# 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 YTGGCAVNGWGCCARG MEME-1 YTGGCAVNGWGCCARG 6.8e-209 9.1e-212 -485.94 0.0 67 485 323 379 0.13814 3.7e-214 242 1 TGTGTGTGTGTGTGTGTGTGTG MEME-2 TGTGTGTGTGTGTGTGTGTGTG 3.3e-001 4.4e-004 -7.73 0.0 79 479 44 134 0.16493 1.8e-006 239 1 TGRTGRTGRTGATGGTGRTGATGGTGRTGATGGTGATGRTG MEME-5 TGRTGRTGRTGATGGTGRTGATGGTGRTGATGGTGATGRTG 7.2e-002 9.6e-005 -9.25 0.0 58 460 12 20 0.12609 4.2e-007 229 1 GAGGTTATCTACTGGGACATCTAGAGCCT MEME-6 GAGGTTATCTACTGGGACATCTAGAGCCT 1.2e-005 1.6e-008 -17.97 0.0 90 472 17 19 0.19068 6.7e-011 235 1 AAGGTTTGCTGAGGGCMATCAC MEME-9 AAGGTTTGCTGAGGGCMATCAC 5.4e-005 7.3e-008 -16.44 0.0 113 479 17 18 0.23591 3.0e-010 239 2 VTGCCAR DREME-1 STGCCAR 6.6e-103 8.9e-106 -241.89 0.0 42 494 200 381 0.08502 3.6e-108 246 2 BTTGGC DREME-2 YTTGGC 1.3e-071 1.8e-074 -169.80 0.0 41 495 171 403 0.08283 7.3e-077 247 3 M1418_1.02 C11orf9 TGGTACCA 1.3e-003 1.7e-006 -13.29 0.0 39 493 73 454 0.07911 6.9e-009 246 3 M1970_1.02 NFIC TGCCAA 1.1e-083 1.4e-086 -197.66 0.0 43 495 223 559 0.08687 5.8e-089 247 3 M2392_1.02 RFX2 GTYDCCATGGCAACVRVNN 7.1e-003 9.5e-006 -11.57 0.0 38 482 61 370 0.07884 4.0e-008 240 3 M4344_1.02 (ARID2)_(Saccharomyces_cerevisiae)_(DBD_0.26) SGTTGCYA 2.5e-005 3.3e-008 -17.22 0.0 75 493 134 513 0.15213 1.3e-010 246 3 M4471_1.02 PAX5 BCAGYSRAGCGTGAC 1.5e-004 2.0e-007 -15.41 0.0 44 486 87 484 0.09053 8.4e-010 242 3 M4850_1.02 (TCF15)_(Drosophila_melanogaster)_(DBD_0.70) TKTWRTNKBBDYDMCATSTGK 9.0e-003 1.2e-005 -11.33 0.0 34 480 76 556 0.07083 5.0e-008 239 3 M5325_1.02 CREB3L1 TGRTGACGTGGCAB 7.1e-004 9.6e-007 -13.86 0.0 49 487 67 313 0.10062 3.9e-009 243 3 M5504_1.02 HES5 YGGCACGTGYCR 6.1e-001 8.2e-004 -7.11 0.0 31 489 30 184 0.06339 3.3e-006 244 3 M5506_1.02 HES7 YGGCACGTGCCR 1.7e-001 2.3e-004 -8.38 0.0 31 489 28 155 0.06339 9.4e-007 244 3 M5512_1.02 HIC2 VSYGGGCAY 7.9e-029 1.1e-031 -71.32 0.0 42 492 146 567 0.08537 4.3e-034 245 3 M5660_1.02 NFIA TTGGCANNDTGCCAR 8.0e-189 1.1e-191 -439.72 0.0 66 486 329 426 0.13580 4.5e-194 242 3 M5662_1.02 NFIB TTGGCAHNDTGCCAR 1.4e-190 1.9e-193 -443.74 0.0 66 486 329 423 0.13580 8.0e-196 242 3 M5664_1.02 NFIX TTGGCANNNHGCCAR 2.3e-170 3.1e-173 -397.21 0.0 50 486 303 473 0.10288 1.3e-175 242 3 M6185_1.02 CXXC1 CGKTGKY 1.2e0000 1.7e-003 -6.39 0.0 42 494 77 544 0.08502 6.8e-006 246 3 M6194_1.02 E2F5 SGCGCSAAAH 1.8e-003 2.4e-006 -12.94 0.0 35 491 50 289 0.07128 9.8e-009 245 3 M6268_1.02 HAND1 AAWKCCAGAYVC 1.5e-001 2.0e-004 -8.50 0.0 121 489 190 562 0.24744 8.4e-007 244 3 M6271_1.02 HES1 KGKCKCGTGBCKB 7.8e-006 1.0e-008 -18.38 0.0 64 488 127 540 0.13115 4.3e-011 243 3 M6272_1.02 HESX1 AKKYYAYKWGCCRSVT 9.9e-004 1.3e-006 -13.53 0.0 31 485 67 491 0.06392 5.5e-009 242 3 M6274_1.02 HIC1 GGGKTGCCC 3.9e-003 5.2e-006 -12.16 0.0 36 492 72 494 0.07317 2.1e-008 245 3 M6344_1.02 MEIS2 KGACAVCTGTCAA 4.7e-003 6.3e-006 -11.97 0.0 32 488 64 464 0.06557 2.6e-008 243 3 M6358_1.02 NEUROD1 SGGCAGRTGKSC 2.4e-001 3.2e-004 -8.06 0.0 33 489 67 535 0.06748 1.3e-006 244 3 M6464_1.02 SMAD2 GTGTCHGKCTV 6.2e-001 8.4e-004 -7.09 0.0 126 490 191 556 0.25714 3.4e-006 244 3 M6525_1.02 TLX1 YGBYAAKDWGS 5.2e-043 7.0e-046 -103.98 0.0 46 490 171 532 0.09388 2.9e-048 244 ## # 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).