# 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 CAASATGGCGGCSSC MEME-1 CAASATGGCGGCSSC 2.8e-116 3.8e-119 -272.69 0.0 174 486 485 584 0.35802 1.6e-121 242 1 CCTYADYMAASATGGC MEME-2 CCTYADYMAASATGGC 1.2e-070 1.7e-073 -167.58 0.0 149 485 320 433 0.30722 6.9e-076 242 1 GGCGGCGGCGGCGGCRGCGSS MEME-3 GGCGGCGGCGGCGGCRGCGSS 2.2e-002 3.0e-005 -10.42 0.0 82 480 100 354 0.17083 1.2e-007 239 2 AANATGGC DREME-1 AAGATGGC 2.3e-079 3.0e-082 -187.70 0.0 159 493 323 407 0.32252 1.2e-084 246 2 ATGGCBGC DREME-2 ATGGCGGC 6.3e-063 8.5e-066 -149.83 0.0 127 493 263 386 0.25761 3.4e-068 246 2 CGYCGCC DREME-4 CGCCGCC 1.4e-006 1.9e-009 -20.06 0.0 66 494 94 346 0.13360 7.9e-012 246 3 M0195_1.02 (TCF23)_(Mus_musculus)_(DBD_0.60) DMCAKMTGKH 9.8e-005 1.3e-007 -15.84 0.0 111 491 194 573 0.22607 5.4e-010 245 3 M0217_1.02 (NEUROG1)_(Mus_musculus)_(DBD_1.00) DCCATATGKB 8.3e-012 1.1e-014 -32.12 0.0 111 491 216 564 0.22607 4.6e-017 245 3 M0609_1.02 DNMT1 NNCCGCNNNN 7.3e0000 9.8e-003 -4.62 0.0 307 491 367 518 0.62525 4.0e-005 245 3 M1919_1.02 YY1 CAARATGGCBGC 2.3e-098 3.1e-101 -231.42 0.0 161 489 450 588 0.32924 1.3e-103 244 3 M2264_1.02 (ATOH1)_(Mus_musculus)_(DBD_1.00) RCCAKCTG 4.1e-010 5.5e-013 -28.23 0.0 159 493 281 585 0.32252 2.2e-015 246 3 M4427_1.02 CTCF NYGGCCASCAGRKGGCRSYVB 5.5e-001 7.4e-004 -7.21 0.0 320 480 390 513 0.66667 3.1e-006 239 3 M4462_1.02 GABPA VVCCGGAAGTG 8.6e0000 1.2e-002 -4.45 0.0 282 490 382 582 0.57551 4.8e-005 244 3 M4636_1.02 THAP1 YTGCCCDBANYMAAGATGGCG 4.0e-041 5.4e-044 -99.62 0.0 152 480 283 435 0.31667 2.3e-046 239 3 M5323_1.02 CREB3 KGRTGACGTCAYNV 6.7e0000 9.0e-003 -4.71 0.0 79 487 74 288 0.16222 3.7e-005 243 3 M5652_1.02 NEUROD2 RMCATATGBY 2.1e-007 2.9e-010 -21.96 0.0 165 491 238 484 0.33605 1.2e-012 245 3 M5693_1.02 OLIG3 AMCATATGBY 3.1e0000 4.2e-003 -5.48 0.0 165 491 188 433 0.33605 1.7e-005 245 3 M5955_1.02 YY2 WAATGGCGGHY 4.6e-071 6.2e-074 -168.56 0.0 136 490 383 598 0.27755 2.6e-076 244 3 M5998_1.02 (CREB5)_(Mus_musculus)_(DBD_1.00) DRTGACGTCATN 7.8e0000 1.1e-002 -4.55 0.0 79 489 73 288 0.16155 4.4e-005 244 3 M6207_1.02 ELK1 RCCGGAAGT 4.2e0000 5.7e-003 -5.16 0.0 282 492 392 598 0.57317 2.3e-005 245 3 M6210_1.02 ENO1 YDSMCACRTGSYS 5.1e-002 7.0e-005 -9.57 0.0 110 488 180 566 0.22541 2.9e-007 243 3 M6213_1.02 ERG ACCGGAARTSM 2.6e0000 3.5e-003 -5.67 0.0 280 490 361 547 0.57143 1.4e-005 244 3 M6540_1.02 ZBTB4 CAATRGCGDTKGYGR 1.5e0000 2.0e-003 -6.21 0.0 128 486 192 553 0.26337 8.3e-006 242 ## # 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).