# 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 CHCAGCAGG MEME-1 CHCAGCAGG 2.8e-053 3.8e-056 -127.61 0.0 198 492 435 597 0.40244 1.6e-058 245 1 CHCWGTGGGDRG MEME-5 CHCWGTGGGDRG 1.8e-003 2.5e-006 -12.91 0.0 191 489 170 308 0.39059 1.0e-008 244 1 CTCCMCAGG MEME-7 CTCCMCAGG 9.7e-003 1.3e-005 -11.26 0.0 334 492 326 408 0.67886 5.3e-008 245 1 ATGADAAAMMACAATBWDYNTTTWTAAMACWHTTACANKKW MEME-10 ATGADAAAMMACAATBWDYNTTTWTAAMACWHTTACANKKW 3.2e0000 4.2e-003 -5.47 0.0 52 460 5 5 0.11304 1.8e-005 229 2 CAGYRGG DREME-1 CAGCAGG 9.0e-034 1.2e-036 -82.71 0.0 174 494 318 496 0.35223 4.9e-039 246 2 CCTGGKGA DREME-4 CCTGGGGA 2.8e-002 3.8e-005 -10.19 0.0 225 493 83 119 0.45639 1.5e-007 246 3 M0422_1.02 (ZIC5)_(Mus_musculus)_(DBD_0.99) SYRGGGGGTM 5.6e-007 7.4e-010 -21.02 0.0 275 491 417 597 0.56008 3.0e-012 245 3 M0428_1.02 (ZNF691)_(Mus_musculus)_(DBD_0.97) RKGAGYAC 8.4e-001 1.1e-003 -6.79 0.0 229 493 331 596 0.46450 4.6e-006 246 3 M0609_1.02 DNMT1 NNCCGCNNNN 7.9e-005 1.1e-007 -16.06 0.0 183 491 211 402 0.37271 4.3e-010 245 3 M1581_1.02 (CIC)_(Mus_musculus)_(DBD_1.00) NNTGCTGACW 1.2e0000 1.6e-003 -6.47 0.0 119 491 188 583 0.24236 6.3e-006 245 3 M1889_1.02 MAX RRGCACATGK 1.9e0000 2.5e-003 -5.98 0.0 413 491 480 530 0.84114 1.0e-005 245 3 M1927_1.02 (MYCL1)_(Mus_musculus)_(DBD_0.66) RCCACGTG 7.1e0000 9.5e-003 -4.66 0.0 213 493 269 517 0.43205 3.9e-005 246 3 M1968_1.02 EBF1 TCCCWGGGGRV 6.4e-002 8.5e-005 -9.37 0.0 346 490 469 589 0.70612 3.5e-007 244 3 M2264_1.02 (ATOH1)_(Mus_musculus)_(DBD_1.00) RCCAKCTG 1.4e-003 1.8e-006 -13.21 0.0 195 493 303 593 0.39554 7.4e-009 246 3 M2299_1.02 (MYF5)_(Mus_musculus)_(DBD_0.90) NRNRRCAGCTGSN 6.2e0000 8.4e-003 -4.78 0.0 304 488 415 591 0.62295 3.5e-005 243 3 M4427_1.02 CTCF NYGGCCASCAGRKGGCRSYVB 3.1e-004 4.2e-007 -14.69 0.0 222 480 310 524 0.46250 1.7e-009 239 3 M4479_1.02 TCF12 VSAGCAGSTGB 7.1e-003 9.5e-006 -11.56 0.0 312 490 441 595 0.63673 3.9e-008 244 3 M4612_1.02 CTCFL CCRSCAGGGGGCGCY 2.0e-010 2.7e-013 -28.95 0.0 232 486 345 532 0.47737 1.1e-015 242 3 M5491_1.02 GLIS2 CDYYGCGGGGGGTC 1.6e-003 2.1e-006 -13.07 0.0 307 487 362 481 0.63039 8.7e-009 243 3 M5627_1.02 MESP1 NVCAGGTGYD 8.3e0000 1.1e-002 -4.50 0.0 315 491 428 596 0.64155 4.6e-005 245 3 M5804_1.02 SCRT1 RWGCAACAGGTGGBH 7.2e0000 9.6e-003 -4.65 0.0 268 486 280 434 0.55144 4.0e-005 242 3 M5965_1.02 ZIC4 DCDCMGCGGGGGGYC 1.1e-034 1.4e-037 -84.84 0.0 244 486 456 595 0.50206 5.9e-040 242 3 M6144_1.02 TFAP2B BCCCBCRGGC 8.9e0000 1.2e-002 -4.43 0.0 327 491 434 585 0.66599 4.9e-005 245 3 M6210_1.02 ENO1 YDSMCACRTGSYB 3.2e0000 4.3e-003 -5.46 0.0 212 488 301 577 0.43443 1.8e-005 243 3 M6267_1.02 GLIS3 GYGGGGGGTM 1.9e-002 2.5e-005 -10.59 0.0 249 491 361 587 0.50713 1.0e-007 245 3 M6270_1.02 NHLH1 RRGGMCGCAGCTGMKMCCCV 7.3e-007 9.8e-010 -20.74 0.0 221 481 304 495 0.45946 4.1e-012 240 3 M6326_1.02 KLF8 CMGGGKGTG 5.9e0000 7.9e-003 -4.84 0.0 232 492 322 579 0.47154 3.2e-005 245 3 M6331_1.02 MAFB WGCTGACDS 2.1e-001 2.7e-004 -8.20 0.0 122 492 199 595 0.24797 1.1e-006 245 3 M6332_1.02 MAF KTGCTGAC 2.1e0000 2.9e-003 -5.86 0.0 163 493 246 594 0.33063 1.2e-005 246 3 M6352_1.02 MYCN CCACGTGS 2.0e0000 2.7e-003 -5.93 0.0 229 493 296 530 0.46450 1.1e-005 246 3 M6355_1.02 MYOG YRACAGCTGCWGC 1.9e-003 2.5e-006 -12.90 0.0 312 488 440 588 0.63934 1.0e-008 243 3 M6358_1.02 NEUROD1 SGGCAGRTGKSC 3.9e-001 5.2e-004 -7.57 0.0 199 489 297 592 0.40695 2.1e-006 244 3 M6422_1.02 PLAGL1 CRGGGGGCCC 2.1e0000 2.8e-003 -5.86 0.0 257 491 353 577 0.52342 1.2e-005 245 3 M6513_1.02 TFAP4 RYCAGCTGYGG 2.8e-010 3.7e-013 -28.62 0.0 254 490 389 571 0.51837 1.5e-015 244 3 M6527_1.02 TWIST1 MCCCAGGTGK 2.4e0000 3.2e-003 -5.75 0.0 143 491 215 577 0.29124 1.3e-005 245 ## # 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).