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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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#Gene Level Annotation Report #2018-05-18 15:18:04.023450 #CRAVAT version: hybrid #Analysis done at http://www.cravat.us. #Job Id: znylund_20180518_111800 #Input file: _VCF_BEDintersect_on_data_65_and_data_6_.vcf #This report shows analysis results at gene level. #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. #hg38 genomic. #N/A #For more information on CRAVAT, visit http://www.cravat.us. 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 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 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 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 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 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 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 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 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