# 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 SYHCCTGCTGDG MEME-1 SYHCCTGCTGDG 2.5e-059 3.3e-062 -141.56 0.0 179 489 420 592 0.36605 1.4e-064 244 1 CCCACWGDG MEME-2 CCCACWGDG 5.2e-012 6.9e-015 -32.61 0.0 194 492 208 333 0.39431 2.8e-017 245 1 GCAGCAGGTGGTCTGRCAGCA MEME-5 GCAGCAGGTGGTCTGRCAGCA 9.3e-001 1.2e-003 -6.69 0.0 180 480 33 46 0.37500 5.2e-006 239 1 GYWCCCTKGCKTMAGCYYSMKKTCCAVKKSMAKGAWCSRNTCYG MEME-7 GYWCCCTKGCKTMAGCYYSMKKTCCAVKKSMAKGAWCSRNTCYG 4.2e-001 5.5e-004 -7.50 0.0 53 457 6 6 0.11597 2.4e-006 228 2 CAGCDGG DREME-1 CAGCAGG 1.2e-039 1.7e-042 -96.20 0.0 170 494 315 476 0.34413 6.8e-045 246 2 CAGGRAGC DREME-3 CAGGRAGC 1.5e-001 2.0e-004 -8.51 0.0 121 493 64 150 0.24544 8.2e-007 246 2 CTGCRGGA DREME-5 CTGCAGGA 3.5e0000 4.7e-003 -5.37 0.0 103 493 42 109 0.20892 1.9e-005 246 2 CCCAKGG DREME-6 CCCAGGG 2.8e0000 3.7e-003 -5.61 0.0 228 494 178 305 0.46154 1.5e-005 246 3 M0198_1.02 (SOHLH2)_(Mus_musculus)_(DBD_0.84) NGYVCGTGCN 3.7e0000 4.9e-003 -5.32 0.0 83 491 132 552 0.16904 2.0e-005 245 3 M0422_1.02 (ZIC5)_(Mus_musculus)_(DBD_0.99) SYRGGGGGTM 1.1e-003 1.5e-006 -13.41 0.0 161 491 264 599 0.32790 6.1e-009 245 3 M0609_1.02 DNMT1 NNCCGCNNNN 5.3e-001 7.1e-004 -7.25 0.0 235 491 213 355 0.47862 2.9e-006 245 3 M1968_1.02 EBF1 TCCCWGGGGRV 1.1e-001 1.5e-004 -8.83 0.0 184 490 277 582 0.37551 6.0e-007 244 3 M2264_1.02 (ATOH1)_(Mus_musculus)_(DBD_1.00) RCCAKCTG 9.8e-004 1.3e-006 -13.55 0.0 155 493 253 591 0.31440 5.3e-009 246 3 M2299_1.02 (MYF5)_(Mus_musculus)_(DBD_0.90) NRNRRCAGCTGSN 7.7e-002 1.0e-004 -9.19 0.0 176 488 269 583 0.36066 4.2e-007 243 3 M4427_1.02 CTCF NYGGCCASCAGRKGGCRSYVB 2.8e-003 3.7e-006 -12.50 0.0 212 480 300 533 0.44167 1.6e-008 239 3 M4479_1.02 TCF12 VSAGCAGSTGB 1.1e-002 1.5e-005 -11.12 0.0 216 490 324 589 0.44082 6.1e-008 244 3 M4612_1.02 CTCFL CCRSCAGGGGGCGCY 5.8e-007 7.7e-010 -20.98 0.0 234 486 332 526 0.48148 3.2e-012 242 3 M4681_1.02 BACH2 TGCTGAGTCA 4.1e-001 5.5e-004 -7.51 0.0 223 491 276 494 0.45418 2.2e-006 245 3 M5430_1.02 FIGLA WMCACCTGKW 5.9e0000 7.8e-003 -4.85 0.0 113 491 178 587 0.23014 3.2e-005 245 3 M5491_1.02 GLIS2 CDYYGCGGGGGGTC 2.6e-004 3.4e-007 -14.89 0.0 159 487 217 472 0.32649 1.4e-009 243 3 M5636_1.02 MSC AACAGCTGTT 4.8e0000 6.5e-003 -5.04 0.0 191 491 240 502 0.38900 2.6e-005 245 3 M5965_1.02 ZIC4 DCDCMGCGGGGGGYC 1.2e-045 1.6e-048 -110.04 0.0 222 486 451 594 0.45679 6.7e-051 242 3 M6267_1.02 GLIS3 GYGGGGGGTM 1.3e-001 1.7e-004 -8.65 0.0 185 491 279 588 0.37678 7.1e-007 245 3 M6270_1.02 NHLH1 RRGGMCGCAGCTGMKMCCCV 9.1e-004 1.2e-006 -13.62 0.0 171 481 235 487 0.35551 5.1e-009 240 3 M6326_1.02 KLF8 CAGGGKGTG 1.7e-003 2.3e-006 -12.97 0.0 164 492 261 585 0.33333 9.5e-009 245 3 M6353_1.02 MYF6 GCAGSTG 8.3e0000 1.1e-002 -4.50 0.0 204 494 291 590 0.41296 4.5e-005 246 3 M6355_1.02 MYOG YRACAGCTGCWGC 3.0e-005 4.0e-008 -17.03 0.0 172 488 278 578 0.35246 1.6e-010 243 3 M6358_1.02 NEUROD1 SGGCAGRTGKSC 1.8e0000 2.4e-003 -6.02 0.0 325 489 438 587 0.66462 1.0e-005 244 3 M6422_1.02 PLAGL1 CRGGGGGCCC 6.0e-002 8.0e-005 -9.43 0.0 277 491 384 576 0.56415 3.3e-007 245 3 M6513_1.02 TFAP4 RYCAGCTGYGG 4.2e-003 5.6e-006 -12.09 0.0 170 490 260 565 0.34694 2.3e-008 244 3 M6527_1.02 TWIST1 MCCCAGGTGK 5.9e-001 7.8e-004 -7.15 0.0 191 491 272 562 0.38900 3.2e-006 245 ## # 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).