# 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 HNNRDTYTTGGCWYRGTGCCAR MEME-1 HNNRDTYTTGGCWYRGTGCCAR 2.2e-207 2.9e-210 -482.46 0.0 79 479 351 404 0.16493 1.2e-212 239 2 STGCCAR DREME-1 STGCCAR 4.5e-072 6.1e-075 -170.89 0.0 48 494 163 323 0.09717 2.5e-077 246 2 CYTGGCW DREME-2 CYTGGCW 4.0e-052 5.4e-055 -124.96 0.0 50 494 141 308 0.10121 2.2e-057 246 2 RCCAAAA DREME-3 RCCAAAA 6.9e-024 9.3e-027 -59.94 0.0 54 494 74 159 0.10931 3.8e-029 246 2 ATCAAAGA DREME-4 ATCAAAGA 4.6e-002 6.2e-005 -9.69 0.0 123 493 98 246 0.24949 2.5e-007 246 3 M1507_1.02 (LCOR)_(Meleagris_gallopavo)_(DBD_1.00) NDWTTNGGNN 1.4e-003 1.9e-006 -13.19 0.0 53 491 102 533 0.10794 7.6e-009 245 3 M1927_1.02 (MYCL1)_(Mus_musculus)_(DBD_0.66) RCCACGTG 3.6e0000 4.9e-003 -5.33 0.0 43 493 67 457 0.08722 2.0e-005 246 3 M1970_1.02 NFIC TGCCAA 6.1e-067 8.2e-070 -159.08 0.0 51 495 218 554 0.10303 3.3e-072 247 3 M4344_1.02 (ARID2)_(Saccharomyces_cerevisiae)_(DBD_0.26) SGTTGCYA 7.1e-001 9.5e-004 -6.96 0.0 73 493 116 520 0.14807 3.9e-006 246 3 M4471_1.02 PAX5 BCAGYSRAGCGTGAC 9.1e0000 1.2e-002 -4.40 0.0 32 486 56 493 0.06584 5.1e-005 242 3 M4522_1.02 ELK4 CCGGAAGYGS 5.4e0000 7.3e-003 -4.92 0.0 1 491 8 494 0.00204 3.0e-005 245 3 M5325_1.02 CREB3L1 TGRTGACGTGGCAB 2.1e-001 2.8e-004 -8.18 0.0 9 487 21 327 0.01848 1.2e-006 243 3 M5512_1.02 HIC2 VSYGGGCAY 4.0e-016 5.4e-019 -42.06 0.0 40 492 119 569 0.08130 2.2e-021 245 3 M5660_1.02 NFIA TTGGCANNDTGCCAR 2.1e-169 2.8e-172 -395.00 0.0 60 486 298 410 0.12346 1.2e-174 242 3 M5662_1.02 NFIB TTGGCAHNDTGCCAR 1.1e-168 1.5e-171 -393.31 0.0 60 486 299 414 0.12346 6.4e-174 242 3 M5664_1.02 NFIX TTGGCANNNHGCCAR 1.8e-151 2.4e-154 -353.73 0.0 60 486 304 465 0.12346 9.8e-157 242 3 M6194_1.02 E2F5 SGCGCSAAAH 2.8e-002 3.8e-005 -10.18 0.0 45 491 54 277 0.09165 1.5e-007 245 3 M6215_1.02 ESRRB TGACCTTGR 3.3e0000 4.4e-003 -5.42 0.0 326 492 384 514 0.66260 1.8e-005 245 3 M6268_1.02 HAND1 AAWKCCAGAYVC 1.1e-003 1.5e-006 -13.39 0.0 29 489 71 570 0.05930 6.3e-009 244 3 M6271_1.02 HES1 KGKCKCGTGBCKB 1.0e-002 1.4e-005 -11.21 0.0 48 488 92 525 0.09836 5.6e-008 243 3 M6272_1.02 HESX1 AKKYYAYKWGCCRSVT 5.8e-005 7.9e-008 -16.35 0.0 61 485 113 498 0.12577 3.3e-010 242 3 M6344_1.02 MEIS2 KGACAVCTGTCAA 4.1e0000 5.6e-003 -5.19 0.0 54 488 82 471 0.11066 2.3e-005 243 3 M6358_1.02 NEUROD1 SGGCAGRTGKSC 1.7e-006 2.3e-009 -19.89 0.0 35 489 85 537 0.07157 9.5e-012 244 3 M6464_1.02 SMAD2 GTGTCHGKCTV 7.6e-002 1.0e-004 -9.19 0.0 30 490 66 560 0.06122 4.2e-007 244 3 M6525_1.02 TLX1 YGBYAAKDWGS 1.1e-034 1.5e-037 -84.77 0.0 42 490 153 547 0.08571 6.3e-040 244 ## # 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).