# 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 AATAAATAAATAAATAAATA MEME-1 AATAAATAAATAAATAAATA 4.2e-045 5.6e-048 -108.80 0.0 45 481 53 56 0.09356 2.3e-050 240 1 AATCCCCWYYBB MEME-2 AATCCCCWYYBB 1.1e-108 1.5e-111 -255.15 0.0 131 489 414 571 0.26789 6.3e-114 244 1 AATAAATAAATAAATA MEME-3 AATAAATAAATAAATA 1.5e-027 2.0e-030 -68.37 0.0 39 485 50 84 0.08041 8.4e-033 242 2 ATCCCB DREME-1 ATCCCC 8.1e-087 1.1e-089 -204.84 0.0 135 495 347 483 0.27273 4.4e-092 247 2 ABTCCCC DREME-2 ABTCCCC 1.2e-018 1.6e-021 -47.87 0.0 116 494 130 242 0.23482 6.6e-024 246 2 AATAAATA DREME-3 AATAAATA 9.3e-033 1.3e-035 -80.36 0.0 47 493 52 71 0.09533 5.1e-038 246 2 TGACTCA DREME-4 TGACTCA 1.8e0000 2.4e-003 -6.05 0.0 188 494 52 85 0.38057 9.6e-006 246 3 M0404_1.02 (ZNF202)_(Mus_musculus)_(DBD_0.87) NNNKGGGGSV 1.3e0000 1.8e-003 -6.33 0.0 233 491 335 594 0.47454 7.3e-006 245 3 M0436_1.02 (ZNF35)_(Mus_musculus)_(DBD_0.96) TTRTTKDHYN 2.1e0000 2.9e-003 -5.85 0.0 47 491 85 556 0.09572 1.2e-005 245 3 M0718_1.02 FOXK1 NNRTMAACAH 2.1e0000 2.8e-003 -5.86 0.0 31 491 63 561 0.06314 1.2e-005 245 3 M0728_1.02 (FOXJ1)_(Mus_musculus)_(DBD_1.00) NRTAAACAAANN 2.4e0000 3.2e-003 -5.74 0.0 47 489 84 542 0.09611 1.3e-005 244 3 M0737_1.02 (FOXB2)_(Mus_musculus)_(DBD_0.94) WRWGTAAAYA 8.0e-003 1.1e-005 -11.43 0.0 31 491 70 552 0.06314 4.4e-008 245 3 M0747_1.02 (FOXL2)_(Mus_musculus)_(DBD_0.70) WNNRTAAAYA 1.2e0000 1.7e-003 -6.39 0.0 75 491 124 553 0.15275 6.9e-006 245 3 M0896_1.02 VENTX TTAATTAG 4.1e0000 5.5e-003 -5.20 0.0 31 493 54 475 0.06288 2.2e-005 246 3 M1583_1.02 (BBX)_(Mus_musculus)_(DBD_0.99) TTCATTGA 1.7e-001 2.3e-004 -8.36 0.0 43 493 83 548 0.08722 9.5e-007 246 3 M1605_1.02 (SOX1)_(Mus_musculus)_(DBD_1.00) ATTSWHNNNN 2.1e0000 2.8e-003 -5.87 0.0 37 491 72 569 0.07536 1.2e-005 245 3 M1968_1.02 EBF1 TCCCWGGGGRV 5.6e0000 7.5e-003 -4.89 0.0 58 490 101 569 0.11837 3.1e-005 244 3 M2281_1.02 FOXH1 BNSAATCCACA 2.8e-002 3.7e-005 -10.20 0.0 84 490 135 515 0.17143 1.5e-007 244 3 M2287_1.02 (HOXC9)_(Mus_musculus)_(DBD_0.98) RGCCATAAATCAB 2.8e-004 3.7e-007 -14.80 0.0 62 488 106 467 0.12705 1.5e-009 243 3 M2385_1.02 FOXP2 RWGTAAACAVR 8.8e-001 1.2e-003 -6.74 0.0 50 490 86 518 0.10204 4.9e-006 244 3 M4444_1.02 RELA DGGGRMTTTCCMVN 1.6e-003 2.1e-006 -13.05 0.0 79 487 135 520 0.16222 8.8e-009 243 3 M4453_1.02 BCL11A ADGRGGAASTGAAAV 1.8e0000 2.5e-003 -5.99 0.0 174 486 258 580 0.35802 1.0e-005 242 3 M4604_1.02 ZNF263 RRGGAGGASGVVGRGGRGGRG 1.1e0000 1.5e-003 -6.53 0.0 262 480 356 557 0.54583 6.1e-006 239 3 M5287_1.02 ALX4 HTAATYNAATTAN 6.4e-002 8.6e-005 -9.36 0.0 32 488 59 450 0.06557 3.5e-007 243 3 M5291_1.02 ARX YTAATTNRATTAN 7.4e-003 1.0e-005 -11.51 0.0 32 488 59 420 0.06557 4.1e-008 243 3 M5335_1.02 CUX2 ATCGATAHNDTTATYGAT 2.0e-022 2.7e-025 -56.55 0.0 31 483 53 139 0.06418 1.1e-027 241 3 M5345_1.02 DMBX1 NHTAATCCBH 2.7e-004 3.7e-007 -14.81 0.0 113 491 195 575 0.23014 1.5e-009 245 3 M5346_1.02 DPRX SHTAATCCNN 1.1e-002 1.5e-005 -11.12 0.0 109 491 183 576 0.22200 6.0e-008 245 3 M5348_1.02 DRGX NTAATYHAATTAN 9.4e-001 1.3e-003 -6.67 0.0 24 488 43 424 0.04918 5.2e-006 243 3 M5446_1.02 FOXD4L2 GTAAACA 1.7e-001 2.3e-004 -8.36 0.0 72 494 122 550 0.14575 9.5e-007 246 3 M5460_1.02 FOXL1 RTAAACA 1.9e-001 2.6e-004 -8.25 0.0 34 494 67 530 0.06883 1.1e-006 246 3 M5500_1.02 GSC VYTAATCCSH 2.9e-005 3.9e-008 -17.05 0.0 115 491 199 566 0.23422 1.6e-010 245 3 M5501_1.02 GSC2 NYTAATCCBH 1.5e-005 2.0e-008 -17.74 0.0 113 491 200 575 0.23014 8.1e-011 245 3 M5584_1.02 ISX YTAATCTAATTAR 1.2e0000 1.6e-003 -6.41 0.0 26 488 39 342 0.05328 6.8e-006 243 3 M5587_1.02 JDP2 ATGASTCAT 6.4e-001 8.6e-004 -7.06 0.0 176 492 175 370 0.35772 3.5e-006 245 3 M5637_1.02 MSX1 TAATTGSWWTTTAATTGS 1.4e0000 1.8e-003 -6.30 0.0 69 483 84 367 0.14286 7.6e-006 241 3 M5697_1.02 ONECUT3 DTTATYGATTTTTY 7.0e-002 9.4e-005 -9.27 0.0 43 487 65 383 0.08830 3.9e-007 243 3 M5714_1.02 PHOX2A TAATYYAATTA 9.7e0000 1.3e-002 -4.34 0.0 46 490 67 442 0.09388 5.4e-005 244 3 M5717_1.02 PITX1 NHTAATCCC 6.6e-007 8.9e-010 -20.84 0.0 118 492 213 580 0.23984 3.6e-012 245 3 M5720_1.02 PITX3 NHTAATCCC 3.7e-007 5.1e-010 -21.40 0.0 118 492 213 577 0.23984 2.1e-012 245 3 M5740_1.02 POU4F1 ATGMATAATTAATG 1.4e0000 1.9e-003 -6.29 0.0 35 487 56 426 0.07187 7.7e-006 243 3 M5743_1.02 POU4F3 RTGMATWATTAATGAV 7.5e-003 1.0e-005 -11.50 0.0 33 485 60 421 0.06804 4.2e-008 242 3 M5970_1.02 ZNF282 VTCGTGTTRKGGGAAAG 8.7e0000 1.2e-002 -4.44 0.0 212 484 169 306 0.43802 4.9e-005 241 3 M5977_1.02 ZNF740 GTGGGGGGGK 8.7e0000 1.2e-002 -4.44 0.0 383 491 459 541 0.78004 4.8e-005 245 3 M6114_1.02 FOXA1 WAWGYAAAYA 1.0e-002 1.4e-005 -11.17 0.0 77 491 131 531 0.15682 5.8e-008 245 3 M6119_1.02 SPI1 RAAAAGAGGAAGTGV 3.4e-003 4.6e-006 -12.30 0.0 62 486 114 529 0.12757 1.9e-008 242 3 M6147_1.02 ARID3A TWWAWTTTGATWYYVWTTAATH 8.7e-002 1.2e-004 -9.05 0.0 29 479 49 382 0.06054 4.9e-007 239 3 M6184_1.02 CUX1 RBRSNDATCGATSB 9.8e0000 1.3e-002 -4.32 0.0 71 487 107 506 0.14579 5.5e-005 243 3 M6187_1.02 DDIT3 GGGGATTGCABBB 1.1e-002 1.4e-005 -11.15 0.0 88 488 153 564 0.18033 5.9e-008 243 3 M6204_1.02 ELF2 TDNCAGGAAGTRRVT 1.1e0000 1.4e-003 -6.55 0.0 212 486 295 556 0.43621 5.9e-006 242 3 M6234_1.02 FOXA3 RVWAARYAAAYAD 3.8e-001 5.2e-004 -7.57 0.0 38 488 73 528 0.07787 2.1e-006 243 3 M6235_1.02 FOXC1 CYWAAGTAAACAWHG 4.2e-001 5.7e-004 -7.47 0.0 42 486 68 444 0.08642 2.4e-006 242 3 M6237_1.02 FOXD3 AAACAAACA 1.2e0000 1.6e-003 -6.44 0.0 42 492 76 532 0.08537 6.5e-006 245 3 M6238_1.02 FOXF1 WAAATAAACAW 1.6e-002 2.2e-005 -10.73 0.0 70 490 115 499 0.14286 9.0e-008 244 3 M6239_1.02 FOXF2 HWADGTAAACA 3.0e-001 4.0e-004 -7.83 0.0 76 490 118 503 0.15510 1.6e-006 244 3 M6241_1.02 FOXJ2 WAAAYAAACA 3.3e-003 4.5e-006 -12.31 0.0 31 491 67 510 0.06314 1.8e-008 245 3 M6244_1.02 FOXM1 RWAAWCAMWCAAV 1.2e-002 1.6e-005 -11.05 0.0 64 488 119 558 0.13115 6.5e-008 243 3 M6245_1.02 FOXO1 AAAWWVWAAACAAVHH 1.7e-003 2.2e-006 -13.01 0.0 41 485 85 526 0.08454 9.3e-009 242 3 M6246_1.02 FOXO3 MKGWAAACAARYM 7.2e-006 9.7e-009 -18.45 0.0 44 488 98 547 0.09016 4.0e-011 243 3 M6250_1.02 FOXQ1 AAATAAACAATD 1.2e0000 1.6e-003 -6.44 0.0 45 489 68 425 0.09202 6.5e-006 244 3 M6269_1.02 HBP1 AYYCATTGA 2.6e-001 3.6e-004 -7.94 0.0 42 492 76 507 0.08537 1.5e-006 245 3 M6281_1.02 HNF1A KGKTAAWBATTAACY 5.5e0000 7.4e-003 -4.91 0.0 32 486 52 435 0.06584 3.1e-005 242 3 M6285_1.02 ONECUT1 WWTATTGATTTWDH 3.7e-006 5.0e-009 -19.11 0.0 35 487 74 445 0.07187 2.1e-011 243 3 M6289_1.02 HOXA9 WCATAAAYYRTH 3.1e0000 4.2e-003 -5.48 0.0 69 489 103 488 0.14110 1.7e-005 244 3 M6295_1.02 HOXB1 CCATCMATCW 8.0e-001 1.1e-003 -6.83 0.0 151 491 172 418 0.30754 4.4e-006 245 3 M6296_1.02 HOXB6 KKCATMAATCAWY 1.6e-002 2.1e-005 -10.77 0.0 38 488 59 365 0.07787 8.7e-008 243 3 M6297_1.02 HOXB7 MATYAATCAA 2.0e-003 2.7e-006 -12.83 0.0 37 491 67 430 0.07536 1.1e-008 245 3 M6298_1.02 HOXB8 BMATTAATCAA 5.6e-003 7.5e-006 -11.80 0.0 54 490 83 407 0.11020 3.1e-008 244 3 M6299_1.02 HOXC6 AAAGTAATAAATCAT 9.7e-007 1.3e-009 -20.45 0.0 54 486 73 283 0.11111 5.4e-012 242 3 M6325_1.02 KLF6 GGGGGCKG 1.4e0000 1.9e-003 -6.25 0.0 345 493 453 581 0.69980 7.8e-006 246 3 M6356_1.02 MZF1 RGDGGGGAD 2.5e-045 3.3e-048 -109.32 0.0 92 492 272 596 0.18699 1.4e-050 245 3 M6370_1.02 NFKB2 GRAATBYCCCT 1.6e-003 2.1e-006 -13.08 0.0 88 490 162 590 0.17959 8.6e-009 244 3 M6378_1.02 NKX3-1 WWTAAGTATWTWW 4.5e-003 6.0e-006 -12.02 0.0 34 488 64 443 0.06967 2.5e-008 243 3 M6381_1.02 NR0B1 YSTCCCMCKC 5.9e0000 8.0e-003 -4.83 0.0 281 491 381 582 0.57230 3.3e-005 245 3 M6399_1.02 ONECUT2 DKSWTKWTATKGATTTTWYYT 4.8e-004 6.5e-007 -14.24 0.0 34 480 60 369 0.07083 2.7e-009 239 3 M6413_1.02 PBX2 VMATCAATCAMWTYM 6.5e-003 8.7e-006 -11.65 0.0 58 486 108 534 0.11934 3.6e-008 242 3 M6418_1.02 PITX2 DBTAATCCMA 1.4e-003 1.9e-006 -13.18 0.0 119 491 201 579 0.24236 7.7e-009 245 3 M6420_1.02 PLAG1 GGRGGSMHNWVKAGGGG 3.8e0000 5.2e-003 -5.27 0.0 144 484 214 565 0.29752 2.1e-005 241 3 M6448_1.02 RELB RGGGRMTTTCCM 8.1e-009 1.1e-011 -25.24 0.0 61 489 140 590 0.12474 4.5e-014 244 3 M6449_1.02 REL DKGGRNWTTCCV 3.1e-001 4.1e-004 -7.79 0.0 95 489 158 576 0.19427 1.7e-006 244 3 M6537_1.02 YBX1 BSKGATTSSCY 1.3e-001 1.8e-004 -8.64 0.0 242 490 352 594 0.49388 7.3e-007 244 3 M6544_1.02 HIVEP1 VGGGATTTCCCA 2.2e-002 3.0e-005 -10.43 0.0 137 489 205 533 0.28016 1.2e-007 244 3 M6546_1.02 ZFHX3 RTTAWTAATTA 3.9e-001 5.3e-004 -7.55 0.0 34 490 54 398 0.06939 2.2e-006 244 ## # 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).