# 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 TKTRTKTRTKTRTKTWTKTRTKTRTKTRTKT MEME-1 TKTRTKTRTKTRTKTWTKTRTKTRTKTRTKT 9.9e-005 1.3e-007 -15.84 0.0 86 470 81 230 0.18298 5.6e-010 234 1 GAACCYRGGAGGYGGAGGTTGCAGTGAG MEME-6 GAACCYRGGAGGYGGAGGTTGCAGTGAG 5.0e0000 6.6e-003 -5.02 0.0 345 473 128 147 0.72939 2.8e-005 236 2 GACTCAK DREME-4 GACTCAK 1.6e-004 2.2e-007 -15.35 0.0 144 494 68 121 0.29150 8.8e-010 246 2 AAATAAAT DREME-12 AAATAAAT 1.9e-004 2.5e-007 -15.22 0.0 43 493 26 79 0.08722 1.0e-009 246 3 M0300_1.02 (ATF2)_(Mus_musculus)_(DBD_1.00) NRTKACGTMA 2.0e0000 2.6e-003 -5.94 0.0 239 491 314 542 0.48676 1.1e-005 245 3 M0728_1.02 (FOXJ1)_(Mus_musculus)_(DBD_1.00) NRTAAACAAANN 1.5e0000 2.0e-003 -6.19 0.0 59 489 103 560 0.12065 8.4e-006 244 3 M0736_1.02 (FOXK2)_(Mus_musculus)_(DBD_0.90) RTAAACAA 3.1e0000 4.1e-003 -5.49 0.0 77 493 127 571 0.15619 1.7e-005 246 3 M0747_1.02 (FOXL2)_(Mus_musculus)_(DBD_0.70) WNNRTAAAYA 1.8e0000 2.4e-003 -6.03 0.0 71 491 120 569 0.14460 9.8e-006 245 3 M1025_1.02 (HOXD1)_(Mus_musculus)_(DBD_0.98) NNYVATYA 6.9e0000 9.2e-003 -4.69 0.0 191 493 176 358 0.38742 3.7e-005 246 3 M2278_1.02 FOS DVTGASTCATB 6.6e-001 8.7e-004 -7.05 0.0 308 490 355 489 0.62857 3.6e-006 244 3 M2289_1.02 JUN DDRATGATGTMAT 4.3e-002 5.7e-005 -9.78 0.0 236 488 288 480 0.48361 2.3e-007 243 3 M2292_1.02 JUND DRTGASTCATS 2.4e0000 3.2e-003 -5.76 0.0 308 490 330 456 0.62857 1.3e-005 244 3 M4526_1.02 SMARCC1 DSRVDGTGASTCAKV 8.4e-002 1.1e-004 -9.11 0.0 312 486 370 496 0.64198 4.6e-007 242 3 M4565_1.02 FOSL2 VDGGATGASTCAYH 1.4e-001 1.8e-004 -8.63 0.0 309 487 345 466 0.63450 7.4e-007 243 3 M4619_1.02 FOSL1 BGGTGASTCAK 1.0e-002 1.4e-005 -11.20 0.0 310 490 352 470 0.63265 5.6e-008 244 3 M4623_1.02 JUNB NDRTGASTCATNYHY 3.7e0000 4.9e-003 -5.32 0.0 304 486 343 479 0.62551 2.0e-005 242 3 M5291_1.02 ARX YTAATTNRATTAN 9.3e0000 1.2e-002 -4.40 0.0 150 488 167 420 0.30738 5.1e-005 243 3 M5292_1.02 ATF4 RKATGAYGCAATM 5.3e0000 7.0e-003 -4.97 0.0 282 488 300 446 0.57787 2.9e-005 243 3 M5293_1.02 ATF7 NKATGACGTCATHN 2.8e-006 3.8e-009 -19.40 0.0 235 487 171 247 0.48255 1.5e-011 243 3 M5302_1.02 BATF3 TGATGACGTCATCA 1.1e-001 1.5e-004 -8.84 0.0 183 487 80 136 0.37577 6.0e-007 243 3 M5323_1.02 CREB3 KGRTGACGTCAYNV 1.5e-003 2.0e-006 -13.12 0.0 227 487 162 251 0.46612 8.2e-009 243 3 M5335_1.02 CUX2 ATCGATAHNDTTATYGAT 1.4e-002 1.8e-005 -10.92 0.0 45 483 30 109 0.09317 7.5e-008 241 3 M5446_1.02 FOXD4L2 RTAAACA 4.5e0000 6.0e-003 -5.12 0.0 52 494 92 569 0.10526 2.4e-005 246 3 M5587_1.02 JDP2 ATGASTCAT 4.5e-001 5.9e-004 -7.43 0.0 112 492 142 440 0.22764 2.4e-006 245 3 M5740_1.02 POU4F1 ATGMATAATTAATG 3.9e0000 5.1e-003 -5.27 0.0 29 487 49 437 0.05955 2.1e-005 243 3 M5998_1.02 (CREB5)_(Mus_musculus)_(DBD_1.00) DRTGACGTCATN 1.2e-005 1.5e-008 -17.99 0.0 235 489 210 318 0.48057 6.3e-011 244 3 M6114_1.02 FOXA1 WAWGYAAAYA 5.3e0000 7.1e-003 -4.95 0.0 83 491 130 548 0.16904 2.9e-005 245 3 M6141_1.02 ALX1 TAATBYAATTAB 6.7e0000 8.9e-003 -4.73 0.0 39 489 65 487 0.07975 3.6e-005 244 3 M6180_1.02 CREB1 RTGACGTMA 7.2e-001 9.5e-004 -6.96 0.0 250 492 327 541 0.50813 3.9e-006 245 3 M6234_1.02 FOXA3 RVWAARYAAAYAD 4.1e0000 5.4e-003 -5.22 0.0 108 488 163 548 0.22131 2.2e-005 243 3 M6239_1.02 FOXF2 HWADGTAAACA 3.9e-001 5.2e-004 -7.57 0.0 86 490 135 526 0.17551 2.1e-006 244 3 M6299_1.02 HOXC6 AAAGTAATAAATCAT 1.1e0000 1.5e-003 -6.50 0.0 126 486 125 340 0.25926 6.2e-006 242 3 M6415_1.02 PDX1 CTAATTACY 8.6e0000 1.1e-002 -4.47 0.0 90 492 120 466 0.18293 4.7e-005 245 ## # 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).