# 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 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAA MEME-1 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAA 6.4e-023 8.7e-026 -57.71 0.0 22 454 27 36 0.04846 3.8e-028 226 1 CYTGGCACMBTGCCAR MEME-2 CYTGGCACMBTGCCAR 8.5e-034 1.1e-036 -82.76 0.0 55 485 82 148 0.11340 4.7e-039 242 1 RAGGTCCCGGGTTCGARTCCCG MEME-3 RAGGTCCCGGGTTCGARTCCCG 6.8e-001 9.1e-004 -7.00 0.0 83 479 29 72 0.17328 3.8e-006 239 1 AGTCCARMGYSYTAACCAYTASRCCAYGGRR MEME-4 AGTCCARMGYSYTAACCAYTASRCCAYGGRR 9.7e-006 1.3e-008 -18.16 0.0 56 470 14 17 0.11915 5.5e-011 234 1 ATCACAAAGAAGTTTCTGAGAATGCTTCTGT MEME-7 ATCACAAAGAAGTTTCTGAGAATGCTTCTGT 7.4e0000 9.9e-003 -4.61 0.0 38 470 4 4 0.08085 4.3e-005 234 1 ATSATTCCMTHSDDYTCMRTTTKRTGATGAWTCCAKKSNAWYMCATTMDA MEME-10 ATSATTCCMTHSDDYTCMRTTTKRTGATGAWTCCAKKSNAWYMCATTMDA 1.7e0000 2.3e-003 -6.05 0.0 49 451 6 7 0.10865 1.0e-005 225 2 ATAAATAA DREME-1 ATAAATAA 1.2e-011 1.7e-014 -31.72 0.0 67 493 37 62 0.13590 6.8e-017 246 3 M1970_1.02 NFIC TGCCAA 1.6e0000 2.1e-003 -6.17 0.0 65 495 116 596 0.13131 8.5e-006 247 3 M2287_1.02 (HOXC9)_(Mus_musculus)_(DBD_0.98) RGCCATAAATCAB 8.9e-001 1.2e-003 -6.73 0.0 54 488 81 446 0.11066 4.9e-006 243 3 M5287_1.02 ALX4 HTAATYNAATTAN 1.8e0000 2.5e-003 -6.00 0.0 24 488 43 428 0.04918 1.0e-005 243 3 M5335_1.02 CUX2 ATCGATAHNDTTATYGAT 5.2e-007 7.0e-010 -21.08 0.0 31 483 35 144 0.06418 2.9e-012 241 3 M5348_1.02 DRGX NTAATYHAATTAN 2.4e0000 3.2e-003 -5.76 0.0 24 488 41 404 0.04918 1.3e-005 243 3 M5584_1.02 ISX YTAATCTAATTAR 6.1e-001 8.2e-004 -7.11 0.0 30 488 44 336 0.06148 3.4e-006 243 3 M5660_1.02 NFIA TTGGCANNDTGCCAR 1.4e-015 1.9e-018 -40.82 0.0 56 486 94 293 0.11523 7.7e-021 242 3 M5662_1.02 NFIB TTGGCAHNDTGCCAR 1.6e-014 2.2e-017 -38.37 0.0 60 486 96 294 0.12346 9.0e-020 242 3 M5664_1.02 NFIX TTGGCANNNNGCCAR 5.6e-009 7.5e-012 -25.62 0.0 60 486 111 431 0.12346 3.1e-014 242 3 M5740_1.02 POU4F1 ATGMATAATTAATG 3.4e-001 4.6e-004 -7.69 0.0 17 487 34 399 0.03491 1.9e-006 243 3 M5743_1.02 POU4F3 RTGMATWATTAATGAV 8.4e-002 1.1e-004 -9.09 0.0 33 485 55 395 0.06804 4.7e-007 242 3 M6241_1.02 FOXJ2 WAAAYAAACA 1.7e0000 2.3e-003 -6.08 0.0 35 491 63 496 0.07128 9.4e-006 245 3 M6245_1.02 FOXO1 AAAWWVWAAACAAVHH 4.7e0000 6.4e-003 -5.06 0.0 61 485 93 484 0.12577 2.6e-005 242 3 M6272_1.02 HESX1 AKKYYAYKWGCCRSVT 5.6e-001 7.5e-004 -7.20 0.0 99 485 157 549 0.20412 3.1e-006 242 3 M6299_1.02 HOXC6 AAAGTAATAAATCAT 2.4e-001 3.3e-004 -8.03 0.0 34 486 43 279 0.06996 1.3e-006 242 3 M6413_1.02 PBX2 VMATCAATCAMWTYM 6.5e0000 8.8e-003 -4.73 0.0 66 486 99 491 0.13580 3.6e-005 242 3 M6426_1.02 POU3F2 CATRAATWWT 7.9e-002 1.1e-004 -9.15 0.0 33 491 64 489 0.06721 4.3e-007 245 3 M6429_1.02 POU6F1 CATAAWTTATGCR 6.7e0000 9.0e-003 -4.71 0.0 30 488 36 285 0.06148 3.7e-005 243 3 M6546_1.02 ZFHX3 RTTAWTAATTA 6.3e-001 8.4e-004 -7.08 0.0 40 490 57 375 0.08163 3.5e-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).