# 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 SYGGGGCCCACM MEME-1 SYGGGGCCCACM 1.6e-185 2.2e-188 -432.12 0.0 87 489 401 521 0.17791 8.9e-191 244 1 CVYKGCCCCTTTAAGR MEME-2 CVYKGCCCCTTTAAGR 7.4e-012 1.0e-014 -32.24 0.0 125 485 148 308 0.25773 4.1e-017 242 1 CTSKSTBTSTSTSYSTGTBTSTSTSTGTSTSTGTSTSTGTSTSTCKSTST MEME-3 CTSKSTBTSTSTSYSTGTBTSTSTSTGTSTSTGTSTSTGTSTSTCKSTST 2.6e0000 3.5e-003 -5.65 0.0 51 451 15 40 0.11308 1.6e-005 225 2 GGNCCCAC DREME-1 GGSCCCAC 6.1e-165 8.3e-168 -384.72 0.0 85 493 330 414 0.17241 3.4e-170 246 2 CTTWAA DREME-2 CTTWAA 1.1e-001 1.4e-004 -8.86 0.0 95 495 83 258 0.19192 5.8e-007 247 3 M0404_1.02 (ZNF202)_(Mus_musculus)_(DBD_0.87) NNNKGGGGSV 5.0e-001 6.8e-004 -7.30 0.0 31 491 68 599 0.06314 2.8e-006 245 3 M0422_1.02 (ZIC5)_(Mus_musculus)_(DBD_0.99) SYRGGGGGTM 1.1e-001 1.5e-004 -8.83 0.0 83 491 148 597 0.16904 5.9e-007 245 3 M1926_1.02 ZEB1 CAGGTGWGB 5.2e0000 7.0e-003 -4.96 0.0 76 492 126 576 0.15447 2.9e-005 245 3 M4532_1.02 MYC CCACGTGSYY 2.6e0000 3.5e-003 -5.67 0.0 103 491 149 518 0.20978 1.4e-005 245 3 M5293_1.02 ATF7 BKATGACGTCATHN 3.0e0000 4.0e-003 -5.52 0.0 191 487 120 226 0.39220 1.7e-005 243 3 M5491_1.02 GLIS2 CDYYGCGGGGGGTC 3.6e-001 4.8e-004 -7.64 0.0 65 487 92 426 0.13347 2.0e-006 243 3 M5962_1.02 ZBTB7C NTCGGTGGTCGY 8.0e-001 1.1e-003 -6.83 0.0 47 489 90 579 0.09611 4.4e-006 244 3 M5965_1.02 ZIC4 DCDCMGCGGGGGGYC 1.7e0000 2.2e-003 -6.10 0.0 76 486 125 551 0.15638 9.3e-006 242 3 M6267_1.02 GLIS3 GYGGGGGGTM 1.5e-001 2.1e-004 -8.48 0.0 67 491 122 581 0.13646 8.5e-007 245 3 M6270_1.02 NHLH1 RRGGMCGCAGCTGMKMCCCV 3.6e0000 4.9e-003 -5.33 0.0 95 481 126 450 0.19751 2.0e-005 240 3 M6322_1.02 KLF1 CAGGGTGKGGC 2.0e-001 2.7e-004 -8.23 0.0 46 490 90 576 0.09388 1.1e-006 244 3 M6422_1.02 PLAGL1 CRGGGGGCCC 9.7e-049 1.3e-051 -117.16 0.0 49 491 195 581 0.09980 5.4e-054 245 3 M6468_1.02 SNAI1 SCAGGTGK 2.5e-002 3.4e-005 -10.30 0.0 29 493 67 584 0.05882 1.4e-007 246 3 M6527_1.02 TWIST1 MCCCAGGTGK 3.3e-002 4.5e-005 -10.02 0.0 41 491 78 509 0.08350 1.8e-007 245 ## # 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).