# 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 CDGCMGAAARGSBSCBBCCC MEME-1 CDGCMGAAARGSBSCBBCCC 5.3e-017 7.1e-020 -44.09 0.0 75 481 107 265 0.15593 3.0e-022 240 1 CTGGCACKSTGCCAAG MEME-2 CTGGCACKSTGCCAAG 1.3e-001 1.8e-004 -8.65 0.0 99 485 53 137 0.20412 7.2e-007 242 1 SVGSSGGCGGSSGCGS MEME-4 SVGSSGGCGGSSGCGS 6.2e0000 8.4e-003 -4.78 0.0 85 485 107 422 0.17526 3.5e-005 242 1 DHTTTATKR MEME-5 DHTTTATKR 1.4e-003 1.9e-006 -13.19 0.0 92 492 64 171 0.18699 7.6e-009 245 1 TCTCAGCAAGGCAADTTTACTT MEME-7 TCTCAGCAAGGCAADTTTACTT 3.4e0000 4.5e-003 -5.39 0.0 77 479 7 8 0.16075 1.9e-005 239 2 GCMGAAA DREME-1 GCAGAAA 7.3e-017 9.8e-020 -43.77 0.0 70 494 70 146 0.14170 4.0e-022 246 3 M0609_1.02 DNMT1 NNCCGCNNNN 9.3e0000 1.3e-002 -4.38 0.0 221 491 260 482 0.45010 5.1e-005 245 3 M1838_1.02 TFAP2A NHYDGCCYSAGGGCA 4.5e0000 6.0e-003 -5.12 0.0 2 486 11 552 0.00412 2.5e-005 242 3 M4427_1.02 CTCF NYGGCCASCAGRKGGCRSYVB 8.5e-002 1.1e-004 -9.07 0.0 270 480 328 488 0.56250 4.8e-007 239 3 M4471_1.02 PAX5 BCAGYSRAGCGTGAC 8.0e0000 1.1e-002 -4.54 0.0 134 486 197 559 0.27572 4.5e-005 242 3 M4612_1.02 CTCFL CCRSCAGGGGGCGCY 1.5e-001 2.0e-004 -8.54 0.0 378 486 421 487 0.77778 8.1e-007 242 3 M5377_1.02 ELF4 AACCCGGAAGTR 2.2e0000 3.0e-003 -5.82 0.0 79 489 107 443 0.16155 1.2e-005 244 3 M5587_1.02 JDP2 ATGASTCAT 9.7e0000 1.3e-002 -4.35 0.0 284 492 200 290 0.57724 5.3e-005 245 3 M5660_1.02 NFIA TTGGCANNDTGCCAR 4.6e-001 6.2e-004 -7.38 0.0 104 486 92 275 0.21399 2.6e-006 242 3 M5662_1.02 NFIB TTGGCAHNDTGCCAR 6.9e-002 9.3e-005 -9.28 0.0 104 486 96 279 0.21399 3.8e-007 242 3 M6326_1.02 KLF8 CMGGGKGTG 4.5e-001 6.0e-004 -7.42 0.0 280 492 361 542 0.56911 2.5e-006 245 3 M6331_1.02 MAFB WGCTGACDS 1.0e0000 1.4e-003 -6.60 0.0 164 492 250 593 0.33333 5.5e-006 245 3 M6339_1.02 MECP2 YYCCGGS 6.9e0000 9.2e-003 -4.69 0.0 304 494 297 419 0.61538 3.8e-005 246 3 M6513_1.02 TFAP4 RYCAGCTGYGG 2.4e0000 3.3e-003 -5.73 0.0 154 490 213 529 0.31429 1.3e-005 244 3 M6529_1.02 UBP1 TYTCTGS 3.7e-001 4.9e-004 -7.62 0.0 70 494 126 595 0.14170 2.0e-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).