# WARNING: this file is not sorted! # db id alt consensus E-value adj_p-value log_adj_p-value bin_location bin_width total_width sites_in_bin total_sites p_success p-value mult_tests 1 TKWTDNTTTDTTTTTYWKTTTT MEME-1 TKWTDNTTTDTTTTTYWKTTTT 4.8e-011 6.5e-014 -30.37 0.0 131 479 199 436 0.27349 2.7e-016 239 1 BHCCCYYCYBYYBVCYTYCYTCHYCYYCTCY MEME-2 BHCCCYYCYBYYBVCYTYCYTCHYCYYCTCY 2.6e-002 3.6e-005 -10.24 0.0 190 470 275 534 0.40426 1.5e-007 234 3 M0104_1.02 (ARID3B)_(Mus_musculus)_(DBD_0.99) AWATTAATWAN 5.8e0000 7.8e-003 -4.85 0.0 24 490 42 430 0.04898 3.2e-005 244 3 M0108_1.02 (ARID5A)_(Mus_musculus)_(DBD_0.97) NNTAATATTKN 1.3e-001 1.7e-004 -8.67 0.0 124 490 137 373 0.25306 7.0e-007 244 3 M0404_1.02 (ZNF202)_(Mus_musculus)_(DBD_0.87) NNNKGGGGSV 5.2e-008 7.0e-011 -23.38 0.0 225 491 363 599 0.45825 2.9e-013 245 3 M0436_1.02 (ZNF35)_(Mus_musculus)_(DBD_0.96) TTRTTKDHYN 1.0e0001 1.4e-002 -4.30 0.0 77 491 123 557 0.15682 5.6e-005 245 3 M0437_1.02 (ZNF32)_(Mus_musculus)_(DBD_0.99) TATRTATRT 5.5e-002 7.5e-005 -9.50 0.0 30 492 52 401 0.06098 3.1e-007 245 3 M0630_1.02 DMRT1 WWTGTWDCNW 4.3e-001 5.8e-004 -7.45 0.0 39 491 75 545 0.07943 2.4e-006 245 3 M0632_1.02 DMRTA2 HHWGTWDYNN 2.1e-002 2.9e-005 -10.46 0.0 37 491 69 473 0.07536 1.2e-007 245 3 M0635_1.02 (DMRTC2)_(Mus_musculus)_(DBD_1.00) NAMATGTATHMWN 1.1e0000 1.5e-003 -6.50 0.0 28 488 53 483 0.05738 6.2e-006 243 3 M0718_1.02 FOXK1 NNRTMAACAH 5.4e0000 7.4e-003 -4.91 0.0 35 491 67 563 0.07128 3.0e-005 245 3 M0728_1.02 (FOXJ1)_(Mus_musculus)_(DBD_1.00) NRTAAACAAANN 1.1e0000 1.4e-003 -6.55 0.0 135 489 193 528 0.27607 5.9e-006 244 3 M0737_1.02 (FOXB2)_(Mus_musculus)_(DBD_0.94) WRWGTAAAYA 7.2e-001 9.8e-004 -6.93 0.0 23 491 50 535 0.04684 4.0e-006 245 3 M0747_1.02 (FOXL2)_(Mus_musculus)_(DBD_0.70) NNNRTAAAYA 1.6e0000 2.2e-003 -6.14 0.0 27 491 56 549 0.05499 8.8e-006 245 3 M0891_1.02 TLX2 NYAAWNNNNN 5.8e0000 7.9e-003 -4.85 0.0 75 491 105 467 0.15275 3.2e-005 245 3 M0894_1.02 LBX1 TTAATTAG 3.4e-001 4.6e-004 -7.69 0.0 21 493 43 453 0.04260 1.9e-006 246 3 M0937_1.02 (SIX6)_(Mus_musculus)_(DBD_1.00) HKATMYN 5.2e-001 7.1e-004 -7.26 0.0 82 494 102 397 0.16599 2.9e-006 246 3 M0952_1.02 (SIX2)_(Mus_musculus)_(DBD_1.00) BGATMCNN 3.5e-002 4.8e-005 -9.95 0.0 77 493 118 478 0.15619 1.9e-007 246 3 M1016_1.02 (SIX3)_(Mus_musculus)_(DBD_1.00) NNGATMY 3.0e-001 4.0e-004 -7.82 0.0 80 494 99 387 0.16194 1.6e-006 246 3 M1034_1.02 (DBX2)_(Mus_musculus)_(DBD_0.93) NYVATNA 1.9e0000 2.6e-003 -5.95 0.0 80 494 87 344 0.16194 1.1e-005 246 3 M1049_1.02 (SIX1)_(Mus_musculus)_(DBD_1.00) NYGATAYBNN 3.5e0000 4.8e-003 -5.34 0.0 91 491 136 523 0.18534 2.0e-005 245 3 M1110_1.02 (HHEX)_(Caenorhabditis_elegans)_(DBD_0.77) NNNYMATNNN 1.9e0000 2.6e-003 -5.97 0.0 77 491 99 413 0.15682 1.0e-005 245 3 M1582_1.02 (HMG20B)_(Mus_musculus)_(DBD_0.94) NWAWATAATWN 6.5e-001 8.9e-004 -7.03 0.0 80 490 105 420 0.16327 3.6e-006 244 3 M1841_1.02 AR GNACABNVTGTTCYY 1.8e0000 2.4e-003 -6.04 0.0 134 486 192 531 0.27572 9.9e-006 242 3 M1868_1.02 GATA2 DSAGATAAGAANYH 3.1e-004 4.2e-007 -14.68 0.0 135 487 196 487 0.27721 1.7e-009 243 3 M1882_1.02 IRF1 AAAVNGAAAGTGAAASYRRRN 5.5e-002 7.5e-005 -9.50 0.0 156 480 205 470 0.32500 3.1e-007 239 3 M2267_1.02 CDX2 TTTTATKRCHB 2.2e0000 3.0e-003 -5.81 0.0 136 490 173 470 0.27755 1.2e-005 244 3 M2283_1.02 FOXP1 MWWADGTAAACAAAR 1.2e-004 1.7e-007 -15.60 0.0 142 486 212 504 0.29218 6.9e-010 242 3 M2286_1.02 HNF4G TGRMCTTTGNHCYYN 3.5e0000 4.8e-003 -5.35 0.0 114 486 173 555 0.23457 2.0e-005 242 3 M2306_1.02 POU2F2 NDNATTTGCATRW 5.8e0000 7.9e-003 -4.84 0.0 78 488 98 414 0.15984 3.3e-005 243 3 M2313_1.02 (SOX6)_(Mus_musculus)_(DBD_1.00) CCWTTGTYYY 7.5e0000 1.0e-002 -4.59 0.0 191 491 264 560 0.38900 4.2e-005 245 3 M2385_1.02 FOXP2 RWGTAAACAVR 7.8e-004 1.1e-006 -13.75 0.0 144 490 206 496 0.29388 4.4e-009 244 3 M4463_1.02 IRF4 DNWSNGGAAVTGAVWSWN 6.9e-001 9.3e-004 -6.98 0.0 79 483 133 559 0.16356 3.9e-006 241 3 M4567_1.02 FOXA2 VCWRWGTAAACANNN 3.3e0000 4.4e-003 -5.42 0.0 22 486 45 507 0.04527 1.8e-005 242 3 M4635_1.02 STAT2 GAAANYGAAACTDAA 1.4e0000 1.9e-003 -6.27 0.0 170 486 221 497 0.34979 7.9e-006 242 3 M4698_1.02 HNF4A BTGRMCTTTGVMCYB 5.4e-001 7.4e-004 -7.22 0.0 122 486 183 538 0.25103 3.0e-006 242 3 M5300_1.02 BARX1 TAATBGNTWTTTAATBG 6.4e-004 8.7e-007 -13.96 0.0 118 484 139 364 0.24380 3.6e-009 241 3 M5308_1.02 BHLHE23 AMCATATGBY 4.0e0000 5.4e-003 -5.23 0.0 247 491 190 306 0.50305 2.2e-005 245 3 M5348_1.02 DRGX NTAATYHAATTAN 4.2e0000 5.7e-003 -5.17 0.0 68 488 83 382 0.13934 2.3e-005 243 3 M5445_1.02 FOXD2 DRTMAATATTWDYD 5.6e-001 7.6e-004 -7.18 0.0 105 487 130 417 0.21561 3.1e-006 243 3 M5530_1.02 HOMEZ TWTAATCGTTTT 7.3e-005 9.9e-008 -16.12 0.0 133 489 175 426 0.27198 4.1e-010 244 3 M5544_1.02 HOXC10 DTTTWATKGB 2.6e0000 3.5e-003 -5.66 0.0 141 491 198 532 0.28717 1.4e-005 245 3 M5547_1.02 HOXC11 DGTCGTWAAAH 8.0e0000 1.1e-002 -4.53 0.0 150 490 184 469 0.30612 4.5e-005 244 3 M5551_1.02 HOXC12 TTTTATTRC 2.7e0000 3.6e-003 -5.63 0.0 142 492 187 498 0.28862 1.5e-005 245 3 M5581_1.02 IRX2 CDTGTCRTGTWN 9.3e0000 1.3e-002 -4.38 0.0 61 489 95 514 0.12474 5.2e-005 244 3 M5584_1.02 ISX YTAATCTAATTAR 8.3e-001 1.1e-003 -6.78 0.0 80 488 77 286 0.16393 4.7e-006 243 3 M5697_1.02 ONECUT3 DTTATYGATTTTTY 1.7e-001 2.3e-004 -8.38 0.0 11 487 25 358 0.02259 9.5e-007 243 3 M5714_1.02 PHOX2A TAATYYAATTA 6.4e-001 8.7e-004 -7.04 0.0 92 490 112 398 0.18776 3.6e-006 244 3 M5715_1.02 PHOX2B TAATBYAATTA 4.1e0000 5.5e-003 -5.19 0.0 88 490 108 413 0.17959 2.3e-005 244 3 M5743_1.02 POU4F3 RTGMATWATTAATGAV 1.9e0000 2.6e-003 -5.94 0.0 27 485 43 381 0.05567 1.1e-005 242 3 M5875_1.02 TBX1 AGGTGTGAAAAAAGGTGTGA 4.6e0000 6.2e-003 -5.08 0.0 169 481 80 156 0.35135 2.6e-005 240 3 M5977_1.02 ZNF740 GTGGGGGGGK 2.0e-005 2.7e-008 -17.44 0.0 299 491 426 579 0.60896 1.1e-010 245 3 M6037_1.02 (IRX1)_(Mus_musculus)_(DBD_1.00) TTTKTCATGTWR 3.3e-001 4.4e-004 -7.72 0.0 139 489 171 441 0.28425 1.8e-006 244 3 M6111_1.02 (ZNF652)_(Mus_musculus)_(DBD_1.00) NBAAAGGGTTAAH 3.2e-001 4.3e-004 -7.75 0.0 84 488 90 325 0.17213 1.8e-006 243 3 M6114_1.02 FOXA1 WAWGYAAAYA 7.6e0000 1.0e-002 -4.58 0.0 21 491 42 505 0.04277 4.2e-005 245 3 M6119_1.02 SPI1 RAAAAGAGGAAGTGV 1.4e0000 1.9e-003 -6.28 0.0 232 486 305 534 0.47737 7.7e-006 242 3 M6140_1.02 AIRE HTTGGWWWWAWTGGDTWH 5.5e-003 7.4e-006 -11.81 0.0 139 483 211 528 0.28778 3.1e-008 241 3 M6141_1.02 ALX1 TAATBYAATTAB 4.2e0000 5.7e-003 -5.17 0.0 79 489 103 433 0.16155 2.3e-005 244 3 M6147_1.02 ARID3A TWWAWTTTGATWYYVWTTAATH 4.4e-002 6.0e-005 -9.72 0.0 159 479 157 336 0.33194 2.5e-007 239 3 M6154_1.02 ATF5 TAAGGRAGARGK 2.7e0000 3.7e-003 -5.60 0.0 139 489 214 587 0.28425 1.5e-005 244 3 M6163_1.02 BPTF KKTBTTGTKKKS 7.5e0000 1.0e-002 -4.59 0.0 137 489 203 569 0.28016 4.2e-005 244 3 M6182_1.02 CRX YTAATCHB 9.8e0000 1.3e-002 -4.32 0.0 15 493 35 554 0.03043 5.4e-005 246 3 M6184_1.02 CUX1 RBRSNDATCGATSB 2.7e0000 3.6e-003 -5.62 0.0 39 487 68 500 0.08008 1.5e-005 243 3 M6188_1.02 DLX2 ATAATTRB 2.1e0000 2.8e-003 -5.88 0.0 35 493 49 361 0.07099 1.1e-005 246 3 M6225_1.02 MECOM WAGAYAAGATAANAKA 9.5e-001 1.3e-003 -6.65 0.0 131 485 146 391 0.27010 5.3e-006 242 3 M6234_1.02 FOXA3 RVWAARYAAAYAD 7.8e0000 1.1e-002 -4.55 0.0 136 488 184 513 0.27869 4.4e-005 243 3 M6235_1.02 FOXC1 CYWAAGTAAACAWHG 7.4e0000 1.0e-002 -4.60 0.0 12 486 25 409 0.02469 4.2e-005 242 3 M6237_1.02 FOXD3 AAACAAACA 9.1e0000 1.2e-002 -4.40 0.0 132 492 180 518 0.26829 5.1e-005 245 3 M6238_1.02 FOXF1 WAAATAAACAW 1.1e-001 1.5e-004 -8.81 0.0 136 490 180 471 0.27755 6.1e-007 244 3 M6241_1.02 FOXJ2 WAAAYAAACA 9.6e-002 1.3e-004 -8.95 0.0 137 491 189 495 0.27902 5.3e-007 245 3 M6242_1.02 FOXJ3 TAAACAWWAAMMA 3.7e-002 5.0e-005 -9.91 0.0 140 488 166 410 0.28689 2.0e-007 243 3 M6245_1.02 FOXO1 AAVWHVWAAACAAVHH 9.3e-003 1.3e-005 -11.28 0.0 143 485 206 505 0.29485 5.2e-008 242 3 M6246_1.02 FOXO3 MKGWAAACAARYM 1.8e-002 2.4e-005 -10.63 0.0 132 488 202 540 0.27049 9.9e-008 243 3 M6249_1.02 FOXP3 AAWCAMATT 3.8e0000 5.1e-003 -5.27 0.0 124 492 177 533 0.25203 2.1e-005 245 3 M6251_1.02 FUBP1 TYGTNTTTTTTT 7.9e-005 1.1e-007 -16.05 0.0 147 489 232 545 0.30061 4.4e-010 244 3 M6256_1.02 GATA4 RSWGATAAV 2.2e0000 3.0e-003 -5.81 0.0 146 492 215 565 0.29675 1.2e-005 245 3 M6257_1.02 GATA5 WVANWGATAABTYRRHK 2.0e0000 2.7e-003 -5.93 0.0 154 484 203 494 0.31818 1.1e-005 241 3 M6258_1.02 GATA6 NWGATAA 2.9e0000 4.0e-003 -5.53 0.0 146 494 206 542 0.29555 1.6e-005 246 3 M6267_1.02 GLIS3 GYGGGGGGTM 1.4e0000 1.9e-003 -6.26 0.0 225 491 320 583 0.45825 7.8e-006 245 3 M6279_1.02 HMGA1 AAAATWN 8.1e0000 1.1e-002 -4.52 0.0 114 494 168 551 0.23077 4.5e-005 246 3 M6281_1.02 HNF1A KGKTAAWBATTAACY 7.8e-001 1.1e-003 -6.85 0.0 64 486 85 398 0.13169 4.4e-006 242 3 M6282_1.02 HNF1B GTTAAWYATTAACY 2.4e0000 3.2e-003 -5.73 0.0 39 487 62 442 0.08008 1.3e-005 243 3 M6285_1.02 ONECUT1 WWTATTGATTTWDH 1.3e0000 1.8e-003 -6.32 0.0 13 487 29 431 0.02669 7.4e-006 243 3 M6289_1.02 HOXA9 WCATAAAYYRTM 1.3e-001 1.7e-004 -8.66 0.0 115 489 154 459 0.23517 7.1e-007 244 3 M6290_1.02 HOXA13 CCAATAAWAHC 1.2e-001 1.6e-004 -8.73 0.0 100 490 151 511 0.20408 6.6e-007 244 3 M6299_1.02 HOXC6 AAAGTAATAAATCAT 2.5e-002 3.4e-005 -10.29 0.0 136 486 107 245 0.27984 1.4e-007 242 3 M6301_1.02 HOXD10 AATTAAAGCA 6.8e-002 9.2e-005 -9.29 0.0 21 491 49 523 0.04277 3.8e-007 245 3 M6304_1.02 HOXD9 HMATNAAWYT 3.1e-001 4.2e-004 -7.78 0.0 85 491 122 470 0.17312 1.7e-006 245 3 M6308_1.02 IRF2 SGAAAGYGAAASYV 7.8e-002 1.1e-004 -9.15 0.0 113 487 176 540 0.23203 4.4e-007 243 3 M6309_1.02 IRF3 GGAAAGBGAAASBRRRA 2.9e-002 4.0e-005 -10.13 0.0 146 484 218 535 0.30165 1.7e-007 241 3 M6311_1.02 IRF5 KAAAGGRAARCMAAAWSWGA 9.3e-004 1.3e-006 -13.59 0.0 151 481 143 302 0.31393 5.2e-009 240 3 M6312_1.02 IRF7 GAAASYGAAA 9.9e-001 1.3e-003 -6.62 0.0 125 491 190 560 0.25458 5.5e-006 245 3 M6314_1.02 IRF9 GAAAGCGAAAYT 3.0e-001 4.1e-004 -7.80 0.0 111 489 139 424 0.22699 1.7e-006 244 3 M6338_1.02 NR3C2 YMCHWCAACCWGKHCTD 9.0e0000 1.2e-002 -4.40 0.0 218 484 280 523 0.45041 5.1e-005 241 3 M6356_1.02 MZF1 RGDGGGGAD 1.4e-006 1.9e-009 -20.07 0.0 220 492 351 600 0.44715 7.9e-012 245 3 M6363_1.02 NFATC2 RWTTTTCCA 9.3e0000 1.3e-002 -4.38 0.0 162 492 237 582 0.32927 5.2e-005 245 3 M6364_1.02 NFATC3 RDTTTTCCA 7.5e0000 1.0e-002 -4.58 0.0 190 492 271 580 0.38618 4.2e-005 245 3 M6378_1.02 NKX3-1 WWTAAGTATWTWW 2.6e-001 3.5e-004 -7.96 0.0 34 488 57 421 0.06967 1.4e-006 243 3 M6387_1.02 NR1I3 HTGAACTYBBYTGACCYY 1.1e0000 1.5e-003 -6.52 0.0 177 483 220 471 0.36646 6.1e-006 241 3 M6392_1.02 NR2F6 YYMNNTGAMCTTTGWCCY 2.6e-001 3.5e-004 -7.96 0.0 125 483 193 552 0.25880 1.4e-006 241 3 M6399_1.02 ONECUT2 DKSWTKWTATKGATTTTWYYT 7.2e-002 9.8e-005 -9.23 0.0 136 480 138 335 0.28333 4.1e-007 239 3 M6401_1.02 OTX2 NYYTAATCCBWKHDM 4.3e0000 5.9e-003 -5.13 0.0 48 486 77 485 0.09877 2.4e-005 242 3 M6412_1.02 PBX1 VHMATCAATCAAWYH 3.0e0000 4.0e-003 -5.52 0.0 90 486 129 494 0.18519 1.7e-005 242 3 M6417_1.02 POU1F1 RWATATTCATKAR 8.7e-002 1.2e-004 -9.04 0.0 70 488 114 505 0.14344 4.9e-007 243 3 M6426_1.02 POU3F2 CATRAATWWT 3.4e0000 4.6e-003 -5.39 0.0 85 491 125 507 0.17312 1.9e-005 245 3 M6432_1.02 PPARD TGACCTTTVNCCTR 1.1e0000 1.4e-003 -6.55 0.0 109 487 174 573 0.22382 5.9e-006 243 3 M6433_1.02 PPARG GKGMMCTTTGACCYASWT 3.9e0000 5.3e-003 -5.24 0.0 105 483 167 574 0.21739 2.2e-005 241 3 M6438_1.02 PROP1 RASHAATTAAHATVR 1.1e-001 1.4e-004 -8.84 0.0 140 486 188 479 0.28807 6.0e-007 242 3 M6475_1.02 SOX2 WTTTGCATRACAAWGG 1.2e0000 1.7e-003 -6.40 0.0 157 485 211 505 0.32371 6.9e-006 242 3 M6476_1.02 SOX4 GAGAACAAAGSG 2.0e-001 2.7e-004 -8.21 0.0 157 489 236 565 0.32106 1.1e-006 244 3 M6508_1.02 TEAD3 GAHATTYYWGCYBYW 6.3e-002 8.6e-005 -9.36 0.0 82 486 134 525 0.16872 3.6e-007 242 3 M6546_1.02 ZFHX3 RTTAWTAATTA 1.5e0000 2.0e-003 -6.22 0.0 36 490 49 345 0.07347 8.2e-006 244 3 M6549_1.02 ZIC2 KGGGTGGTC 9.9e-001 1.3e-003 -6.61 0.0 246 492 354 599 0.50000 5.5e-006 245 3 M6550_1.02 ZIC3 BGGGTGGYC 2.6e0000 3.5e-003 -5.65 0.0 224 492 323 597 0.45528 1.4e-005 245 3 M6555_1.02 ZNF333 SKATAATGA 9.2e0000 1.2e-002 -4.39 0.0 32 492 52 446 0.06504 5.1e-005 245 ## # Detailed descriptions of columns in this file: # # db: The name of the database (file name) that contains the motif. # id: A name for the motif that is unique in the motif database file. # alt: An alternate name of the motif that may be provided # in the motif database file. # consensus: A consensus sequence computed from the motif. # E-value: The expected number motifs that would have least one. # region as enriched for best matches to the motif as the reported region. # The E-value is the p-value multiplied by the number of motifs in the # input database(s). # adj_p-value: The probability that any tested region would be as enriched for # best matches to this motif as the reported region is. # By default the p-value is calculated by using the one-tailed binomial # test on the number of sequences with a match to the motif # that have their best match in the reported region, corrected for # the number of regions and score thresholds tested. # The test assumes that the probability that the best match in a sequence # falls in the region is the region width divided by the # number of places a motif # can align in the sequence (sequence length minus motif width plus 1). # When CentriMo is run in discriminative mode with a negative # set of sequences, the p-value of a region is calculated # using the Fisher exact test on the # enrichment of best matches in the positive sequences relative # to the negative sequences, corrected # for the number of regions and score thresholds tested. # The test assumes that the probability that the best match (if any) # falls into a given region # is the same for all positive and negative sequences. # log_adj_p-value: Log of adjusted p-value. # bin_location: Location of the center of the most enriched region. # bin_width: The width (in sequence positions) of the most enriched region. # A best match to the motif is counted as being in the region if the # center of the motif falls in the region. # total_width: The window maximal size which can be reached for this motif: # rounded(sequence length - motif length +1)/2 # sites_in_bin: The number of (positive) sequences whose best match to the motif # falls in the reported region. # Note: This number may be less than the number of # (positive) sequences that have a best match in the region. # The reason for this is that a sequence may have many matches that score # equally best. # If n matches have the best score in a sequence, 1/n is added to the # appropriate bin for each match. # total_sites: The number of sequences containing a match to the motif # above the score threshold. # p_success: The probability of falling in the enriched window: # bin width / total width # p-value: The uncorrected p-value before it gets adjusted to the # number of multiple tests to give the adjusted p-value. # mult_tests: This is the number of multiple tests (n) done for this motif. # It was used to correct the original p-value of a region for # multiple tests using the formula: # p' = 1 - (1-p)^n where p is the uncorrected p-value. # The number of multiple tests is the number of regions # considered times the number of score thresholds considered. # It depends on the motif length, sequence length, and the type of # optimizations being done (central enrichment, local enrichment, # score optimization).