# HG changeset patch # User saketkc # Date 1405557101 14400 # Node ID 47ca5fb1b3f7b506a35ca5b35d6a9816f222adef # Parent af0c2fa5bc764bc15ce60402e56fc1058cd552c2 Uploaded diff -r af0c2fa5bc76 -r 47ca5fb1b3f7 chasm_webservice/test-data/chasm_input.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chasm_webservice/test-data/chasm_input.txt Wed Jul 16 20:31:41 2014 -0400 @@ -0,0 +1,5 @@ +TR1 chr22 30421786 + A T +TR2 chr22 29446079 + A G +TR3 chr22 29446079 + A G +TR4 chr22 40814500 - A G +TR5 chr22 40815256 + C T diff -r af0c2fa5bc76 -r 47ca5fb1b3f7 chasm_webservice/test-data/chasm_output_aminoacids.tabular diff -r af0c2fa5bc76 -r 47ca5fb1b3f7 chasm_webservice/test-data/chasm_output_codons.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chasm_webservice/test-data/chasm_output_codons.tabular Wed Jul 16 20:31:41 2014 -0400 @@ -0,0 +1,13 @@ +#Amino Acid Level Analysis Report +#2014-07-15 03:23:43.460539 +#Analysis done at http://www.cravat.us. +#Input file: dataset_346.dat +#This report shows analysis results at amino acid level. +#Input coordinate was hg19 genomic. +#For more information on CRAVAT, visit http://www.cravat.us. +# +Transcript Amino acid position Sequence Ontology Reference amino acid(s) Alternate amino acid(s) HUGO symbol Other transcripts Occurrences in study [amino acid change] Transcript in COSMIC Protein sequence change in COSMIC Occurrences in COSMIC [amino acid change] Occurrences in COSMIC by primary sites [amino acid change] +NM_021090.3 1198 MS N I MTMR3 NM_153051.2:aAc>aTc:N1161I, NM_153050.2:aAc>aTc:N1170I, ENST00000323630:aAc>aTc:N1062I, ENST00000351488:aAc>aTc:N1161I, ENST00000333027:aAc>aTc:N1170I, ENST00000406629:aAc>aTc:N1170I, ENST00000401950:aAc>aTc:N1198I 1 0 +NM_001206998.1 637 MS H R ZNRF3 NM_032173.3:cAc>cGc:H537R, ENST00000406323:cAc>cGc:H537R, ENST00000332811:cAc>cGc:H537R, ENST00000402174:cAc>cGc:H537R, ENST00000544604:cAc>cGc:H637R 2 0 +NM_020831.3 648 MS S G MKL1 ENST00000396617:Agc>Ggc:S648G, ENST00000402042:Agc>Ggc:S598G, ENST00000407029:Agc>Ggc:S648G, ENST00000355630:Agc>Ggc:S648G 1 0 +NM_020831.3 396 MS A T MKL1 ENST00000396617:Gcc>Acc:A396T, ENST00000402042:Gcc>Acc:A346T, ENST00000407029:Gcc>Acc:A396T, ENST00000355630:Gcc>Acc:A396T 1 0 diff -r af0c2fa5bc76 -r 47ca5fb1b3f7 chasm_webservice/test-data/chasm_output_errors.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chasm_webservice/test-data/chasm_output_errors.tabular Wed Jul 16 20:31:41 2014 -0400 @@ -0,0 +1,1 @@ +# End of input format error output. If nothing is above this line, there was no format error in the input. \ No newline at end of file diff -r af0c2fa5bc76 -r 47ca5fb1b3f7 chasm_webservice/test-data/chasm_output_genes.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chasm_webservice/test-data/chasm_output_genes.tabular Wed Jul 16 20:31:41 2014 -0400 @@ -0,0 +1,14 @@ +#Gene Level Analysis Report +#2014-07-15 03:23:43.461186 +#Analysis done at http://www.cravat.us. +#Input file: dataset_346.dat +#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. +#Input coordinate was hg19 genomic. +#Tissue type for CHASM analysis: Other +#For more information on CRAVAT, visit http://www.cravat.us. +# +HUGO symbol Best driver score from representative transcripts Composite p value Composite FDR Occurrences in study [gene mutated] Occurrences in COSMIC [gene mutated] Occurrences in COSMIC by primary sites [gene mutated] MuPIT link +MTMR3 0.6 0.3364 0.55 1 102 upper_aerodigestive_tract(2);large_intestine(24);haematopoietic_and_lymphoid_tissue(5);endometrium(12);urinary_tract(4);oesophagus(1);liver(3);skin(17);lung(17);ovary(5);prostate(2);kidney(4);breast(6 ) +ZNRF3 0.514 0.171 0.55 2 73 upper_aerodigestive_tract(2);large_intestine(19);autonomic_ganglia(1);haematopoietic_and_lymphoid_tissue(2);endometrium(12);urinary_tract(2);lung(16);liver(5);skin(1);oesophagus(3);ovary(2);NS(1);prostate(2);kidney(3);breast(2 ) +MKL1 0.728 0.793956248886469 1 2 68 large_intestine(15);stomach(2);central_nervous_system(1);haematopoietic_and_lymphoid_tissue(3);endometrium(13);urinary_tract(1);lung(19);breast(3);skin(1);ovary(5);kidney(4);liver(1 ) diff -r af0c2fa5bc76 -r 47ca5fb1b3f7 chasm_webservice/test-data/chasm_output_variants.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chasm_webservice/test-data/chasm_output_variants.tabular Wed Jul 16 20:31:41 2014 -0400 @@ -0,0 +1,15 @@ +#Variant Level Analysis Report +#2014-07-15 03:23:43.461879 +#Analysis done at http://www.cravat.us. +#Input file: dataset_346.dat +#This report shows analysis results at variant level. +#Input coordinate was hg19 genomic. +#Tissue type for CHASM analysis: Other +#For more information on CRAVAT, visit http://www.cravat.us. +# +ID Chromosome Position Strand Reference base Alternate base Sample ID HUGO symbol Transcript Transcript strand Codon change Amino acid position Sequence Ontology Reference amino acid(s) Alternate amino acid(s) Other transcripts Mappability Warning Driver score of representative transcript (driver mutations close to 0) Empirical p-value FDR (Benjamini-Hochberg) (not available with less than 10 unique mutations) Best driver score and transcript All transcripts and driver scores dbSNP 1000 Genomes allele frequency ESP6500 allele frequency (European American) ESP6500 allele frequency (African American) Occurrences in study [exact nucleotide change] Transcript in COSMIC Protein sequence change in COSMIC Occurrences in COSMIC [exact nucleotide change] Occurrences in COSMIC by primary sites [exact nucleotide change] MuPIT Link +TR1 chr22 30421786 + A T No_sample_ID MTMR3 NM_021090.3 + aAc>aTc 1198 MS N I NM_153051.2:aAc>aTc:N1161I, NM_153050.2:aAc>aTc:N1170I, ENST00000323630:aAc>aTc:N1062I, ENST00000351488:aAc>aTc:N1161I, ENST00000333027:aAc>aTc:N1170I, ENST00000406629:aAc>aTc:N1170I, ENST00000401950:aAc>aTc:N1198I 0.6(NM_021090.3:N1198I) 0.3364 0.60 0.572(ENST00000323630:N1062I) ENST00000323630:N1062I(0.572),ENST00000406629:N1170I(0.602),ENST00000401950:N1198I(0.6),ENST00000351488:N1161I(0.572),NM_153050.2:N1170I(0.572),ENST00000333027:N1170I(0.572),NM_021090.3:N1198I(0.6),NM_153051.2:N1161I(0.572) rs75623810 0.00778388278388 0 0.0226963 1 +TR2 chr22 29446079 + A G No_sample_ID ZNRF3 NM_001206998.1 + cAc>cGc 637 MS H R NM_032173.3:cAc>cGc:H537R, ENST00000406323:cAc>cGc:H537R, ENST00000332811:cAc>cGc:H537R, ENST00000402174:cAc>cGc:H537R, ENST00000544604:cAc>cGc:H637R 0.514(NM_001206998.1:H637R) 0.1710 0.60 0.442(ENST00000544604:H637R) ENST00000544604:H637R(0.442),NM_032173.3:H537R(0.514),ENST00000402174:H537R(0.514),ENST00000406323:H537R(0.514),NM_001206998.1:H637R(0.514),ENST00000332811:H537R(0.514) rs62641746 0 0.00598145 0.00104004 2 +TR3 chr22 29446079 + A G No_sample_ID ZNRF3 NM_001206998.1 + cAc>cGc 637 MS H R NM_032173.3:cAc>cGc:H537R, ENST00000406323:cAc>cGc:H537R, ENST00000332811:cAc>cGc:H537R, ENST00000402174:cAc>cGc:H537R, ENST00000544604:cAc>cGc:H637R 0.514(NM_001206998.1:H637R) 0.1710 0.60 0.442(ENST00000544604:H637R) ENST00000544604:H637R(0.442),NM_032173.3:H537R(0.514),ENST00000402174:H537R(0.514),ENST00000406323:H537R(0.514),NM_001206998.1:H637R(0.514),ENST00000332811:H537R(0.514) rs62641746 0 0.00598145 0.00104004 2 +TR4 chr22 40814500 - A G No_sample_ID MKL1 NM_020831.3 - Agc>Ggc 648 MS S G ENST00000396617:Agc>Ggc:S648G, ENST00000402042:Agc>Ggc:S598G, ENST00000407029:Agc>Ggc:S648G, ENST00000355630:Agc>Ggc:S648G 0.728(NM_020831.3:S648G) 0.6890 0.80 0.708(ENST00000402042:S598G) ENST00000407029:S648G(0.728),NM_020831.3:S648G(0.728),ENST00000396617:S648G(0.728),ENST00000355630:S648G(0.728),ENST00000402042:S598G(0.708) rs878756 0.419871794872 0.396977 0.860645 1 +TR5 chr22 40815256 + C T No_sample_ID MKL1 NM_020831.3 - Gcc>Acc 396 MS A T ENST00000396617:Gcc>Acc:A396T, ENST00000402042:Gcc>Acc:A346T, ENST00000407029:Gcc>Acc:A396T, ENST00000355630:Gcc>Acc:A396T 0.748(NM_020831.3:A396T) 0.7476 0.80 0.748(ENST00000407029:A396T) ENST00000407029:A396T(0.748),NM_020831.3:A396T(0.748),ENST00000396617:A396T(0.748),ENST00000355630:A396T(0.748),ENST00000402042:A346T(0.754) rs34736200 0.0201465201465 0.00127937 0.0834091 1