# 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 KGKGKGKRCAGGTGWGBRKGBR MEME-1 KGKGKGKRCAGGTGWGBRKGBR 2.0e-006 2.7e-009 -19.72 0.0 79 479 131 448 0.16493 1.1e-011 239 1 BVCAGGTGDGBR MEME-2 BVCAGGTGDGBR 1.2e-018 1.6e-021 -47.90 0.0 161 489 272 494 0.32924 6.5e-024 244 1 KGKGKGYAGGTG MEME-3 KGKGKGYAGGTG 7.4e-007 9.9e-010 -20.73 0.0 145 489 211 472 0.29652 4.1e-012 244 1 CAGGTGWGK MEME-4 CAGGTGWGK 1.8e-012 2.3e-015 -33.69 0.0 146 492 205 411 0.29675 9.6e-018 245 2 VCAGGTR DREME-1 VCAGGTG 3.1e-014 4.2e-017 -37.71 0.0 134 494 214 456 0.27126 1.7e-019 246 2 CAGGTR DREME-2 CAGGTG 8.5e-012 1.1e-014 -32.11 0.0 131 495 214 484 0.26465 4.6e-017 247 2 CCGGAA DREME-3 CCGGAA 6.0e0000 8.1e-003 -4.82 0.0 265 495 87 121 0.53535 3.3e-005 247 3 M0189_1.02 (ID2)_(Mus_musculus)_(DBD_0.98) RCACGTGR 8.7e-002 1.2e-004 -9.06 0.0 243 493 324 541 0.49290 4.7e-007 246 3 M0211_1.02 (MLXIP)_(Mus_musculus)_(DBD_0.82) BCACGTGK 7.7e-003 1.0e-005 -11.48 0.0 247 493 334 542 0.50101 4.2e-008 246 3 M0305_1.02 (CREB3L2)_(Mus_musculus)_(DBD_1.00) GCCACGTGD 4.6e0000 6.2e-003 -5.08 0.0 156 492 188 461 0.31707 2.5e-005 245 3 M1917_1.02 USF1 GGTCACRTGRB 7.3e0000 9.8e-003 -4.63 0.0 106 490 142 483 0.21633 4.0e-005 244 3 M1926_1.02 ZEB1 CAGGTGWGB 4.5e-008 6.0e-011 -23.53 0.0 82 492 167 579 0.16667 2.5e-013 245 3 M2299_1.02 (MYF5)_(Mus_musculus)_(DBD_0.90) NRNRRCAGCTGSN 9.9e0000 1.3e-002 -4.33 0.0 276 488 357 552 0.56557 5.5e-005 243 3 M4479_1.02 TCF12 VSAGCAGSTGB 1.3e0000 1.7e-003 -6.38 0.0 262 490 351 560 0.53469 6.9e-006 244 3 M4553_1.02 BHLHE40 NGKCACGTGC 1.4e-001 1.9e-004 -8.59 0.0 135 491 195 524 0.27495 7.6e-007 245 3 M5116_1.02 (ATOH8)_(Drosophila_melanogaster)_(DBD_0.70) RCCACCTGK 2.1e-001 2.8e-004 -8.20 0.0 268 492 368 572 0.54472 1.1e-006 245 3 M5323_1.02 CREB3 KGRTGACGTCAYNV 4.4e0000 5.8e-003 -5.14 0.0 293 487 163 222 0.60164 2.4e-005 243 3 M5430_1.02 FIGLA WMCACCTGKW 1.8e-003 2.4e-006 -12.92 0.0 83 491 152 578 0.16904 1.0e-008 245 3 M5509_1.02 HEY1 GRCACGTGBC 2.8e0000 3.8e-003 -5.58 0.0 207 491 246 475 0.42159 1.5e-005 245 3 M5571_1.02 ID4 DVCAGGTGYN 1.0e-004 1.4e-007 -15.81 0.0 267 491 380 567 0.54379 5.6e-010 245 3 M5627_1.02 MESP1 NVCAGGTGYD 3.5e-002 4.7e-005 -9.97 0.0 267 491 376 580 0.54379 1.9e-007 245 3 M5980_1.02 ZNF784 AGGTAGGTAC 2.4e-002 3.2e-005 -10.36 0.0 373 491 369 429 0.75967 1.3e-007 245 3 M6162_1.02 ARNTL GRGTCACGTGTYCM 1.5e0000 2.0e-003 -6.21 0.0 125 487 144 405 0.25667 8.3e-006 243 3 M6316_1.02 TCF4 VCAGGTGCD 6.2e-005 8.3e-008 -16.30 0.0 276 492 382 553 0.56098 3.4e-010 245 3 M6345_1.02 MITF VKCACATGWY 6.8e-001 9.1e-004 -7.00 0.0 135 491 201 554 0.27495 3.7e-006 245 3 M6353_1.02 MYF6 GCAGSTG 1.3e0000 1.7e-003 -6.37 0.0 86 494 141 572 0.17409 6.9e-006 246 3 M6358_1.02 NEUROD1 SGGCAGRTGKSC 1.9e0000 2.5e-003 -5.98 0.0 183 489 259 560 0.37423 1.0e-005 244 3 M6468_1.02 SNAI1 SCAGGTGK 1.9e-007 2.6e-010 -22.08 0.0 271 493 400 577 0.54970 1.0e-012 246 3 M6469_1.02 SNAI2 BCAGGTG 1.3e-004 1.7e-007 -15.58 0.0 94 494 175 594 0.19028 7.0e-010 246 3 M6527_1.02 TWIST1 MCCCAGGTGK 9.1e-002 1.2e-004 -9.02 0.0 273 491 347 524 0.55601 5.0e-007 245 ## # 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).