# 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 MTGRACCYYRAYAAGAACAGCV MEME-1 MTGRACCYYRAYAAGAACAGCV 1.5e-144 1.9e-147 -337.82 0.0 61 479 244 318 0.12735 8.1e-150 239 1 CYTGGCACBBTGCCAR MEME-2 CYTGGCACBBTGCCAR 2.4e-060 3.3e-063 -143.88 0.0 63 485 122 177 0.12990 1.3e-065 242 1 YHRKTTTTCTTGAATA MEME-3 YHRKTTTTCTTGAATA 7.2e-017 9.6e-020 -43.79 0.0 97 485 94 177 0.20000 4.0e-022 242 1 TTGTGGYATTTTAACTTGYCCTATTCCC MEME-4 TTGTGGYATTTTAACTTGYCCTATTCCC 1.4e-019 1.8e-022 -50.05 0.0 91 473 53 69 0.19239 7.8e-025 236 1 YAAKCSVRRGRTYSYGGGTTCGADYCCCRSC MEME-7 YAAKCSVRRGRTYSYGGGTTCGADYCCCRSC 2.3e-003 3.1e-006 -12.68 0.0 158 470 21 23 0.33617 1.3e-008 234 1 TRKGAGRRARDGRGRWRRGRATGGGTYKTGGHTCAAATRYHAMARACTCT MEME-8 TRKGAGRRARDGRGRWRRGRATGGGTYKTGGHTCAAATRYHAMARACTCT 4.5e-003 6.0e-006 -12.02 0.0 51 451 8 8 0.11308 2.7e-008 225 1 CAAGTTAAAATRCCACARABCT MEME-9 CAAGTTAAAATRCCACARABCT 4.5e-020 6.1e-023 -51.16 0.0 71 479 53 80 0.14823 2.5e-025 239 2 AAGADCAG DREME-1 AAGAACAG 6.9e-097 9.2e-100 -228.03 0.0 51 493 147 193 0.10345 3.8e-102 246 2 GRAAAM DREME-2 GRAAAM 8.4e-004 1.1e-006 -13.70 0.0 63 495 108 486 0.12727 4.5e-009 247 2 AGDTTCAG DREME-3 AGATTCAG 9.7e-015 1.3e-017 -38.88 0.0 71 493 52 95 0.14402 5.3e-020 246 2 TTGGCAB DREME-4 TTGGCAB 2.0e-015 2.7e-018 -40.44 0.0 54 494 66 171 0.10931 1.1e-020 246 2 CTATTCY DREME-6 CTATTCY 4.7e-001 6.3e-004 -7.37 0.0 106 494 40 93 0.21457 2.6e-006 246 3 M1359_1.02 (MYPOP)_(Mus_musculus)_(DBD_0.97) NWTTGCGCCR 5.0e0000 6.6e-003 -5.01 0.0 31 491 51 441 0.06314 2.7e-005 245 3 M1528_1.02 (RFX6)_(Mus_musculus)_(DBD_0.66) VCNTRGYWAC 2.4e0000 3.3e-003 -5.73 0.0 247 491 342 579 0.50305 1.3e-005 245 3 M1841_1.02 AR GNACABNVTGTTCYY 1.6e-011 2.1e-014 -31.49 0.0 42 486 110 547 0.08642 8.7e-017 242 3 M1868_1.02 GATA2 DSAGATAAGAANYH 5.3e0000 7.0e-003 -4.96 0.0 65 487 101 511 0.13347 2.9e-005 243 3 M1970_1.02 NFIC TGCCAA 4.9e-010 6.6e-013 -28.05 0.0 49 495 123 595 0.09899 2.7e-015 247 3 M2264_1.02 (ATOH1)_(Mus_musculus)_(DBD_1.00) RCCAKCTG 4.2e0000 5.7e-003 -5.17 0.0 349 493 435 554 0.70791 2.3e-005 246 3 M2299_1.02 (MYF5)_(Mus_musculus)_(DBD_0.90) NRNRRCAGCTGSN 2.2e-001 3.0e-004 -8.12 0.0 250 488 341 557 0.51230 1.2e-006 243 3 M2310_1.02 RUNX2 MAAACCACARAMMMM 6.2e0000 8.2e-003 -4.80 0.0 30 486 60 563 0.06173 3.4e-005 242 3 M4469_1.02 REST TCCRTGGTGCTGAA 7.5e0000 1.0e-002 -4.61 0.0 183 487 200 425 0.37577 4.1e-005 243 3 M5325_1.02 CREB3L1 TGRTGACGTGGCAB 4.8e0000 6.4e-003 -5.06 0.0 5 487 13 311 0.01027 2.6e-005 243 3 M5512_1.02 HIC2 VSYGGGCAY 5.8e0000 7.8e-003 -4.86 0.0 52 492 94 587 0.10569 3.2e-005 245 3 M5594_1.02 LBX2 CTBRANSTRATTA 5.1e0000 6.8e-003 -4.99 0.0 46 488 82 547 0.09426 2.8e-005 243 3 M5636_1.02 MSC AACAGCTGTT 1.9e0000 2.5e-003 -5.98 0.0 41 491 66 460 0.08350 1.0e-005 245 3 M5660_1.02 NFIA TTGGCANNDTGCCAR 1.2e-034 1.6e-037 -84.73 0.0 64 486 145 345 0.13169 6.6e-040 242 3 M5662_1.02 NFIB TTGGCAHNDTGCCAR 2.6e-033 3.5e-036 -81.65 0.0 38 486 112 355 0.07819 1.4e-038 242 3 M5664_1.02 NFIX TTGGCANNNHGCCAR 7.9e-025 1.1e-027 -62.12 0.0 64 486 159 471 0.13169 4.4e-030 242 3 M5976_1.02 ZNF713 TTCGTGGCATTYTTCTA 1.4e0000 1.9e-003 -6.27 0.0 54 484 34 136 0.11157 7.9e-006 241 3 M6225_1.02 MECOM WAGAYAAGATAANAKA 9.0e0000 1.2e-002 -4.42 0.0 59 485 83 441 0.12165 5.0e-005 242 3 M6436_1.02 PGR DACAGRNTGTTCY 7.9e-004 1.1e-006 -13.76 0.0 36 488 83 569 0.07377 4.3e-009 243 3 M6453_1.02 RFX3 TYRCCATGGYAACV 7.8e0000 1.0e-002 -4.56 0.0 253 487 237 381 0.51951 4.3e-005 243 3 M6457_1.02 RUNX1 WAACCACARW 6.1e0000 8.1e-003 -4.82 0.0 229 491 319 580 0.46640 3.3e-005 245 3 M6525_1.02 TLX1 YGBYAAKDWGS 4.7e-006 6.3e-009 -18.88 0.0 30 490 80 588 0.06122 2.6e-011 244 ## # 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).