# 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 ACACACACACACACACACACACACACACACACACACACACRCAYASAS MEME-1 ACACACACACACACACACACACACACACACACACACACACRCAYASAS 2.7e-009 3.6e-012 -26.34 0.0 197 453 42 43 0.43488 1.6e-014 226 1 GRTGATGTCAY MEME-3 GRTGATGTCAY 1.3e-003 1.7e-006 -13.27 0.0 180 490 100 172 0.36735 7.1e-009 244 1 AARGYGYBDGBCTMVTRABCCVGRGRTYGTGGGTTCGADTCCC MEME-7 AARGYGYBDGBCTMVTRABCCVGRGRTYGTGGGTTCGADTCCC 1.5e0000 2.0e-003 -6.20 0.0 52 458 8 12 0.11354 8.9e-006 228 2 TGACTCAB DREME-2 TGACTCAB 8.7e-001 1.2e-003 -6.75 0.0 253 493 73 99 0.51318 4.8e-006 246 2 CGGAAC DREME-3 CGGAAC 4.2e-003 5.6e-006 -12.10 0.0 125 495 80 182 0.25253 2.3e-008 247 3 M0300_1.02 (ATF2)_(Mus_musculus)_(DBD_1.00) NRTKACGTMA 4.4e-002 5.9e-005 -9.73 0.0 185 491 261 539 0.37678 2.4e-007 245 3 M2289_1.02 JUN DDRATGATGTMAT 2.5e-001 3.3e-004 -8.01 0.0 226 488 237 408 0.46311 1.4e-006 243 3 M2388_1.02 SREBF2 RTGGGGTGAY 1.1e0000 1.5e-003 -6.52 0.0 181 491 234 504 0.36864 6.0e-006 245 3 M4619_1.02 FOSL1 BGGTGASTCAK 7.8e0000 1.0e-002 -4.56 0.0 74 490 87 382 0.15102 4.3e-005 244 3 M5292_1.02 ATF4 GKATGAYGCAATM 2.3e-001 3.0e-004 -8.10 0.0 212 488 223 404 0.43443 1.3e-006 243 3 M5293_1.02 ATF7 NKATGACGTCATHN 1.9e-003 2.5e-006 -12.90 0.0 181 487 147 271 0.37166 1.0e-008 243 3 M5302_1.02 BATF3 TGATGACGTCATCA 1.9e-002 2.5e-005 -10.59 0.0 181 487 98 171 0.37166 1.0e-007 243 3 M5323_1.02 CREB3 KGRTGACGTCAYNV 8.6e-002 1.1e-004 -9.07 0.0 181 487 146 283 0.37166 4.7e-007 243 3 M5882_1.02 TBX19 DTTMRCACVTAGGTGTGAAW 5.8e0000 7.8e-003 -4.85 0.0 181 481 108 210 0.37630 3.3e-005 240 3 M5883_1.02 TBX20 TCACACSTTCACACCT 3.9e0000 5.3e-003 -5.25 0.0 59 485 61 292 0.12165 2.2e-005 242 3 M5998_1.02 (CREB5)_(Mus_musculus)_(DBD_1.00) DRTGACGTCATN 6.9e-004 9.2e-007 -13.90 0.0 185 489 172 318 0.37832 3.8e-009 244 3 M6152_1.02 ATF1 VTGACGTCAV 3.4e0000 4.5e-003 -5.40 0.0 253 491 287 469 0.51527 1.8e-005 245 3 M6180_1.02 CREB1 RTGACGTMA 1.6e0000 2.1e-003 -6.15 0.0 184 492 248 532 0.37398 8.7e-006 245 3 M6181_1.02 CREM CRVTGACGTCA 2.2e0000 2.9e-003 -5.85 0.0 402 490 436 490 0.82041 1.2e-005 244 3 M6276_1.02 HINFP DMSNHMGCGGACGTTV 1.7e0000 2.3e-003 -6.07 0.0 299 485 287 398 0.61649 9.6e-006 242 3 M6277_1.02 HLF SKRTTACRYAAYC 3.4e-002 4.6e-005 -10.00 0.0 58 488 84 399 0.11885 1.9e-007 243 3 M6333_1.02 MAFG MATGACT 4.7e-001 6.3e-004 -7.37 0.0 104 494 163 554 0.21053 2.6e-006 246 3 M6359_1.02 NFE2L1 NATGACD 9.5e0000 1.3e-002 -4.36 0.0 64 494 107 568 0.12955 5.2e-005 246 ## # 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).