# 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 GTGTGTGTGTGTGTGTGTGT MEME-1 GTGTGTGTGTGTGTGTGTGT 1.8e-014 2.5e-017 -38.24 0.0 105 481 57 82 0.21830 1.0e-019 240 1 CACACACACACA MEME-2 CACACACACACA 3.1e-008 4.2e-011 -23.89 0.0 121 489 77 143 0.24744 1.7e-013 244 1 GYAYGCYGYCACCARGTGGCGG MEME-3 GYAYGCYGYCACCARGTGGCGG 3.3e-008 4.5e-011 -23.82 0.0 69 479 24 34 0.14405 1.9e-013 239 2 TGACTCAB DREME-1 TGACTCAB 4.7e-003 6.4e-006 -11.96 0.0 231 493 72 96 0.46856 2.6e-008 246 2 GGTTCCK DREME-2 GGTTCCG 1.5e0000 2.1e-003 -6.17 0.0 114 494 41 95 0.23077 8.5e-006 246 3 M0300_1.02 (ATF2)_(Mus_musculus)_(DBD_1.00) NRTKACGTMA 1.5e0000 2.0e-003 -6.19 0.0 223 491 291 530 0.45418 8.3e-006 245 3 M2289_1.02 JUN DDRATGATGTMAT 3.8e0000 5.2e-003 -5.26 0.0 242 488 244 407 0.49590 2.1e-005 243 3 M2292_1.02 JUND DRTGASTCATS 3.0e0000 4.1e-003 -5.51 0.0 80 490 97 396 0.16327 1.7e-005 244 3 M4619_1.02 FOSL1 BGGTGASTCAK 7.9e0000 1.1e-002 -4.54 0.0 66 490 83 401 0.13469 4.4e-005 244 3 M5292_1.02 ATF4 GKATGAYGCAATM 7.6e-003 1.0e-005 -11.49 0.0 214 488 216 373 0.43852 4.2e-008 243 3 M5293_1.02 ATF7 NKATGACGTCATHN 1.7e-001 2.3e-004 -8.36 0.0 235 487 151 237 0.48255 9.6e-007 243 3 M5302_1.02 BATF3 TGATGACGTCATCA 1.7e-001 2.4e-004 -8.35 0.0 297 487 104 129 0.60986 9.7e-007 243 3 M5883_1.02 TBX20 TCACACSTTCACACCT 5.7e-002 7.8e-005 -9.46 0.0 31 485 45 310 0.06392 3.2e-007 242 3 M5998_1.02 (CREB5)_(Mus_musculus)_(DBD_1.00) DRTGACGTCATN 2.0e-001 2.7e-004 -8.21 0.0 235 489 183 295 0.48057 1.1e-006 244 3 M6139_1.02 AHR KCACGCRAH 1.6e-001 2.1e-004 -8.46 0.0 90 492 143 535 0.18293 8.6e-007 245 3 M6180_1.02 CREB1 RTGACGTMA 6.2e0000 8.4e-003 -4.78 0.0 308 492 382 539 0.62602 3.4e-005 245 3 M6200_1.02 EGR3 WGAGTGGGYGT 8.6e-001 1.2e-003 -6.76 0.0 116 490 176 550 0.23673 4.8e-006 244 3 M6333_1.02 MAFG MATGACT 1.3e0000 1.8e-003 -6.34 0.0 72 494 120 559 0.14575 7.2e-006 246 ## # 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).