https://sourceforge.net/p/soapfuse/wiki/simulated-case.for.SOAPfuse/Recent changes to simulated-case.for.SOAPfuseenSat, 27 Jul 2013 03:24:15 -0000https://sourceforge.net/p/soapfuse/wiki/simulated-case.for.SOAPfuse/<div class="markdown_content"><pre>--- v1 +++ v2 @@ -167,13 +167,13 @@ 3 up_chr 4 up_strand 5 up_loc - 6 up_dna_breakpoint + 6 up_dna_junction_pos 7 down_gene 8 down_trans 9 down_chr 10 down_strand 11 down_loc - 12 down_dna_breakpoint + 12 down_dna_junction_pos </pre> <p>info of simulated cases<br /> </p></div>NOBEL89Sat, 27 Jul 2013 03:24:15 -0000https://sourceforge.net7586a3f8cabc984b3c568b7d5ac3e4f45cd43922https://sourceforge.net/p/soapfuse/wiki/simulated-case.for.SOAPfuse/<div class="markdown_content"><h1 id="simulated-fusions-150-cases">simulated fusions, 150 cases</h1> <pre class="code"> ABHD14B ABHD14B-201 chr3 - E<b style="color: red;">*</b> 52002569 MCF2L2 MCF2L2-014 chr3 - M 182897969 ACP5 ACP5-204 chr19 - M 11688465 FUZ FUZ-204 chr19 - E 50314724 ACVR2B ACVR2B-003 chr3 + M 38520696 LMLN LMLN-004 chr3 + E 197710814 AFM AFM-001 chr4 + M 74353454 ANXA3 ANXA3-001 chr4 + E 79507414 AGAP7 AGAP7-001 chr10 - E 51483174 SLC16A9 SLC16A9-001 chr10 - E 61444085 AHR AHR-002 chr7 + E 17370510 ZNF3 ZNF3-009 chr7 - E 99672884 AKT2 AKT2-018 chr19 - E 40741797 PIK3R2 PIK3R2-201 chr19 + E 18272776 ALDH1A2 ALDH1A2-002 chr15 - E 58245629 MYO5A MYO5A-002 chr15 - E 52615641 AMOT AMOT-001 chrX - E 112025768 CLCN5 CLCN5-003 chrX + E 49845251 ATAD3C ATAD3C-001 chr1 + E 1389880 GBP7 GBP7-001 chr1 - E 89641723 BOD1L BOD1L-001 chr4 - E 13610154 GRPEL1 GRPEL1-004 chr4 - E 7069274 BRCC3 BRCC3-005 chrX + E 154348443 SFRS5 SFRS5-201 chr14 + E 70234874 BTF3 BTF3-007 chr5 + E 72795027 RELL2 RELL2-201 chr5 + E 141020238 C1QTNF1 C1QTNF1-204 chr17 + M 77045486 SHISA6 SHISA6-201 chr17 + M 11461172 CA6 CA6-004 chr1 + E 9017304 MAGOH MAGOH-002 chr1 - E 53704171 CAPRIN2 CAPRIN2-201 chr12 - E 30876193 ELOVL4 ELOVL4-001 chr6 - M 80657023 CBWD5 CBWD5-025 chr9 - E 70434178 PDLIM5 PDLIM5-004 chr4 + E 95373037 CD1D CD1D-001 chr1 + E 158149952 UBQLN4 UBQLN4-201 chr1 - E 156011778 CDC20B CDC20B-201 chr5 - E 54439341 PHACTR4 PHACTR4-003 chr1 + E 28733921 CELF5 CELF5-201 chr19 + E 3282265 CYP4F8 CYP4F8-201 chr19 + E 15726427 CENPV CENPV-003 chr17 - M 16252565 PTRH2 PTRH2-002 chr17 - E 57775339 CHAD CHAD-004 chr17 - E 48542655 CACNG5 CACNG5-201 chr17 + M 64875175 CLCA1 CLCA1-001 chr1 + M 86947915 MARK3 MARK3-205 chr14 + E 103946724 COL23A1 COL23A1-201 chr5 - M 177694327 MIER3 MIER3-202 chr5 - E 56219660 CPVL CPVL-008 chr7 - M 29160674 ANAPC5 ANAPC5-203 chr12 - E 121756227 CSMD2 CSMD2-007 chr1 - E 34280897 GBP5 GBP5-201 chr1 - E 89728468 CTDSPL2 CTDSPL2-001 chr15 + E 44788656 ADAL ADAL-201 chr15 + E 43639214 CTSS CTSS-201 chr1 - E 150730334 ACTN2 ACTN2-002 chr1 + E 236924315 CYB561D1 CYB561D1-004 chr1 + E 110036909 PIGT PIGT-003 chr20 + E 44048776 CYTIP CYTIP-007 chr2 - E 158300359 OTUD3 OTUD3-001 chr1 + E 20209006 DGKD DGKD-004 chr2 + E 234343545 PTPRN PTPRN-009 chr2 - E 220172279 DLD DLD-014 chr7 + E 107545503 NPTX2 NPTX2-001 chr7 + E 98256477 ENPP5 ENPP5-001 chr6 - E 46138545 SLC17A1 SLC17A1-201 chr6 - E 25832287 ETV3L ETV3L-202 chr1 - E 157068933 CALML6 CALML6-003 chr1 + E 1846848 FAM177B FAM177B-005 chr1 + E 222920423 RORC RORC-201 chr1 - M 151803447 FAM72A FAM72A-002 chr1 + E 206145578 RGS1 RGS1-004 chr1 + E 192547352 FAM75A4 FAM75A4-001 chr9 - E 41327147 CYLC2 CYLC2-002 chr9 + M 105767129 FRG2C FRG2C-002 chr3 + M 75714303 WNT7A WNT7A-002 chr3 - M 13917429 GAGE2C GAGE2C-001 chrX + M 49230861 MAGEB1 MAGEB1-201 chrX + E 30268551 GALP GALP-201 chr19 + E 56697144 FAM5C FAM5C-001 chr1 - E 190250880 GDPD2 GDPD2-002 chrX + M 69652469 MTMR8 MTMR8-202 chrX - E 63579407 GIGYF2 GIGYF2-019 chr2 + E 233625269 PCGF1 PCGF1-007 chr2 - E 74732737 GIMAP6 GIMAP6-203 chr7 - E 150324807 EPHA1 EPHA1-005 chr7 - E 143092275 GPBP1 GPBP1-006 chr5 + M 56531838 PPARGC1B PPARGC1B-008 chr5 + E 149227021 GRIN1 GRIN1-003 chr9 + E 140053169 DNLZ DNLZ-001 chr9 - E 139257580 GSPT1 GSPT1-202 chr16 - E 11976872 GAN GAN-001 chr16 + E 81385188 HMOX1 HMOX1-005 chr22 + E 35779219 ARHGAP8 ARHGAP8-014 chr22 + E 45204187 HOXD3 HOXD3-001 chr2 + M 177034326 MSH6 MSH6-006 chr2 + E 48023033 IGF2BP1 IGF2BP1-005 chr17 + M 47114022 LRRC37A2 LRRC37A2-202 chr17 + E 44590076 IL1F7 IL1F7-002 chr2 + E 113674825 TACR1 TACR1-001 chr2 - M 75278442 INPP5E INPP5E-201 chr9 - E 139327607 CAMSAP1 CAMSAP1-010 chr9 - E 138758382 IRAK1 IRAK1-018 chrX - E 153284050 XAGE2B XAGE2B-001 chrX + M 52115723 ITGA3 ITGA3-003 chr17 + E 48151368 CSHL1 CSHL1-201 chr17 - M 61987593 JMY JMY-001 chr5 + E 78596141 AP3S1 AP3S1-007 chr5 + E 115205714 KCNH5 KCNH5-202 chr14 - E 63269047 AKT1 AKT1-203 chr14 - M 105240304 KHDRBS2 KHDRBS2-001 chr6 - E 62407100 SYTL1 SYTL1-007 chr1 + E 27676238 KIFC1 KIFC1-004 chr6 + M 33374394 FAM54A FAM54A-202 chr6 - E 136562814 KRT4 KRT4-203 chr12 - M 53201551 TAOK3 TAOK3-201 chr12 - E 118650800 LAP3 LAP3-009 chr4 + M 17608493 ING4 ING4-003 chr12 - E 6765964 LARP4 LARP4-204 chr12 + M 50867861 HOXC6 HOXC6-003 chr12 + E 54422360 LHPP LHPP-204 chr10 + E 126186697 PAOX PAOX-001 chr10 + E 135193503 LIN9 LIN9-002 chr1 - E 226420797 SV2A SV2A-002 chr1 - M 149881354 LRRFIP1 LRRFIP1-003 chr2 + E 238662122 GALNT3 GALNT3-001 chr2 - M 166650760 MAPK1 MAPK1-001 chr22 - E 22127162 RGL4 RGL4-006 chr22 + M 24040483 MAPKAPK3 MAPKAPK3-005 chr3 + E 50684256 TBCCD1 TBCCD1-002 chr3 - E 186272873 MASP1 MASP1-004 chr3 - E 186969422 PPIC PPIC-002 chr5 - E 122372420 MBNL3 MBNL3-004 chrX - M 131524957 G6PD G6PD-006 chrX - E 153762375 MDS2 MDS2-001 chr1 + E 23954488 HP1BP3 HP1BP3-002 chr1 - E 21076375 MED6 MED6-204 chr14 - E 71063328 WISP2 WISP2-005 chr20 + E 43355728 MTF2 MTF2-005 chr1 + E 93545088 KPNA6 KPNA6-002 chr1 + E 32622454 MYBPHL MYBPHL-001 chr1 - E 109840044 MIER1 MIER1-004 chr1 + E 67424534 MYO3B MYO3B-003 chr2 + E 171070993 COX5B COX5B-002 chr2 + E 98262980 NBL1 NBL1-005 chr1 + E 19983404 NECAP2 NECAP2-202 chr1 + M 16775636 NES NES-202 chr1 - M 156639387 DISP1 DISP1-003 chr1 + E 223101783 NEU1 NEU1-005 chr6 - E 31825436 SUPT3H SUPT3H-205 chr6 - E 45333038 NSUN3 NSUN3-007 chr3 + E 93803294 FAM160A1 FAM160A1-004 chr4 + E 152487290 OCA2 OCA2-201 chr15 - E 28326794 TAC1 TAC1-002 chr7 + E 97364138 PAPD5 PAPD5-201 chr16 + E 50258905 MT1A MT1A-202 chr16 + M 56673229 PECI PECI-003 chr6 - E 4115923 ZC3H12D ZC3H12D-003 chr6 - E 149773858 PHKB PHKB-203 chr16 + M 47533705 SPNS3 SPNS3-202 chr17 + E 4381867 PHOSPHO2 PHOSPHO2-003 chr2 + E 170551757 HTR4 HTR4-204 chr5 - M 147902793 PHYHIPL PHYHIPL-002 chr10 + E 60937378 RP1 RP1-202 chr8 + E 55471745 PICK1 PICK1-006 chr22 + M 38453540 CBX6 CBX6-001 chr22 - E 39263206 PIK3AP1 PIK3AP1-006 chr10 - E 98363736 UPF2 UPF2-202 chr10 - E 12043824 PPIB PPIB-001 chr15 - E 64448924 TM2D3 TM2D3-201 chr15 - M 102190362 PPP5C PPP5C-003 chr19 + E 46888166 ARMC6 ARMC6-202 chr19 + M 19165086 PRKRIP1 PRKRIP1-002 chr7 + E 102067113 MUC3A MUC3A-003 chr7 + E 100552886 PRPH PRPH-202 chr12 + M 49690739 MVK MVK-201 chr12 + E 110012612 PSMD6 PSMD6-004 chr3 - M 64008139 RAD54L2 RAD54L2-002 chr3 + E 51664721 PSMD8 PSMD8-201 chr19 + E 38866872 ICAM1 ICAM1-201 chr19 + M 10394866 PVALB PVALB-006 chr22 - E 37211147 SCARA5 SCARA5-001 chr8 - E 27762351 QKI QKI-205 chr6 + E 163983101 ZUFSP ZUFSP-003 chr6 - M 116987858 RAPGEF5 RAPGEF5-203 chr7 - E 22306583 OGDH OGDH-008 chr7 + E 44646194 RASSF4 RASSF4-010 chr10 + M 45486525 THAP8 THAP8-201 chr19 - E 36526494 REG3G REG3G-005 chr2 + E 79254376 KCTD1 KCTD1-201 chr18 - E 24035865 REV1 REV1-002 chr2 - E 100019107 NEK4 NEK4-005 chr3 - E 52786086 RGPD4 RGPD4-201 chr2 + E 108477787 ROCK2 ROCK2-004 chr2 - E 11335242 RPGRIP1L RPGRIP1L-201 chr16 - M 53692365 NOB1 NOB1-001 chr16 - E 69786274 RPS6KB1 RPS6KB1-201 chr17 + E 58022879 MCART1 MCART1-002 chr9 - E 37888589 RRAGB RRAGB-003 chrX + M 55777798 UBA1 UBA1-202 chrX + E 47070435 RREB1 RREB1-202 chr6 + E 7240775 CYHR1 CYHR1-202 chr8 - E 145689995 RYR1 RYR1-201 chr19 + E 39057627 GRIN3B GRIN3B-201 chr19 + E 1007627 SACS SACS-003 chr13 - E 23949258 SYNJ2 SYNJ2-001 chr6 + M 158476058 SELENBP1 SELENBP1-006 chr1 - M 151338878 IARS2 IARS2-004 chr1 + E 220316286 SEPT8 SEPT8-201 chr5 - E 132091697 RASA1 RASA1-002 chr5 + E 86659165 SIGLEC1 SIGLEC1-001 chr20 - E 3667617 TBC1D2B TBC1D2B-006 chr15 - E 78290697 SLC35E3 SLC35E3-201 chr12 + E 69153019 MLXIP MLXIP-201 chr12 + M 122625505 SLC45A3 SLC45A3-002 chr1 - E 205626979 KCND3 KCND3-002 chr1 - E 112323413 SMARCC1 SMARCC1-009 chr3 - M 47652038 SH3RF3 SH3RF3-002 chr2 + E 109964130 SNHG3 SNHG3-002 chr1 + E 28836145 NFASC NFASC-015 chr1 + E 204951012 SNRPG SNRPG-001 chr2 - E 70520750 ORC2L ORC2L-002 chr2 - M 201790631 SPON1 SPON1-201 chr11 + M 14279316 CNGA4 CNGA4-202 chr11 + M 6261838 SS18L1 SS18L1-003 chr20 + E 60749700 HAPLN4 HAPLN4-201 chr19 - E 19373605 SSX2B SSX2B-201 chrX + E 52781826 BIVM BIVM-002 chr13 + E 103473387 STAMBP STAMBP-201 chr2 + M 74071986 RGPD1 RGPD1-201 chr2 + E 87180621 STX6 STX6-002 chr1 - M 180953887 LNX2 LNX2-001 chr13 - M 28127469 SYT9 SYT9-202 chr11 + E 7335172 CEACAM4 CEACAM4-001 chr19 - E 42126615 TBC1D3 TBC1D3-201 chr17 + M 36292441 TMC6 TMC6-201 chr17 - M 76122640 TCTEX1D1 TCTEX1D1-003 chr1 + M 67241987 RFC5 RFC5-004 chr12 + E 118455800 TEX13A TEX13A-201 chrX - E 104463646 FHL1 FHL1-001 chrX + E 135229624 TGIF2LX TGIF2LX-001 chrX + E 89177882 TREX2 TREX2-002 chrX - M 152730456 THAP6 THAP6-003 chr4 + E 76442189 BBS7 BBS7-003 chr4 - M 122770028 THRAP3 THRAP3-004 chr1 + E 36762381 FAM78B FAM78B-004 chr1 - M 166039581 TJAP1 TJAP1-003 chr6 + E 43471405 NEDD9 NEDD9-005 chr6 - E 11382571 TLE1 TLE1-204 chr9 - E 84226684 GBGT1 GBGT1-003 chr9 - E 136037919 TMED5 TMED5-002 chr1 - E 93617415 ATF3 ATF3-201 chr1 + E 212792700 TMED8 TMED8-201 chr14 - E 77818016 FLYWCH1 FLYWCH1-202 chr16 + M 3000226 TMEM132E TMEM132E-001 chr17 + M 32955685 EPN2 EPN2-203 chr17 + M 19185375 TNPO1 TNPO1-004 chr5 + E 72179059 FAM173B FAM173B-005 chr5 - M 10249980 TP53I3 TP53I3-001 chr2 - E 24303689 ACVR1 ACVR1-201 chr2 - E 158634854 TREM2 TREM2-202 chr6 - E 41127530 HBS1L HBS1L-004 chr6 - E 135371785 TSC2 TSC2-009 chr16 + M 2112984 ACSM2A ACSM2A-204 chr16 + E 20471429 TSN TSN-002 chr2 + E 122513529 PDE9A PDE9A-013 chr21 + E 44188298 TXNDC5 TXNDC5-002 chr6 - E 7888938 GUCA1A GUCA1A-003 chr6 + E 42146981 TYRP1 TYRP1-008 chr9 + E 12704705 CLCN6 CLCN6-004 chr1 + E 11879545 UACA UACA-201 chr15 - E 70969447 ADPGK ADPGK-201 chr15 - E 73048788 UBR4 UBR4-010 chr1 - E 19421400 AMT AMT-009 chr3 - M 49459824 UCHL1 UCHL1-010 chr4 + E 41266178 CASP3 CASP3-202 chr4 - E 185550655 UGT1A8 UGT1A8-001 chr2 + E 234675811 CDC42EP1 CDC42EP1-003 chr22 + E 37960413 UGT3A2 UGT3A2-001 chr5 - E 36051972 RBM4 RBM4-009 chr11 + M 66406214 UNC5CL UNC5CL-203 chr6 - M 40996291 INO80E INO80E-001 chr16 + E 30012735 UQCRC2 UQCRC2-001 chr16 + M 21991941 POLR2C POLR2C-001 chr16 + E 57496299 VOPP1 VOPP1-003 chr7 - E 55565306 ZKSCAN1 ZKSCAN1-001 chr7 + E 99613204 VRK2 VRK2-203 chr2 + E 58366967 ITGB1BP1 ITGB1BP1-020 chr2 - E 9548533 VWA5A VWA5A-206 chr11 + M 123988406 SAC3D1 SAC3D1-201 chr11 + M 64809086 WBP4 WBP4-001 chr13 + E 41646993 UNC5B UNC5B-001 chr10 + E 73052224 WIPF2 WIPF2-002 chr17 + E 38418893 TAOK1 TAOK1-201 chr17 + M 27825382 WWC1 WWC1-202 chr5 + M 167868827 ETF1 ETF1-002 chr5 - E 137878625 YTHDF2 YTHDF2-001 chr1 + E 29063659 CHIA CHIA-201 chr1 + E 111860608 ZBTB9 ZBTB9-001 chr6 + E 33422552 TIMM17A TIMM17A-001 chr1 + E 201926639 <b style="color: red;">*</b> 'E' mean the breakpoint is at exon boundary(Edge). 'M' mean the breakpoint is at the exon internal part. </pre> <h1 id="format">Format</h1> <pre class="code"> <b>Column_NO.</b> <b>Descriptions</b> 1 up_gene 2 up_trans 3 up_chr 4 up_strand 5 up_loc 6 up_dna_breakpoint 7 down_gene 8 down_trans 9 down_chr 10 down_strand 11 down_loc 12 down_dna_breakpoint </pre> <h1 id="info-of-simulated-cases">info of simulated cases</h1> <pre class="code"> shortest fused sequence: 520nt longest fused sequence: 14829nt shortest up fusion segment: 109nt shortest down fusion segment: 105nt intra-chromosome fusions: 109 inter-chromosome fusions: 41 </pre> </div>NOBEL89Sat, 27 Jul 2013 03:23:08 -0000https://sourceforge.net5487d712bd87a95a850f4c110d7871f92210bef0