists and endothelial function. - Curr Opin Investig Drugs - 2008 - Maron BA - Leopold JA - - - mesangial cell - CL:0000650 - Cell Type - - - hypertension - DOID:10763 - Disease - - - signaling pathway - PW:0000003 - Pathway Ontology - - - 17464936 - PubMed - The emerging role of ACE2 in physiology and disease. - J Pathol - 2007 - Hamming I - Cooper ME - Haagmans BL - Hooper NM - Korstanje R - Osterhaus AD - Timens W - Turner AJ - Navis G - van Goor H - - - 15174896 - PubMed - Pharmacogenetics of antihypertensive drug responses. - Am J Pharmacogenomics - 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