Mercurial > repos > galaxyp > cravatool
annotate test-results/Gene_Level_Analysis.tsv @ 0:83181dabeb90 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
author | galaxyp |
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date | Fri, 18 May 2018 13:25:29 -0400 |
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83181dabeb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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1 #Gene Level Annotation Report |
83181dabeb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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2 #2018-05-18 15:18:04.023450 |
83181dabeb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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3 #CRAVAT version: hybrid |
83181dabeb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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4 #Analysis done at http://www.cravat.us. |
83181dabeb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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5 #Job Id: znylund_20180518_111800 |
83181dabeb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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6 #Input file: _VCF_BEDintersect_on_data_65_and_data_6_.vcf |
83181dabeb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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7 #This report shows analysis results at gene level. |
83181dabeb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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8 #The composite p-value (Stouffer's combined p-value) and composite FDR of a gene show how probable it is to get the same p-value distribution for the gene as that obtained from the input variants by chance. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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9 #hg38 genomic. |
83181dabeb90
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10 #N/A |
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11 #For more information on CRAVAT, visit http://www.cravat.us. |
83181dabeb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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12 |
83181dabeb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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13 HUGO symbol Number of variants Sequence ontology CGC driver class CGC inheritance CGC tumor types somatic CGC tumor types germline ClinVar disease identifier ClinVar XRef Occurrences in COSMIC COSMIC gene count (tissue) Number of samples with gene mutated CHASM gene score CHASM gene p-value CHASM gene FDR VEST gene score (non-silent) VEST gene p-value VEST gene FDR Protein 3D gene Has a mutation in a TCGA Mutation Cluster NCI pathway hits NCI pathway IDs NCI pathway names TARGET CGL driver class |
83181dabeb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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14 CRABP2 1 MS 37 upper_aerodigestive_tract(3);large_intestine(9);stomach(4);soft_tissue(3);endometrium(4);lung(3);liver(2);skin(4);NS(1);prostate(1);bone(1);kidney(1);breast(1) 1 0.2 0.53061 0.65 ../MuPIT_Interactive?gm=chr1:156705422 0 |
83181dabeb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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15 NOP2 1 MS 133 large_intestine(22);endometrium(8);lung(8);skin(20);kidney(5);thyroid(1);cervix(2);central_nervous_system(3);oesophagus(4);NS(2);upper_aerodigestive_tract(5);stomach(8);soft_tissue(1);urinary_tract(4);breast(12);prostate(5);pituitary(1);pancreas(5);adrenal_gland(1);haematopoietic_and_lymphoid_tissue(2);ovary(5);liver(9) 1 0.958 0.00324 0.05 ../MuPIT_Interactive?gm=chr12:6561055 0 |
83181dabeb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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16 ATP2A2 1 MS C0022595 OMIM:124200 200 large_intestine(31);endometrium(12);lung(7);skin(43);autonomic_ganglia(1);kidney(9);thyroid(3);cervix(2);testis(1);oesophagus(4);NS(2);upper_aerodigestive_tract(6);biliary_tract(6);stomach(14);soft_tissue(2);urinary_tract(8);breast(7);prostate(8);pancreas(6);small_intestine(2);haematopoietic_and_lymphoid_tissue(5);ovary(3);bone(2);liver(16) 1 0.951 0.00374 0.05 ../MuPIT_Interactive?gm=chr12:110339630 0 |
83181dabeb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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17 DYNC1H1 1 MS C1834690 OMIM:158600 955 large_intestine(151);pleura(1);endometrium(79);lung(62);skin(151);autonomic_ganglia(1);kidney(27);thyroid(8);cervix(13);testis(1);central_nervous_system(12);oesophagus(28);NS(19);upper_aerodigestive_tract(31);biliary_tract(6);stomach(60);soft_tissue(13);urinary_tract(25);breast(50);prostate(38);pancreas(18);adrenal_gland(3);meninges(1);small_intestine(3);haematopoietic_and_lymphoid_tissue(37);ovary(20);bone(4);liver(93) 1 0.829 0.02307 0.1 ../MuPIT_Interactive?gm=chr14:102011985 1 94da5dd8-5521-11e7-8f50-0ac135e8bacf Lissencephaly gene (LIS1) in neuronal migration and development |
83181dabeb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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18 HSP90AA1 1 MS somatic NHL 174 large_intestine(19);endometrium(9);lung(9);skin(25);kidney(12);thyroid(2);cervix(4);central_nervous_system(2);oesophagus(9);NS(5);biliary_tract(2);stomach(16);soft_tissue(5);urinary_tract(15);liver(11);prostate(3);pancreas(1);salivary_gland(1);haematopoietic_and_lymphoid_tissue(5);ovary(8);bone(1);breast(10) 1 0.84 0.02014 0.1 ../MuPIT_Interactive?gm=chr14:102083954 15 3814fa62-5521-11e7-8f50-0ac135e8bacf,32ff1916-5521-11e7-8f50-0ac135e8bacf,a8411a5c-5521-11e7-8f50-0ac135e8bacf,541d7e20-5521-11e7-8f50-0ac135e8bacf,98ad85f0-5521-11e7-8f50-0ac135e8bacf,9697501e-5521-11e7-8f50-0ac135e8bacf,e6f69242-5521-11e7-8f50-0ac135e8bacf,603902ca-5521-11e7-8f50-0ac135e8bacf,bb3d7c4a-5521-11e7-8f50-0ac135e8bacf,b1ac7318-5521-11e7-8f50-0ac135e8bacf,cb348d72-5521-11e7-8f50-0ac135e8bacf,945aa686-5521-11e7-8f50-0ac135e8bacf,4c90f780-5521-11e7-8f50-0ac135e8bacf,e4e93610-5521-11e7-8f50-0ac135e8bacf,6f7a316e-5521-11e7-8f50-0ac135e8bacf Validated targets of C-MYC transcriptional activation@VEGFR1 specific signals@IL2 signaling events mediated by PI3K@Signaling events mediated by HDAC Class II@Integrin-linked kinase signaling@Integrins in angiogenesis@Class I PI3K signaling events mediated by Akt@Regulation of Telomerase@Glucocorticoid receptor regulatory network@Hypoxic and oxygen homeostasis regulation of HIF-1-alpha@ErbB receptor signaling network@LKB1 signaling events@Signaling events mediated by VEGFR1 and VEGFR2@Class I PI3K signaling events@Regulation of Androgen receptor activity |
83181dabeb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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19 FASN 1 MS 621 large_intestine(163);endometrium(22);lung(19);skin(82);autonomic_ganglia(1);kidney(9);thyroid(7);cervix(9);central_nervous_system(7);genital_tract(1);oesophagus(24);NS(13);upper_aerodigestive_tract(21);biliary_tract(12);stomach(39);soft_tissue(9);urinary_tract(2);liver(79);prostate(20);pancreas(14);adrenal_gland(2);salivary_gland(3);small_intestine(4);haematopoietic_and_lymphoid_tissue(14);ovary(3);bone(5);breast(37) 1 0.501 0.18611 0.25 ../MuPIT_Interactive?gm=chr17:82082606 2 34a994cc-5521-11e7-8f50-0ac135e8bacf,812903c2-5521-11e7-8f50-0ac135e8bacf Validated transcriptional targets of deltaNp63 isoforms@p73 transcription factor network |
83181dabeb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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20 MYO9B 2 MS C1857847 OMIM:609753 424 large_intestine(96);endometrium(33);lung(17);skin(57);kidney(12);thyroid(9);cervix(4);central_nervous_system(9);oesophagus(22);NS(8);upper_aerodigestive_tract(22);biliary_tract(9);stomach(24);soft_tissue(10);urinary_tract(8);breast(17);prostate(14);pancreas(15);adrenal_gland(4);haematopoietic_and_lymphoid_tissue(8);ovary(1);bone(4);liver(21) 1 0.473 0.721215732958585 1 ../MuPIT_Interactive?gm=chr19:17205335,chr19:17205973 1 60f3521c-5521-11e7-8f50-0ac135e8bacf Regulation of RhoA activity |
83181dabeb90
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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21 UPF1 1 MS 267 large_intestine(57);endometrium(18);lung(13);skin(45);meninges(1);kidney(9);thyroid(3);cervix(4);central_nervous_system(7);oesophagus(5);NS(4);upper_aerodigestive_tract(10);biliary_tract(2);stomach(15);soft_tissue(6);urinary_tract(12);breast(11);prostate(7);pancreas(7);haematopoietic_and_lymphoid_tissue(10);ovary(4);bone(2);liver(15) 1 0.662 0.09372 0.15 ../MuPIT_Interactive?gm=chr19:18856059 |