# 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 2.3e-010 3.1e-013 -28.79 0.0 78 470 33 48 0.16596 1.3e-015 234 1 GGGCGKGGC MEME-2 GGGCGKGGC 4.5e-013 6.0e-016 -35.06 0.0 112 492 218 555 0.22764 2.4e-018 245 1 GRGRVRRRRRGRSAGRGARRGR MEME-3 GRGRVRRRRRGRSAGRGARRGR 1.8e-002 2.4e-005 -10.62 0.0 87 479 146 535 0.18163 1.0e-007 239 1 ACACMYMCACACASABMCMMAC MEME-8 ACACMYMCACACASABMCMMAC 2.4e0000 3.3e-003 -5.73 0.0 75 479 41 137 0.15658 1.4e-005 239 2 CMMCGCCC DREME-1 CCMCGCCC 2.5e-004 3.3e-007 -14.93 0.0 101 493 123 362 0.20487 1.3e-009 246 2 CACRCCC DREME-2 CACACCC 1.7e-006 2.2e-009 -19.93 0.0 194 494 166 280 0.39271 9.0e-012 246 2 SCGGAA DREME-3 SCGGAA 9.5e-002 1.3e-004 -8.97 0.0 223 495 186 315 0.45051 5.2e-007 247 3 M0405_1.02 (KLF7)_(Mus_musculus)_(DBD_1.00) DGGGCGKGGY 1.8e-018 2.4e-021 -47.46 0.0 193 491 355 595 0.39308 1.0e-023 245 3 M0443_1.02 (KLF12)_(Mus_musculus)_(DBD_1.00) DGGGCGKGKY 6.9e-017 9.2e-020 -43.83 0.0 191 491 350 598 0.38900 3.8e-022 245 3 M1871_1.02 (KLF2)_(Mus_musculus)_(DBD_0.95) DGGGYGKGGC 8.9e-015 1.2e-017 -38.97 0.0 131 491 260 587 0.26680 4.8e-020 245 3 M2391_1.02 KLF5 DGGGHGGGGC 2.1e-004 2.9e-007 -15.06 0.0 157 491 260 593 0.31976 1.2e-009 245 3 M5209_1.02 (SP5)_(Drosophila_melanogaster)_(DBD_0.93) GKGGGCGKRKC 9.1e-004 1.2e-006 -13.62 0.0 188 490 295 589 0.38367 5.0e-009 244 3 M5592_1.02 KLF14 ARGKGGGCGTGGYM 1.9e0000 2.6e-003 -5.96 0.0 223 487 307 559 0.45791 1.1e-005 243 3 M5593_1.02 KLF16 GGGGGCGTGKC 3.2e-003 4.2e-006 -12.37 0.0 130 490 216 584 0.26531 1.7e-008 244 3 M5856_1.02 SP8 RGKGGGCGTGGY 5.5e-002 7.3e-005 -9.52 0.0 219 489 325 590 0.44785 3.0e-007 244 3 M6191_1.02 E2F2 GGCGCGAAAC 7.1e0000 9.5e-003 -4.65 0.0 149 491 193 498 0.30346 3.9e-005 245 3 M6194_1.02 E2F5 SGCGCSAAAH 9.4e0000 1.3e-002 -4.38 0.0 391 491 386 444 0.79633 5.2e-005 245 3 M6200_1.02 EGR3 WGAGTGGGYGT 1.9e-002 2.6e-005 -10.56 0.0 66 490 120 555 0.13469 1.1e-007 244 3 M6322_1.02 KLF1 CAGGGTGKGGC 2.6e-003 3.5e-006 -12.57 0.0 146 490 239 589 0.29796 1.4e-008 244 3 M6324_1.02 KLF4 DGGGYGKGGC 2.5e-013 3.3e-016 -35.64 0.0 133 491 260 592 0.27088 1.4e-018 245 3 M6326_1.02 KLF8 CMGGGKGTG 1.7e-001 2.2e-004 -8.41 0.0 32 492 68 567 0.06504 9.1e-007 245 3 M6482_1.02 SP3 VGVVGGGGGCGGGGCBRGSS 2.9e0000 3.9e-003 -5.56 0.0 109 481 176 583 0.22661 1.6e-005 240 ## # 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).