edit to reference gene list (AlexsLemonade#539)

* edit to reference gene list * updated kinase list * added GIST for reference list Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
UCSC-Treehouse · Feb 18, 2020 · c6e6261 · c6e6261
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diff --git a/analyses/fusion_filtering/README.md b/analyses/fusion_filtering/README.md
@@ -20,9 +20,11 @@ We also gather counts for recurrent fusions and fused genes found in more than 3
 * pbta-gene-expression-rsem-fpkm.stranded.rds : aggregated stranded fpm data
 
 #### Inputs used as reference
-* genelistreference.txt : known kinases, oncogenes, tumor suppressors, curated transcription factors [@doi:10.1016/j.cell.2018.01.029], COSMIC Cancer Gene Census list[https://cancer.sanger.ac.uk/census] . MYBL1 [@doi:10.1073/pnas.1300252110], SNCAIP [@doi:10.1038/nature11327], FOXR2 [@doi:10.1016/j.cell.2016.01.015], TTYH1 [@doi:10.1038/ng.2849], and TERT [@doi:10.1038/ng.3438; @doi:10.1002/gcc.22110; @doi:10.1016/j.canlet.2014.11.057; @doi:10.1007/s11910-017-0722-5] were added to the oncogene list and BCOR [@doi:10.1016/j.cell.2016.01.015] and QKI [@doi:10.1038/ng.3500] were added to the tumor suppressor gene list based on pediatric cancer literature review
+* genelistreference.txt : known kinases, oncogenes, tumor suppressors, curated transcription factors [@doi:10.1016/j.cell.2018.01.029], COSMIC Cancer Gene Census list[https://cancer.sanger.ac.uk/census] . MYBL1 [@doi:10.1073/pnas.1300252110], SNCAIP [@doi:10.1038/nature11327], FOXR2 [@doi:10.1016/j.cell.2016.01.015], TTYH1 [@doi:10.1038/ng.2849], and TERT [@doi:10.1038/ng.3438; @doi:10.1002/gcc.22110; @doi:10.1016/j.canlet.2014.11.057; @doi:10.1007/s11910-017-0722-5] were added to the oncogene list and BCOR [@doi:10.1016/j.cell.2016.01.015] and QKI [@doi:10.1038/ng.3500] were added to the tumor suppressor gene list based on pediatric cancer literature review. 
 * fusionreference.txt :  known TCGA fusions
 * Brain_FPKM_hg38_matrix.txt.zip : GTex brain samples FPKM data
+The code to generate genelistreference.txt and fusionreference.txt is available here: https://gist.github.com/kgaonkar6/02b3fbcfeeddfa282a1cdf4803704794#file-format_reference_gene_list-r
+
 
 #### Outputs saved to data download
 * pbta-fusion-putative-oncogenic.tsv

diff --git a/analyses/fusion_filtering/references/genelistreference.txt b/analyses/fusion_filtering/references/genelistreference.txt
diff --git a/analyses/fusion_filtering/results/FilteredFusion.tsv b/analyses/fusion_filtering/results/FilteredFusion.tsv
diff --git a/analyses/fusion_filtering/results/pbta-fusion-putative-oncogenic.tsv b/analyses/fusion_filtering/results/pbta-fusion-putative-oncogenic.tsv
diff --git a/...c_fusions_participant_histology_level.tsv → ...a-fusion-recurrent-fusion-byhistology.tsv b/...c_fusions_participant_histology_level.tsv → ...a-fusion-recurrent-fusion-byhistology.tsv
diff --git a/...fusions_matrix_sample_histology_level.tsv → ...pbta-fusion-recurrent-fusion-bysample.tsv b/...fusions_matrix_sample_histology_level.tsv → ...pbta-fusion-recurrent-fusion-bysample.tsv
@@ -5,7 +5,6 @@ BS_03FT4S8B	0	0	0	1	0
 BS_0448A413	0	1	0	0	0
 BS_044XZ8ST	0	0	0	1	0
 BS_052PZFMK	0	0	0	1	0
-BS_05TTCK08	0	0	0	1	0
 BS_063ERW0R	0	0	1	0	0
 BS_06AMMCXR	0	0	1	0	0
 BS_06XH7EVF	0	0	0	1	0
@@ -23,6 +22,7 @@ BS_0SCXXM6N	0	0	1	0	0
 BS_0SPCTBZY	0	0	0	1	0
 BS_0T17SY47	0	0	0	1	0
 BS_0VRSD9V3	0	0	0	1	0
+BS_0VXZCRJS	0	0	0	1	0
 BS_0WQJP6ZG	1	0	0	0	0
 BS_0WVJYM9R	0	0	1	0	0
 BS_0X9EGHY2	0	0	0	1	0
@@ -42,6 +42,7 @@ BS_1EBQ3T20	0	0	0	1	0
 BS_1EN5V3XW	0	0	0	1	0
 BS_1G3WYEN3	0	0	0	1	0
 BS_1HFK0SXV	0	0	0	1	0
+BS_1HQ76V6D	0	0	0	1	0
 BS_1J2WQ08M	0	0	0	1	0
 BS_1JDG6JV5	0	0	0	1	0
 BS_1N9XZXGE	0	1	0	0	0
@@ -62,7 +63,6 @@ BS_258RRGDM	0	0	0	1	0
 BS_25T139TX	0	0	0	1	0
 BS_264RCK7G	0	0	0	1	0
 BS_273HKCT4	0	0	0	1	0
-BS_277SBSCP	0	0	0	1	0
 BS_27QE6BV7	0	0	0	1	0
 BS_29006KEX	0	0	0	1	0
 BS_29CPJ040	0	0	0	1	0
@@ -141,6 +141,7 @@ BS_4JWBB28H	0	0	0	1	0
 BS_4NF35AF6	0	0	0	1	0
 BS_4NWHYH53	1	0	0	0	0
 BS_4PH1MBGR	0	0	0	1	0
+BS_4PPHAQXF	0	0	0	1	0
 BS_4PWDGEB0	0	0	0	1	0
 BS_4QW2S1Q8	0	0	0	1	0
 BS_4SCWT0FX	0	0	0	1	0
@@ -157,12 +158,12 @@ BS_52MPKTJH	0	0	0	1	0
 BS_53GQKVEX	0	0	1	0	0
 BS_55JW3HFM	0	0	0	1	0
 BS_55P8HPYD	0	0	1	0	0
-BS_56Z15924	0	0	0	1	0
 BS_58YXHGAJ	0	0	0	1	0
 BS_593HEWBF	0	0	0	1	0
 BS_5965SFPZ	0	0	0	1	0
 BS_5AF6ZNJF	0	0	0	1	0
 BS_5CMGN56B	0	0	0	1	0
+BS_5CTVXVRX	0	0	0	1	0
 BS_5JM573JC	0	0	0	1	0
 BS_5K3R0F5D	0	0	0	1	0
 BS_5NWDARXG	0	0	0	1	0
@@ -177,7 +178,6 @@ BS_5YJEPPTP	0	0	1	0	0
 BS_60K3EQ9S	0	0	0	1	0
 BS_61E80SD6	0	0	0	1	0
 BS_64HCD9K3	0	0	0	1	0
-BS_65VFS9N1	0	0	0	1	0
 BS_66ABA973	0	0	1	0	0
 BS_66HQ3E4Z	0	0	1	0	0
 BS_67PX06P3	0	0	0	1	0
@@ -198,10 +198,10 @@ BS_6MZ7FRZH	1	0	0	0	0
 BS_6N3AFF66	0	0	1	0	0
 BS_6NRTJSYK	0	0	0	1	0
 BS_6NTXGQAC	0	0	0	1	0
-BS_6PRD2CF1	0	0	0	1	0
 BS_6R7SFVV2	0	0	0	1	0
 BS_6T4JGBGY	0	0	0	1	0
 BS_6VF6VPCG	0	0	0	1	0
+BS_6VPKXXMR	0	0	0	1	0
 BS_6WP1FHTE	0	0	0	1	0
 BS_6YMJ621P	0	0	0	1	0
 BS_70FFPA51	0	0	0	1	0
@@ -221,7 +221,6 @@ BS_7G42J2SK	1	0	0	0	0
 BS_7GJT4A6A	0	0	0	1	0
 BS_7H4RFCW9	0	0	0	1	0
 BS_7N0B2CY1	0	0	0	1	0
-BS_7N8XY997	0	0	0	1	0
 BS_7P83Z28P	0	0	1	0	0
 BS_7T1J3KET	0	0	0	1	0
 BS_7WM3MNZ0	0	0	0	1	0
@@ -235,6 +234,7 @@ BS_850BAHH9	0	0	0	1	0
 BS_86Q14TZG	0	0	0	1	0
 BS_8D0NYM46	0	0	0	1	0
 BS_8F9BDWY4	0	0	0	1	0
+BS_8GW1TMV2	0	0	0	1	0
 BS_8J09S6MZ	0	0	0	1	0
 BS_8J3B6ZB6	0	0	1	0	0
 BS_8NY9J9NQ	0	0	0	1	0
@@ -249,7 +249,6 @@ BS_8VAZSJEN	0	0	1	0	0
 BS_8WPNFT03	0	0	0	1	0
 BS_8Z3SCKB5	0	0	0	1	0
 BS_8ZP3CBQA	0	0	0	1	0
-BS_8ZS9F31R	0	0	0	1	0
 BS_8ZY4GST0	0	0	0	1	0
 BS_90B22NGP	0	0	0	1	0
 BS_912NX4Y0	0	0	0	1	0
@@ -268,7 +267,6 @@ BS_9GJ23RHH	0	0	0	1	0
 BS_9HA238XS	0	0	0	1	0
 BS_9HSGV9TJ	0	0	0	1	0
 BS_9M5XJ10G	0	0	0	1	0
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 BS_9NJHQE9F	0	0	0	1	0
 BS_9NZ2D6AD	0	0	0	1	0
 BS_9P9MB8X8	0	0	0	1	0
@@ -333,7 +331,6 @@ BS_BVSW4GTG	0	0	0	1	0
 BS_BXXJ9P8C	0	0	0	1	0
 BS_BYCX6VK1	0	0	0	1	0
 BS_C05FKR8X	1	0	0	0	0
-BS_C0AY0XC5	0	0	0	1	0
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 BS_C41DJZ1F	0	0	0	1	0
 BS_C51RB0YR	0	0	0	1	0
@@ -343,11 +340,9 @@ BS_C7A2TYAC	0	0	1	0	0
 BS_C7N3J4NW	0	0	0	1	0
 BS_C80S5N37	0	0	0	1	0
 BS_C83TK159	0	0	0	1	0
-BS_C97AE5XA	0	0	0	1	0
 BS_CB6VK7PB	0	0	1	0	0
 BS_CGB2WS2A	0	0	1	0	0
 BS_CHDGRYHJ	0	0	0	1	0
-BS_CMM1Q934	0	0	0	1	0
 BS_CQEETJ66	0	0	0	1	0
 BS_CQSAJ7BF	0	0	0	1	0
 BS_CREQ97QC	0	0	0	1	0
@@ -392,10 +387,8 @@ BS_E4F1D721	0	0	0	1	0
 BS_E4QK839R	0	0	0	1	0
 BS_E94QRJDW	0	0	0	1	0
 BS_EBMCTR80	0	0	0	1	0
-BS_EE17YHEH	0	0	0	1	0
 BS_EF775B3K	0	0	0	1	0
 BS_EFE4YEK3	0	0	0	1	0
-BS_EFEB483R	0	0	0	1	0
 BS_EFEZB0ZH	0	0	1	0	0
 BS_EHVYJAVA	0	0	0	1	0
 BS_EK5PCKY0	1	0	0	0	0
@@ -414,7 +407,6 @@ BS_EZ3147MX	0	0	0	0	1
 BS_F0JB4EAK	0	0	0	1	0
 BS_F4E8R9VY	0	0	0	1	0
 BS_F5BZSF3Q	0	0	0	1	0
-BS_F63KKBGX	0	0	0	1	0
 BS_F6V1Y4QS	0	0	0	1	0
 BS_F6Z5HFWH	0	0	0	1	0
 BS_F8N6CFQE	0	0	1	0	0
@@ -470,7 +462,6 @@ BS_H3FE3TH9	0	0	1	0	0
 BS_H3Y8FWHV	0	0	0	1	0
 BS_H4B5Y6S0	0	0	0	1	0
 BS_H4NXBD2D	1	0	0	0	0
-BS_H64GWVJQ	0	0	0	1	0
 BS_H8A9PSYA	0	0	1	0	0
 BS_H97S5SQN	0	0	0	0	1
 BS_HB03GSHF	0	0	0	1	0
@@ -489,7 +480,6 @@ BS_HTEPAKCM	0	0	0	1	0
 BS_HV8PFRBR	0	0	0	1	0
 BS_HWGWYCY7	0	0	0	1	0
 BS_HX0S30NE	0	0	0	1	0
-BS_HYMWP6WF	0	0	0	1	0
 BS_HZE3KYZ1	0	0	0	1	0
 BS_HZRM07TW	0	0	0	1	0
 BS_J1AB8PMA	0	0	0	1	0
@@ -519,14 +509,12 @@ BS_JS95PE0J	0	0	0	1	0
 BS_JSPR854S	0	0	0	1	0
 BS_JT82QGXF	0	0	0	1	0
 BS_JTMXAMB7	0	0	0	1	0
-BS_JV9G8CNX	0	0	0	1	0
 BS_JVA2NQFF	0	0	1	0	0
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 BS_JWCX8R17	0	0	0	1	0
 BS_JWSR581E	0	0	1	0	0
 BS_JX449BF5	0	0	0	1	0
 BS_JX7S9MY7	0	0	0	1	0
-BS_JXAVKXZE	0	0	0	1	0
 BS_JXF8A2A6	0	0	0	1	0
 BS_JXNZYGCR	0	0	0	1	0
 BS_JZRM1S3T	0	0	0	1	0
@@ -552,7 +540,6 @@ BS_KP735TJ6	0	0	0	1	0
 BS_KPT2WPHW	0	0	0	1	0
 BS_KQ6ZW085	0	0	0	1	0
 BS_KSKZ9J7J	0	0	0	1	0
-BS_KSS4AAPP	0	0	0	1	0
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 BS_KVNGNETA	0	0	0	1	0
 BS_KVV7001W	0	0	0	1	0
@@ -571,7 +558,6 @@ BS_M4923M40	0	0	0	1	0
 BS_M4NVX721	0	0	0	1	0
 BS_M4TTKPNR	0	0	1	0	0
 BS_M84H3KXA	0	0	0	1	0
-BS_M85CXHDV	0	0	0	1	0
 BS_M86ECPHK	0	0	0	1	0
 BS_M8M56Z4Y	0	0	1	0	0
 BS_M8WP5T16	0	0	0	1	0
@@ -589,7 +575,6 @@ BS_MGAMKKBD	0	0	0	1	0
 BS_MKM0EEN1	0	0	0	1	0
 BS_MM20BVW9	0	0	0	1	0
 BS_MMNRZ1EQ	0	0	0	1	0
-BS_MN5XVP5A	0	0	0	1	0
 BS_MQCKXD60	0	0	0	1	0
 BS_MT15SGJN	1	0	0	0	0
 BS_MVW01FPB	0	0	0	1	0
@@ -617,10 +602,8 @@ BS_NGSG2KB6	0	0	0	1	0
 BS_NGY0TE6S	0	0	0	1	0
 BS_NH7K4CD9	0	0	0	1	0
 BS_NJ4WPQVK	0	0	0	1	0
-BS_NK7K4GFE	0	0	0	1	0
 BS_NKEAAFMW	0	0	0	1	0
 BS_NKRYMHEP	0	0	0	1	0
-BS_NNVEQTEW	0	0	0	1	0
 BS_NPA6CZQF	0	0	0	1	0
 BS_NQB91P48	0	0	1	0	0
 BS_NQFH3GZH	0	0	0	1	0
@@ -693,6 +676,7 @@ BS_R7NTZR4C	0	0	0	1	0
 BS_R9B92M75	0	0	0	1	0
 BS_RB2S0KDF	0	0	0	1	0
 BS_RCC8BXVE	0	0	0	1	0
+BS_RCCN63K6	0	0	0	1	0
 BS_RCFQ31XF	0	0	0	1	0
 BS_RD4D5F9F	0	0	0	1	0
 BS_RFMQ7T0T	0	0	0	1	0
@@ -701,7 +685,6 @@ BS_RGSMX7QD	0	0	1	0	0
 BS_RHD7XPNP	0	0	0	1	0
 BS_RR12T74P	0	0	0	1	0
 BS_RRAEQZ97	0	0	0	1	0
-BS_RSRPX3S8	0	0	0	1	0
 BS_RVSEDNJ4	0	0	1	0	0
 BS_RWJZFTP9	0	0	1	0	0
 BS_RX1YTZ7F	0	0	0	0	1
@@ -727,7 +710,6 @@ BS_SES41DAX	0	0	0	1	0
 BS_SFKZSJN1	0	0	0	1	0
 BS_SFRQXM76	0	0	0	1	0
 BS_SHMC4902	0	0	1	0	0
-BS_SHZZ99DT	0	0	0	1	0
 BS_SKGJ5SY9	0	0	0	1	0
 BS_SM8VQFPD	0	0	0	1	0
 BS_SNVM7CZT	0	0	0	1	0
@@ -758,7 +740,6 @@ BS_TK84K675	0	0	0	1	0
 BS_TMTV769C	0	0	0	1	0
 BS_TNRHHYNC	0	0	0	1	0
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-BS_TR0FSM4R	0	0	0	1	0
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 BS_TW8DQH8J	0	0	0	1	0
 BS_TXY8QYWA	0	0	0	1	0
@@ -827,7 +808,6 @@ BS_WJ9H4NZZ	0	0	0	1	0
 BS_WJGFDRWK	0	1	0	0	0
 BS_WKESC3XN	0	0	0	1	0
 BS_WMEHNDSK	0	0	0	1	0
-BS_WN90GPFR	0	0	0	1	0
 BS_WRHDP7WF	0	0	0	1	0
 BS_WRQHPSXQ	0	0	0	1	0
 BS_WSQMAA33	0	0	0	1	0
@@ -858,10 +838,10 @@ BS_XKKB4MZV	0	0	1	0	0
 BS_XM1AHBDJ	0	0	0	1	0
 BS_XQ5SFW35	0	0	0	1	0
 BS_XQYHPBFS	0	0	0	1	0
+BS_XZM79E42	0	0	0	1	0
 BS_XZTV0J8W	0	0	0	1	0
 BS_Y08D5P8N	0	0	0	1	0
 BS_Y0PCBNJV	0	0	1	0	0
-BS_Y1ZP55ZK	0	0	0	1	0
 BS_Y7F9E2E9	0	0	0	1	0
 BS_Y8D1F5WW	0	0	0	1	0
 BS_YA8RBGD8	0	0	0	1	0

diff --git a/...rec_genes_participant_histology_level.tsv → ...n-recurrently-fused-genes-byhistology.tsv b/...rec_genes_participant_histology_level.tsv → ...n-recurrently-fused-genes-byhistology.tsv