# 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 YTGGCASNGWGCCARG MEME-1 YTGGCASNGWGCCARG 4.2e-207 5.7e-210 -481.80 0.0 73 485 346 413 0.15052 2.4e-212 242 2 BTGCCAR DREME-1 STGCCAR 1.7e-094 2.3e-097 -222.50 0.0 74 494 253 421 0.14980 9.5e-100 246 2 CYTGGC DREME-2 CYTGGC 1.4e-052 1.9e-055 -125.98 0.0 67 495 207 474 0.13535 7.9e-058 247 3 M0178_1.02 (ASCL2)_(Mus_musculus)_(DBD_0.98) NVCAGCTGBN 8.0e0000 1.1e-002 -4.52 0.0 49 491 87 567 0.09980 4.5e-005 245 3 M0305_1.02 (CREB3L2)_(Mus_musculus)_(DBD_1.00) GCCACGTGD 4.6e0000 6.2e-003 -5.08 0.0 72 492 89 400 0.14634 2.6e-005 245 3 M1528_1.02 (RFX6)_(Mus_musculus)_(DBD_0.66) VCNTRGYWAC 3.9e0000 5.3e-003 -5.24 0.0 81 491 136 590 0.16497 2.2e-005 245 3 M1838_1.02 TFAP2A NHYDGCCYSAGGGCA 5.0e0000 6.8e-003 -4.99 0.0 102 486 151 532 0.20988 2.8e-005 242 3 M1970_1.02 NFIC TGCCAA 4.3e-073 5.9e-076 -173.23 0.0 81 495 296 599 0.16364 2.4e-078 247 3 M2264_1.02 (ATOH1)_(Mus_musculus)_(DBD_1.00) RCCAKCTG 8.9e0000 1.2e-002 -4.42 0.0 81 493 127 555 0.16430 4.9e-005 246 3 M2392_1.02 RFX2 GTYDCCATGGCAACVRVNN 2.9e-002 3.9e-005 -10.16 0.0 92 482 133 455 0.19087 1.6e-007 240 3 M4344_1.02 (ARID2)_(Saccharomyces_cerevisiae)_(DBD_0.26) SGTTGCYA 9.7e-007 1.3e-009 -20.46 0.0 35 493 87 554 0.07099 5.3e-012 246 3 M4471_1.02 PAX5 BCAGYSRAGCGTGAC 9.6e-004 1.3e-006 -13.56 0.0 80 486 143 543 0.16461 5.3e-009 242 3 M4971_1.02 (FERD3L)_(Drosophila_melanogaster)_(DBD_0.89) GTVACAGVTG 2.5e0000 3.4e-003 -5.67 0.0 477 491 558 560 0.97149 1.4e-005 245 3 M5325_1.02 CREB3L1 TGRTGACGTGGCAB 6.6e-003 8.9e-006 -11.63 0.0 61 487 82 357 0.12526 3.7e-008 243 3 M5512_1.02 HIC2 VSYGGGCAY 4.8e-028 6.5e-031 -69.51 0.0 62 492 188 598 0.12602 2.6e-033 245 3 M5660_1.02 NFIA TTGGCANNDTGCCAR 6.8e-181 9.2e-184 -421.46 0.0 70 486 354 485 0.14403 3.8e-186 242 3 M5662_1.02 NFIB TTGGCAHNDTGCCAR 1.3e-179 1.7e-182 -418.54 0.0 70 486 355 489 0.14403 7.0e-185 242 3 M5664_1.02 NFIX TTGGCANNNNGCCAR 3.8e-156 5.1e-159 -364.47 0.0 72 486 361 550 0.14815 2.1e-161 242 3 M5753_1.02 PROX1 YAAGACGYCTTA 9.9e0000 1.3e-002 -4.31 0.0 9 489 15 243 0.01840 5.5e-005 244 3 M6161_1.02 BHLHE41 WSVRKSYCACGTGMHGRRRV 1.5e0000 2.1e-003 -6.19 0.0 49 481 82 495 0.10187 8.6e-006 240 3 M6174_1.02 CEBPZ AGCCAATSAGH 3.4e0000 4.6e-003 -5.39 0.0 34 490 57 460 0.06939 1.9e-005 244 3 M6185_1.02 CXXC1 CGKTGKY 9.8e0000 1.3e-002 -4.32 0.0 44 494 80 580 0.08907 5.4e-005 246 3 M6194_1.02 E2F5 SGCGCSAAAH 8.1e-005 1.1e-007 -16.02 0.0 57 491 85 368 0.11609 4.5e-010 245 3 M6268_1.02 HAND1 AAWKCCAGAYVC 5.0e-004 6.7e-007 -14.21 0.0 17 489 51 585 0.03476 2.8e-009 244 3 M6271_1.02 HES1 KGKCKCGTGBCKB 6.5e-003 8.8e-006 -11.64 0.0 72 488 132 561 0.14754 3.6e-008 243 3 M6272_1.02 HESX1 AKKYYAYKWGCCRSVT 3.6e-003 4.8e-006 -12.24 0.0 21 485 55 557 0.04330 2.0e-008 242 3 M6274_1.02 HIC1 GGGKTGCCC 6.3e-004 8.5e-007 -13.97 0.0 32 492 75 558 0.06504 3.5e-009 245 3 M6344_1.02 MEIS2 KGACAVCTGTCAA 5.8e-005 7.8e-008 -16.36 0.0 90 488 147 488 0.18443 3.2e-010 243 3 M6358_1.02 NEUROD1 SGGCAGRTGKSC 2.6e-001 3.5e-004 -7.97 0.0 47 489 91 574 0.09611 1.4e-006 244 3 M6373_1.02 NFYC YAGCCAATSAGVGS 4.4e-002 5.9e-005 -9.73 0.0 113 487 181 555 0.23203 2.4e-007 243 3 M6379_1.02 NKX3-2 ARYTAAGTGGV 5.5e0000 7.4e-003 -4.91 0.0 222 490 310 576 0.45306 3.0e-005 244 3 M6464_1.02 SMAD2 GTGTCHGKCTV 1.8e-001 2.4e-004 -8.32 0.0 36 490 76 587 0.07347 1.0e-006 244 3 M6468_1.02 SNAI1 SCAGGTGK 1.6e-001 2.1e-004 -8.46 0.0 49 493 95 577 0.09939 8.6e-007 246 3 M6525_1.02 TLX1 YGBYAAKDWGS 1.1e-036 1.5e-039 -89.38 0.0 72 490 220 589 0.14694 6.2e-042 244 3 M6527_1.02 TWIST1 MCCCAGGTGK 9.4e-001 1.3e-003 -6.67 0.0 47 491 81 511 0.09572 5.2e-006 245 ## # 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).