# 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 CAGCGCCMCCTDGTGG MEME-1 CAGCGCCMCCTDGTGG 3.6e-076 4.9e-079 -180.32 0.0 73 485 246 459 0.15052 2.0e-081 242 1 CTGCAYCWAWAHAAAC MEME-3 CTGCAYCWAWAHAAAC 4.3e-002 5.9e-005 -9.74 0.0 83 485 59 180 0.17113 2.4e-007 242 2 AGRKGGCG DREME-1 AGRKGGCG 6.3e-016 8.5e-019 -41.60 0.0 65 493 76 182 0.13185 3.5e-021 246 2 ACAGCGMC DREME-2 ACAGCGMC 2.4e-023 3.2e-026 -58.70 0.0 71 493 57 84 0.14402 1.3e-028 246 2 CCACHAGG DREME-3 CCACMAGG 7.2e-015 9.7e-018 -39.17 0.0 107 493 68 107 0.21704 3.9e-020 246 3 M0178_1.02 (ASCL2)_(Mus_musculus)_(DBD_0.98) NVCAGCTGBN 4.3e-001 5.8e-004 -7.45 0.0 203 491 291 571 0.41344 2.4e-006 245 3 M0413_1.02 (ZBTB1)_(Mus_musculus)_(DBD_0.99) NDTGCGKGDN 4.2e0000 5.6e-003 -5.18 0.0 313 491 403 560 0.63747 2.3e-005 245 3 M0422_1.02 (ZIC5)_(Mus_musculus)_(DBD_0.99) SYRGGGGGTM 2.2e-005 3.0e-008 -17.32 0.0 47 491 106 584 0.09572 1.2e-010 245 3 M0609_1.02 DNMT1 NNCCGMNNNN 6.0e-002 8.1e-005 -9.43 0.0 217 491 262 470 0.44196 3.3e-007 245 3 M1927_1.02 (MYCL1)_(Mus_musculus)_(DBD_0.66) RCCACGTG 1.8e-001 2.4e-004 -8.32 0.0 171 493 228 506 0.34686 9.9e-007 246 3 M2264_1.02 (ATOH1)_(Mus_musculus)_(DBD_1.00) RCCAKCTG 1.5e-001 2.0e-004 -8.51 0.0 201 493 290 571 0.40771 8.2e-007 246 3 M2299_1.02 (MYF5)_(Mus_musculus)_(DBD_0.90) NRNRRCAGCTGSN 1.3e-001 1.7e-004 -8.68 0.0 174 488 261 573 0.35656 7.0e-007 243 3 M4427_1.02 CTCF NYGGCCASCAGRKGGCRSYVB 1.6e-057 2.1e-060 -137.39 0.0 76 480 250 536 0.15833 9.0e-063 239 3 M4479_1.02 TCF12 VSAGCAGSTGB 2.9e-002 4.0e-005 -10.13 0.0 72 490 132 581 0.14694 1.6e-007 244 3 M4532_1.02 MYC CCACGTGSYY 3.1e0000 4.1e-003 -5.49 0.0 183 491 248 537 0.37271 1.7e-005 245 3 M4536_1.02 E2F1 VRRVRGVGCGCGCRS 1.6e0000 2.2e-003 -6.13 0.0 206 486 254 487 0.42387 9.0e-006 242 3 M4543_1.02 MXI1 VVVVCCACGTG 4.9e0000 6.6e-003 -5.02 0.0 108 490 152 510 0.22041 2.7e-005 244 3 M4612_1.02 CTCFL CCRSCAGGGGGCGCY 2.2e-052 2.9e-055 -125.56 0.0 88 486 261 538 0.18107 1.2e-057 242 3 M5116_1.02 (ATOH8)_(Drosophila_melanogaster)_(DBD_0.70) RCCACCTGK 3.6e0000 4.8e-003 -5.34 0.0 42 492 80 578 0.08537 2.0e-005 245 3 M5430_1.02 FIGLA WMCACCTGKW 3.1e-001 4.1e-004 -7.79 0.0 61 491 112 581 0.12424 1.7e-006 245 3 M5965_1.02 ZIC4 DCDCMGCGGGGGGYC 8.7e-005 1.2e-007 -15.96 0.0 42 486 91 531 0.08642 4.8e-010 242 3 M6316_1.02 TCF4 VCAGGTGCD 4.4e0000 6.0e-003 -5.12 0.0 58 492 97 544 0.11789 2.5e-005 245 3 M6326_1.02 KLF8 CAGGGKGTG 7.2e-001 9.7e-004 -6.94 0.0 316 492 411 562 0.64228 4.0e-006 245 3 M6346_1.02 MLXIPL VCACGVSGKKGBCMCRTGC 7.2e0000 9.7e-003 -4.64 0.0 50 482 69 409 0.10373 4.1e-005 240 3 M6348_1.02 MTF1 MGKGCCGTGYGCAAARS 2.4e-001 3.2e-004 -8.04 0.0 28 484 51 431 0.05785 1.3e-006 241 3 M6355_1.02 MYOG YRACAGCTGCWGC 5.2e-007 7.0e-010 -21.08 0.0 64 488 132 546 0.13115 2.9e-012 243 3 M6358_1.02 NEUROD1 SGGCAGRTGKSC 1.6e-004 2.1e-007 -15.35 0.0 179 489 280 571 0.36605 8.8e-010 244 3 M6468_1.02 SNAI1 SCAGGTGK 1.2e-004 1.6e-007 -15.67 0.0 55 493 116 587 0.11156 6.4e-010 246 3 M6513_1.02 TFAP4 RYCAGCTGYGG 9.5e-001 1.3e-003 -6.66 0.0 44 490 80 535 0.08980 5.3e-006 244 3 M6527_1.02 TWIST1 MCCCAGGTGK 7.4e-007 9.9e-010 -20.73 0.0 59 491 119 522 0.12016 4.1e-012 245 ## # 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).