-
Notifications
You must be signed in to change notification settings - Fork 67
/
final-list_candidate-fusion-genes.txt
executable file
·26 lines (26 loc) · 8.11 KB
/
final-list_candidate-fusion-genes.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
Gene_1_symbol(5end_fusion_partner) Gene_2_symbol(3end_fusion_partner) Fusion_description Counts_of_common_mapping_reads Spanning_pairs Spanning_unique_reads Longest_anchor_found Fusion_finding_method Fusion_point_for_gene_1(5end_fusion_partner) Fusion_point_for_gene_2(3end_fusion_partner) Gene_1_id(5end_fusion_partner) Gene_2_id(3end_fusion_partner) Exon_1_id(5end_fusion_partner) Exon_2_id(3end_fusion_partner) Fusion_sequence Predicted_effect
FGFR3 TACC3 known,adjacent,oncogene,cosmic,ticdb,tcga,cell_lines,18cancers,gliomas,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,oesophagus,10K<gap<100K 0 820 66 43 BOWTIE+BLAT;BOWTIE+STAR 4:1806934:+ 4:1727977:+ ENSG00000068078 ENSG00000013810 AGCAGCTGGTGGAGGACCTGGACCGTGTCCTTACCGTGACGTCCACCGAC*ACAGAAGAGTGACACCCGCCTCTGAGACCCTAGAAGACCCTTGCAGGACA in-frame
FGFR3 TACC3 known,adjacent,oncogene,cosmic,ticdb,tcga,cell_lines,18cancers,gliomas,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,oesophagus,10K<gap<100K 0 820 13 45 BOWTIE+BLAT;BOWTIE+STAR 4:1806934:+ 4:1727981:+ ENSG00000068078 ENSG00000013810 AGCAGCTGGTGGAGGACCTGGACCGTGTCCTTACCGTGACGTCCACCGAC*AAGAGTGACACCCGCCTCTGAGACCCTAGAAGACCCTTGCAGGACAGAGT out-of-frame
FGFR3 TACC3 known,adjacent,oncogene,cosmic,ticdb,tcga,cell_lines,18cancers,gliomas,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,oesophagus,10K<gap<100K 0 820 10 43 BOWTIE+BLAT;BOWTIE+STAR 4:1807033:+ 4:1727832:+ ENSG00000068078 ENSG00000013810 CCGTCCCCGGCCATCCTGCCCCCCAGAGTGCTGAGGTGTGGGGCGGGCCT*TCTGGCCCAGGTGCCCTGGCTGACCTGGACTGCTCAAGCTCTTCCCAGAG intronic/CDS(truncated)
GOPC ROS1 known,oncogene,cosmic,chimerdb2,cgp,ticdb,cacg,chimerdb3kb,chimerdb3pub,cancer,tumor,100K<gap<200K,exon-exon 0 73 22 30 BOWTIE;BOWTIE+BLAT;BOWTIE+STAR 6:117566854:- 6:117321394:- ENSG00000047932 ENSG00000047936 ENSE00003526662 ENSE00000442460 GCTAGTTGCAAAGACACAAGTGGGGAAATCAAAGTATTACAAG*TCTGGCATAGAAGATTAAAGAATCAAAAAAGTGCCAAGGAAGG in-frame
GOPC ROS1 known,oncogene,cosmic,chimerdb2,cgp,ticdb,cacg,chimerdb3kb,chimerdb3pub,cancer,tumor,100K<gap<200K,exon-exon 0 73 2 26 BOWTIE 6:117566854:- 6:117320030:- ENSG00000047932 ENSG00000047936 ENSE00003526662 ENSE00003478828 GCTAGTTGCAAAGACACAAGTGGGGAAATCAAAGTATTACAAG*TACTCTTCCAACCCAAGAGGAGATTGAAAATCTTCCTGCCTTC out-of-frame
FIP1L1 PDGFRA known,oncogene,chimerdb2,cgp,ticdb,cacg,tcga,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,tumor 0 50 48 48 BOWTIE+BLAT;BOWTIE+STAR 4:53425965:+ 4:54274925:+ ENSG00000145216 ENSG00000134853 TCAGCCGAGTAGAAGGCAGGCGACGGGCAAATGAGAACAGCAACATACAG*CTGCCTTATGACTCAAGATGGGAGTTTCCAAGAGATGGACTAGTGCTTGG in-frame
IGH@ CRLF2 known,oncogene,cancer 0 32 4 33 BOWTIE+STAR 14:105863263:+ X:1228687:- ENSG09000000014 ENSG00000205755 CGTGGTCCCTTTGCCCCAGACGTCCATGTAGTAGTAGTAGTAGTAATCAC*NNNNNNNNNNNNNNNNNNNNNGAAGCTGTGAGCTGGGGAGAGGATATATAAGAACTTTCTGTACTTTCTGC ---/intergenic
IGH@ CRLF2 known,oncogene,cancer 0 32 3 34 BOWTIE+STAR 14:105863264:+ X:1228687:- ENSG09000000014 ENSG00000205755 GTGGTCCCTTTGCCCCAGACGTCCATGTAGTAGTAGTAGTAGTAATCACA*NNNNNNNNNNNNNNNNNNNNNGAAGCTGTGAGCTGGGGAGAGGATATATAAGAACTTTCTGTACTTTCTGC ---/intergenic
IGH@ CRLF2 known,oncogene,cancer 0 32 3 33 BOWTIE+STAR 14:105863263:+ X:1228688:- ENSG09000000014 ENSG00000205755 CGTGGTCCCTTTGCCCCAGACGTCCATGTAGTAGTAGTAGTAGTAATCAC*NNNNNNNNNNNNNNNNNNNNNCGAAGCTGTGAGCTGGGGAGAGGATATATAAGAACTTTCTGTACTTTCTG ---/intergenic
AKAP9 BRAF known,oncogene,cosmic,chimerdb2,cgp,ticdb,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,tumor,exon-exon 0 10 11 29 BOWTIE;BOWTIE+BLAT;BOWTIE+STAR 7:92003235:+ 7:140787584:- ENSG00000127914 ENSG00000157764 ENSE00003484877 ENSE00003680515 TGATAAACTTCAGAAAGAACTCAATGTACTTAAATCAGAACAG*GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAA in-frame
EWSR1 ATF1 known,oncogene,cosmic,cgp,ticdb,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,tumor,m4,exon-exon 0 10 10 30 BOWTIE;BOWTIE+BLAT;BOWTIE+STAR 22:29287134:+ 12:50814280:+ ENSG00000182944 ENSG00000123268 ENSE00003570564 ENSE00003675908 CCAAGTCAATATAGCCAACAGAGCAGCAGCTACGGGCAGCAGA*CTGCATCAGGAGATATGCAAACATATCAGATCCGAACTACACC in-frame
HOOK3 RET known,oncogene,cosmic,cgp,ticdb,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,tumor,exon-exon 0 10 10 29 BOWTIE;BOWTIE+BLAT;BOWTIE+STAR 8:42968214:+ 10:43116584:+ ENSG00000168172 ENSG00000165731 ENSE00003485179 ENSE00001095944 GGCCAACGCAGCGCGAAGTCAACTTGAAACCTACAAGAGACAG*GAGGATCCAAAGTGGGAATTCCCTCGGAAGAACTTGGTTCTTG in-frame
EWSR1 FLI1 known,oncogene,cosmic,cgp,ticdb,cell_lines,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,tumor,m6,exon-exon 0 9 11 28 BOWTIE;BOWTIE+BLAT;BOWTIE+STAR 22:29287134:+ 11:128807180:+ ENSG00000182944 ENSG00000151702 ENSE00003570564 ENSE00003702967 CCAAGTCAATATAGCCAACAGAGCAGCAGCTACGGGCAGCAGA*GTCCTCCCCTTGGAGGGGCACAAACGATCAGTAAGAATACAGA in-frame
TMPRSS2 ETV1 known,oncogene,cosmic,chimerdb2,cgp,ticdb,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,tumor 0 7 10 38 BOWTIE+BLAT 21:41494380:- 7:13935843:- ENSG00000184012 ENSG00000006468 GGTCCTGACGCAGGCTTCCAACCCCGTCGTCTGCACGCAGCCCAAATCCC*CATCCAGCACGCCAGTGTCCCCACTGCATCATGCATCTCCAAACTCAACT in-frame
TMPRSS2 ETV1 known,oncogene,cosmic,chimerdb2,cgp,ticdb,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,tumor 0 7 10 38 BOWTIE+STAR 21:41494381:- 7:13935844:- ENSG00000184012 ENSG00000006468 GGGTCCTGACGCAGGCTTCCAACCCCGTCGTCTGCACGCAGCCCAAATCC*CCATCCAGCACGCCAGTGTCCCCACTGCATCATGCATCTCCAAACTCAAC in-frame
ETV6 NTRK3 known,oncogene,cosmic,chimerdb2,cgp,ticdb,tcga,cell_lines,18cancers,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,tumor,exon-exon 0 6 8 29 BOWTIE 12:11869969:+ 15:87940753:- ENSG00000139083 ENSG00000140538 ENSE00001788162 ENSE00001134154 TCCCCGCCTGAAGAGCACGCCATGCCCATTGGGAGAATAGCAG*ATGTGCAGCACATTAAGAGGAGAGACATCGTGCTGAAGCGAGA in-frame
BRD4 NUTM1 known,oncogene,cosmic,chimerdb2,cgp,ticdb,cell_lines,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,exon-exon 0 5 9 30 BOWTIE;BOWTIE+BLAT;BOWTIE+STAR 19:15254152:- 15:34347969:+ ENSG00000141867 ENSG00000184507 ENSE00001187704 ENSE00001367212 TCCAGTGAGTCCAGCTCCTCTGACAGCGAAGACTCCGAAACAG*CATCTGCATTGCCGGGACCGGATATGAGCATGAAACCTAGTGC in-frame
CIC DUX4 known,cosmic,chimerdb2,cgp,ticdb,chimerdb3kb,chimerdb3pub,cancer 0 5 5 34 BOWTIE+STAR 19:42295047:+ 4:190174446:+ ENSG00000079432 ENSG00000260596 CTGCCCCTGCCCCCACTCCCAGCCCCGCAGGGGGCCCTGACCCCACCTCA*CCGGCAGAGGGGATCTCCCAACCTGCCCCGGCGCGCGGGGATTTCGCCTA in-frame
CIC DUX4 known,cosmic,chimerdb2,cgp,ticdb,chimerdb3kb,chimerdb3pub,cancer 0 5 4 35 BOWTIE+BLAT 19:42295048:+ 4:190174447:+ ENSG00000079432 ENSG00000260596 TGCCCCTGCCCCCACTCCCAGCCCCGCAGGGGGCCCTGACCCCACCTCAC*CGGCAGAGGGGATCTCCCAACCTGCCCCGGCGCGCGGGGATTTCGCCTAC in-frame
DUX4 IGH@ known,cancer 0 5 5 84 BOWTIE+SPOTLIGHT 4:190174997:+ 14:190287409:+ ENSG00000260596 ENSG09000000014 CGCAACCTCTCCTAGAAACGGAGGCCCCGGGGGAGCTGGAGGCCTCGGAAGAGGCCGCCTCGCTG*CGATCCCTCAGGGTTGGCTGTAGTCACCGTATGGGGGAAGCCTGTGTCATCATTTATTTACCCAACCTGGGTTAATGTCTTTGCTATTATGAATAGTGCTGG CDS(truncated)/---
DUX4 IGH@ known,cancer 0 4 8 38 BOWTIE+BLAT;BOWTIE+STAR 4:190175284:+ 14:106638525:- ENSG00000260596 ENSG09000001017 TTCTTTCCTGGGCATCCCGGGGATCCCAGAGCCGGCCCAGGTACCAGCAG*GCAGAGAAGAGGCCATGTGGAGACATAGTGCACTAGAAGGTGGCCCAGTG UTR/---
EML4 ALK known,oncogene,cosmic,chimerdb2,cgp,ticdb,tcga,cell_lines,18cancers,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,tumor 0 4 4 33 BOWTIE+STAR 2:42301391:+ 2:29223587:- ENSG00000143924 ENSG00000171094 AGAAAAATAATTCTGTGGGATCATGATCTGAATCCTGAAAGAGAAATAGA*GTGTAGTGCTTCAAGGGCCAGGCTGCCAGGCCATGTTGCAGCTGACCACC CDS(truncated)/intronic
CD74 ROS1 known,oncogene,cosmic,chimerdb2,cgp,ticdb,tcga,cell_lines,18cancers,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,tumor,exon-exon 0 3 7 30 BOWTIE;BOWTIE+BLAT;BOWTIE+STAR 5:150404680:- 6:117324415:- ENSG00000019582 ENSG00000047936 ENSE00000841201 ENSE00000762702 AGGCACTCCTTGGAGCAAAAGCCCACTGACGCTCCACCGAAAG*ATGATTTTTGGATACCAGAAACAAGTTTCATACTTACTATTAT in-frame
MALT1 IGH@ known,oncogene,chimerdb2,chimerdb3kb,cancer 0 3 3 34 BOWTIE+STAR 18:58669909:+ 14:105888559:+ ENSG00000172175 ENSG09000000014 AGCTATATTGGCTAAGAGTAAATAACACTGGCACCCATTTAACTCGTATG*AGTCACCACCACAATATGCTCACAGTGACACGAACCCCCACAAAATCCTC intergenic/---
NPM1 ALK known,oncogene,cosmic,chimerdb2,cgp,ticdb,cell_lines,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,tumor,exon-exon 0 3 3 30 BOWTIE 5:171391799:+ 2:29223528:- ENSG00000181163 ENSG00000171094 ENSE00003625205 ENSE00001154407 TGTGGTTCAGGGCCAGTGCATATTAGTGGACAGCACTTAGTAG*TGTACCGCCGGAAGCACCAGGAGCTGCAAGCCATGCAGATGGA in-frame