# 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 GTGTGTGTGTGTGTGT MEME-1 GTGTGTGTGTGTGTGT 8.7e-009 1.2e-011 -25.17 0.0 119 485 95 192 0.24536 4.8e-014 242 1 TGTGTGTSTGTGTGTSTGTGTGTGTGTGTGT MEME-2 TGTGTGTSTGTGTGTSTGTGTGTGTGTGTGT 4.9e-008 6.6e-011 -23.44 0.0 130 470 113 222 0.27660 2.8e-013 234 1 YTGGCACYGTGCCARG MEME-3 YTGGCACYGTGCCARG 1.9e-038 2.5e-041 -93.47 0.0 131 485 121 148 0.27010 1.1e-043 242 1 GRWGRDDGDRWGGRWG MEME-5 GRWGRDDGDRWGGRWG 1.0e-001 1.4e-004 -8.89 0.0 259 485 354 556 0.53402 5.7e-007 242 1 TCCTGAGGCCTCMCCAGAAGCHRAGCAGATG MEME-6 TCCTGAGGCCTCMCCAGAAGCHRAGCAGATG 3.9e-016 5.2e-019 -42.10 0.0 106 470 36 38 0.22553 2.2e-021 234 1 GTGTGTGTG MEME-9 GTGTGTGTG 1.4e-002 1.9e-005 -10.89 0.0 96 492 106 332 0.19512 7.6e-008 245 2 SYTGGCA DREME-1 SYTGGCA 8.2e-014 1.1e-016 -36.75 0.0 94 494 96 208 0.19028 4.5e-019 246 2 GAGGCCTC DREME-2 GAGGCCTC 6.2e-001 8.3e-004 -7.09 0.0 131 493 58 127 0.26572 3.4e-006 246 2 GAGCCAA DREME-4 GAGCCAA 7.0e-005 9.3e-008 -16.19 0.0 122 494 39 63 0.24696 3.8e-010 246 3 M1970_1.02 NFIC TGCCAA 1.9e-005 2.6e-008 -17.48 0.0 49 495 102 531 0.09899 1.0e-010 247 3 M5512_1.02 HIC2 VSYGGGCAY 5.3e0000 7.0e-003 -4.96 0.0 22 492 46 544 0.04472 2.9e-005 245 3 M5660_1.02 NFIA TTGGCANNDTGCCAR 1.8e-025 2.4e-028 -63.59 0.0 78 486 124 271 0.16049 1.0e-030 242 3 M5662_1.02 NFIB TTGGCAHNDTGCCAR 1.1e-023 1.5e-026 -59.45 0.0 78 486 124 279 0.16049 6.3e-029 242 3 M5664_1.02 NFIX TTGGCANNNHGCCAR 4.6e-017 6.1e-020 -44.24 0.0 46 486 98 359 0.09465 2.5e-022 242 3 M6200_1.02 EGR3 WGAGTGGGYGT 1.5e0000 2.0e-003 -6.22 0.0 48 490 83 521 0.09796 8.2e-006 244 3 M6212_1.02 EPAS1 CMCACGYAYDCAC 8.8e-002 1.2e-004 -9.05 0.0 196 488 264 518 0.40164 4.8e-007 243 3 M6456_1.02 RREB1 DKGKKKGKGGKTGKTTKGGGKT 3.0e-002 4.1e-005 -10.11 0.0 49 479 86 480 0.10230 1.7e-007 239 ## # 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).