# 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 YTGGCACHDTGCCA MEME-1 YTGGCACHDTGCCA 1.9e-167 2.5e-170 -390.52 0.0 65 487 280 354 0.13347 1.0e-172 243 1 SSMGYCSGGGHMBCGVVCSCSSGGGACSGGGSKSRGVGVBSGG MEME-2 SSMGYCSGGGHMBCGVVCSCSSGGGACSGGGSKSRGVGVBSGG 1.4e0000 1.9e-003 -6.28 0.0 44 458 9 17 0.09607 8.2e-006 228 2 VTGCCAR DREME-1 STGCCAR 3.4e-084 4.5e-087 -198.82 0.0 44 494 179 357 0.08907 1.8e-089 246 2 GCCAR DREME-2 GCCAR 6.5e-053 8.7e-056 -126.78 0.0 58 496 191 464 0.11694 3.5e-058 247 3 M0198_1.02 (SOHLH2)_(Mus_musculus)_(DBD_0.84) NRYNCGTGCN 2.7e-002 3.6e-005 -10.24 0.0 35 491 63 445 0.07128 1.5e-007 245 3 M1418_1.02 C11orf9 TGGTACCA 1.1e-004 1.4e-007 -15.75 0.0 33 493 60 374 0.06694 5.9e-010 246 3 M1507_1.02 (LCOR)_(Meleagris_gallopavo)_(DBD_1.00) NDWTTNGGNN 5.5e-001 7.4e-004 -7.21 0.0 49 491 81 480 0.09980 3.0e-006 245 3 M1528_1.02 (RFX6)_(Mus_musculus)_(DBD_0.66) NCNTRGYWAC 7.6e-002 1.0e-004 -9.19 0.0 39 491 72 491 0.07943 4.2e-007 245 3 M1838_1.02 TFAP2A NHYWGCCYSAGGGCA 3.0e-001 4.1e-004 -7.81 0.0 46 486 69 407 0.09465 1.7e-006 242 3 M1917_1.02 USF1 GGTCACRTGRB 3.2e0000 4.3e-003 -5.44 0.0 70 490 86 387 0.14286 1.8e-005 244 3 M1934_1.02 ESR1 RGGTCAGGGTGACCTKGVNN 2.6e-001 3.5e-004 -7.96 0.0 33 481 55 407 0.06861 1.5e-006 240 3 M1970_1.02 NFIC TGCCAA 1.1e-074 1.5e-077 -176.93 0.0 39 495 191 496 0.07879 5.9e-080 247 3 M2264_1.02 (ATOH1)_(Mus_musculus)_(DBD_1.00) RCCAKCTG 1.9e0000 2.5e-003 -5.98 0.0 135 493 161 437 0.27383 1.0e-005 246 3 M2286_1.02 HNF4G TGRMCTTTGNHCYYN 9.4e0000 1.3e-002 -4.37 0.0 34 486 57 468 0.06996 5.3e-005 242 3 M2392_1.02 RFX2 GTYDCCATGGCAACVRNNN 2.5e-006 3.3e-009 -19.52 0.0 50 482 82 364 0.10373 1.4e-011 240 3 M4344_1.02 (ARID2)_(Saccharomyces_cerevisiae)_(DBD_0.26) BGTTGCYA 1.1e-005 1.4e-008 -18.06 0.0 111 493 172 483 0.22515 5.9e-011 246 3 M4473_1.02 PBX3 NBCDGCCAATSRGVR 7.0e-001 9.3e-004 -6.98 0.0 50 486 78 452 0.10288 3.9e-006 242 3 M4525_1.02 TFAP2C NGCCYSAGGSCANDB 2.4e-001 3.3e-004 -8.02 0.0 56 486 79 400 0.11523 1.4e-006 242 3 M4636_1.02 THAP1 YTGCCCDBANYMAAGATGGCG 3.9e-001 5.3e-004 -7.55 0.0 60 480 55 230 0.12500 2.2e-006 239 3 M4698_1.02 HNF4A BTGRMCTTTGVHCYB 2.9e0000 3.8e-003 -5.57 0.0 34 486 58 459 0.06996 1.6e-005 242 3 M5284_1.02 ALX3 BNTAATTRRY 5.8e0000 7.8e-003 -4.85 0.0 65 491 91 453 0.13238 3.2e-005 245 3 M5325_1.02 CREB3L1 TGRTGACGTGGCAB 1.1e-002 1.4e-005 -11.17 0.0 43 487 55 290 0.08830 5.8e-008 243 3 M5506_1.02 HES7 YGGCACGTGCCR 5.7e0000 7.7e-003 -4.86 0.0 13 489 14 134 0.02658 3.2e-005 244 3 M5509_1.02 HEY1 GRCACGTGYC 1.5e-001 2.1e-004 -8.48 0.0 37 491 49 311 0.07536 8.5e-007 245 3 M5512_1.02 HIC2 VSYGGGCAY 5.6e-039 7.5e-042 -94.69 0.0 38 492 143 492 0.07724 3.1e-044 245 3 M5568_1.02 HSFY2 TTCGAAHVRTTCGAA 1.5e-004 2.0e-007 -15.43 0.0 50 486 72 331 0.10288 8.2e-010 242 3 M5621_1.02 MEIS3 SCTGTCAH 2.6e-003 3.5e-006 -12.57 0.0 81 493 130 491 0.16430 1.4e-008 246 3 M5660_1.02 NFIA TTGGCANNDTGCCAR 1.3e-149 1.7e-152 -349.46 0.0 64 486 283 397 0.13169 7.1e-155 242 3 M5662_1.02 NFIB TTGGCAHNDTGCCAR 1.2e-149 1.6e-152 -349.54 0.0 64 486 285 402 0.13169 6.5e-155 242 3 M5664_1.02 NFIX TTGGCANNNHGCCAR 1.7e-136 2.3e-139 -319.21 0.0 64 486 289 443 0.13169 9.6e-142 242 3 M6161_1.02 BHLHE41 WSVRKSYCACGTGMWGRRRV 6.8e0000 9.1e-003 -4.70 0.0 47 481 60 358 0.09771 3.8e-005 240 3 M6173_1.02 CEBPG VAGATTGCAHAAT 9.0e-002 1.2e-004 -9.02 0.0 42 488 73 465 0.08607 5.0e-007 243 3 M6185_1.02 CXXC1 CGKTGKY 8.6e-001 1.2e-003 -6.76 0.0 54 494 85 473 0.10931 4.7e-006 246 3 M6192_1.02 E2F3 SSCGCSAAAC 4.5e-008 6.0e-011 -23.54 0.0 35 491 61 305 0.07128 2.5e-013 245 3 M6194_1.02 E2F5 SGCGCSAAAH 2.8e-008 3.8e-011 -24.00 0.0 51 491 74 289 0.10387 1.5e-013 245 3 M6210_1.02 ENO1 YDSMCACRTGSYB 4.1e-002 5.5e-005 -9.80 0.0 76 488 115 463 0.15574 2.3e-007 243 3 M6268_1.02 HAND1 AAWDCCAGAYVC 8.0e-005 1.1e-007 -16.05 0.0 55 489 101 479 0.11247 4.4e-010 244 3 M6271_1.02 HES1 KGKCKCGTGBCKB 2.9e-005 3.9e-008 -17.07 0.0 84 488 133 452 0.17213 1.6e-010 243 3 M6272_1.02 HESX1 AKKYYAYKWGCCRSVT 3.6e-011 4.8e-014 -30.66 0.0 55 485 113 444 0.11340 2.0e-016 242 3 M6274_1.02 HIC1 GGGKTGCCC 1.6e-006 2.2e-009 -19.94 0.0 42 492 85 454 0.08537 8.9e-012 245 3 M6275_1.02 HIF1A SBSTACGTGCSB 6.4e-004 8.6e-007 -13.97 0.0 37 489 59 344 0.07566 3.5e-009 244 3 M6278_1.02 HLTF KANKKCTGSMAM 1.2e-001 1.6e-004 -8.76 0.0 45 489 79 487 0.09202 6.4e-007 244 3 M6306_1.02 INSM1 TGTMAGGGGGCR 4.9e0000 6.6e-003 -5.02 0.0 217 489 187 337 0.44376 2.7e-005 244 3 M6344_1.02 MEIS2 KGACAVCTGTCAA 2.3e-005 3.0e-008 -17.31 0.0 40 488 76 423 0.08197 1.2e-010 243 3 M6345_1.02 MITF VKCACATGWY 2.4e-002 3.2e-005 -10.34 0.0 63 491 101 470 0.12831 1.3e-007 245 3 M6358_1.02 NEUROD1 BGGCAGRTGKSC 5.1e-009 6.8e-012 -25.71 0.0 65 489 123 461 0.13292 2.8e-014 244 3 M6373_1.02 NFYC YAGCCAATSAGVGS 3.9e0000 5.2e-003 -5.25 0.0 135 487 168 459 0.27721 2.2e-005 243 3 M6374_1.02 NKX2-1 STCAAGKGCH 5.0e-001 6.7e-004 -7.31 0.0 35 491 64 491 0.07128 2.7e-006 245 3 M6464_1.02 SMAD2 GTGTCHGKCTV 7.4e-003 1.0e-005 -11.52 0.0 30 490 61 472 0.06122 4.1e-008 244 3 M6525_1.02 TLX1 YGBYAAKDWGS 2.8e-058 3.8e-061 -139.13 0.0 46 490 184 490 0.09388 1.5e-063 244 3 M6537_1.02 YBX1 BSKGATTSSCY 5.8e-003 7.8e-006 -11.76 0.0 52 490 91 478 0.10612 3.2e-008 244 ## # 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).