# 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 ACACACACACACACACACACACACACACACA MEME-1 ACACACACACACACACACACACACACACACA 2.0e-041 2.6e-044 -100.35 0.0 80 470 106 153 0.17021 1.1e-046 234 1 AGAGAGAGAGAGAGAGAGAGAG MEME-2 AGAGAGAGAGAGAGAGAGAGAG 4.5e-002 6.0e-005 -9.72 0.0 83 479 56 167 0.17328 2.5e-007 239 1 KGTGTGTGTGTGTGTGTGTGTG MEME-3 KGTGTGTGTGTGTGTGTGTGTG 3.2e-029 4.2e-032 -72.24 0.0 93 479 121 210 0.19415 1.8e-034 239 1 TGTGTGTGTGTG MEME-5 TGTGTGTGTGTG 9.4e-023 1.3e-025 -57.34 0.0 91 489 129 267 0.18609 5.1e-028 244 1 YAAHYYGRRGGTCSHGGGTTCRADTCCCRBY MEME-6 YAAHYYGRRGGTCSHGGGTTCRADTCCCRBY 8.9e-003 1.2e-005 -11.34 0.0 62 470 21 45 0.13191 5.1e-008 234 1 AGAGAGAGAGAGAVAG MEME-7 AGAGAGAGAGAGAVAG 3.5e-003 4.6e-006 -12.28 0.0 79 485 57 170 0.16289 1.9e-008 242 1 GRTGATGTMAT MEME-8 GRTGATGTMAT 3.8e-001 5.0e-004 -7.59 0.0 180 490 126 246 0.36735 2.1e-006 244 3 M5302_1.02 BATF3 TGATGACGTCATCA 3.5e-002 4.7e-005 -9.97 0.0 191 487 82 133 0.39220 1.9e-007 243 3 M5875_1.02 TBX1 AGGTGTGAAAAAAGGTGTGA 4.0e-004 5.4e-007 -14.44 0.0 143 481 107 219 0.29730 2.2e-009 240 3 M5883_1.02 TBX20 TCACACSTTCACACCT 6.4e-005 8.6e-008 -16.27 0.0 73 485 93 325 0.15052 3.6e-010 242 3 M5981_1.02 ZSCAN4 TTTTCAGKGTGTGCA 5.0e-008 6.7e-011 -23.42 0.0 106 486 135 345 0.21811 2.8e-013 242 3 M5998_1.02 (CREB5)_(Mus_musculus)_(DBD_1.00) DRTGACGTCATN 9.6e0000 1.3e-002 -4.36 0.0 153 489 124 295 0.31288 5.3e-005 244 3 M6139_1.02 AHR KCACGCRAH 9.4e-004 1.3e-006 -13.58 0.0 146 492 222 535 0.29675 5.2e-009 245 3 M6151_1.02 ARNT BYRCGTGC 5.9e0000 8.0e-003 -4.83 0.0 135 493 167 463 0.27383 3.2e-005 246 3 M6200_1.02 EGR3 WGAGTGGGYGT 4.6e-009 6.2e-012 -25.81 0.0 66 490 140 544 0.13469 2.5e-014 244 3 M6212_1.02 EPAS1 CMCACGYAYDCAC 7.7e-009 1.0e-011 -25.30 0.0 90 488 170 530 0.18443 4.2e-014 243 3 M6275_1.02 HIF1A SBSTACGTGCSB 1.2e0000 1.7e-003 -6.41 0.0 71 489 107 488 0.14519 6.8e-006 244 3 M6323_1.02 KLF3 HRCYWGGGTGKGGCT 2.2e-003 3.0e-006 -12.73 0.0 34 486 72 504 0.06996 1.2e-008 242 3 M6326_1.02 KLF8 CAGGGKGTG 1.3e0000 1.7e-003 -6.36 0.0 206 492 275 536 0.41870 7.1e-006 245 3 M6456_1.02 RREB1 DKGKKKGKGGKTGKTTKGGGKT 8.8e-007 1.2e-009 -20.56 0.0 75 479 135 484 0.15658 4.9e-012 239 3 M6464_1.02 SMAD2 GTGTCHGKCTV 8.8e-001 1.2e-003 -6.75 0.0 248 490 344 575 0.50612 4.8e-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).