# 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 CMCCCCCVGCCMCGCCCMYYCC MEME-1 CMCCCCCVGCCMCGCCCMYYCC 3.6e-004 4.8e-007 -14.55 0.0 205 479 321 583 0.42797 2.0e-009 239 1 CCWCACCSRKGCACACCCWCACCCRSRCACA MEME-5 CCWCACCSRKGCACACCCWCACCCRSRCACA 3.3e-001 4.4e-004 -7.72 0.0 98 470 18 29 0.20851 1.9e-006 234 1 RCCMCGCCC MEME-8 RCCMCGCCC 6.7e-008 8.9e-011 -23.14 0.0 250 492 305 451 0.50813 3.6e-013 245 2 CMMCGCCC DREME-1 CCMCGCCC 1.5e-007 1.9e-010 -22.36 0.0 219 493 254 410 0.44422 7.9e-013 246 2 TTCCGB DREME-2 TTCCGS 5.3e-007 7.1e-010 -21.07 0.0 171 495 190 364 0.34545 2.9e-012 247 2 CTCCDCC DREME-3 CTCCDCC 7.1e0000 9.5e-003 -4.66 0.0 258 494 257 414 0.52227 3.9e-005 246 3 M0405_1.02 (KLF7)_(Mus_musculus)_(DBD_1.00) DGGGCGKGGY 5.4e-016 7.2e-019 -41.78 0.0 183 491 334 592 0.37271 2.9e-021 245 3 M0443_1.02 (KLF12)_(Mus_musculus)_(DBD_1.00) DGGGCGKGGY 7.5e-016 1.0e-018 -41.44 0.0 183 491 334 594 0.37271 4.1e-021 245 3 M1871_1.02 (KLF2)_(Mus_musculus)_(DBD_0.95) DGGGYGKGGC 2.1e-009 2.8e-012 -26.61 0.0 219 491 355 587 0.44603 1.1e-014 245 3 M1906_1.02 SP1 GGGGGMGGGGC 1.6e-001 2.1e-004 -8.47 0.0 212 490 308 579 0.43265 8.6e-007 244 3 M2314_1.02 SP2 SSSVRGRGGCGGGRC 6.9e-002 9.2e-005 -9.30 0.0 246 486 353 579 0.50617 3.8e-007 242 3 M2391_1.02 KLF5 DGGGHGGGGC 1.7e-004 2.3e-007 -15.28 0.0 203 491 316 587 0.41344 9.4e-010 245 3 M4459_1.02 EGR1 SBGCGKGGGCGGVGGSGSGS 7.9e0000 1.1e-002 -4.55 0.0 195 481 277 568 0.40541 4.4e-005 240 3 M4537_1.02 E2F4 SGCGGGAARWTBVRR 7.2e-001 9.6e-004 -6.95 0.0 186 486 266 557 0.38272 4.0e-006 242 3 M5209_1.02 (SP5)_(Drosophila_melanogaster)_(DBD_0.93) GKGGGCGKRKC 1.1e-009 1.4e-012 -27.28 0.0 216 490 352 586 0.44082 5.8e-015 244 3 M5302_1.02 BATF3 TGATGACGTCATCA 2.8e0000 3.7e-003 -5.60 0.0 279 487 75 96 0.57290 1.5e-005 243 3 M5591_1.02 KLF13 CAAAAAGGGGCGTGKCAY 2.1e-001 2.8e-004 -8.17 0.0 97 483 116 382 0.20083 1.2e-006 241 3 M5592_1.02 KLF14 ARGKGGGCGTGGYM 4.3e-004 5.8e-007 -14.37 0.0 215 487 317 561 0.44148 2.4e-009 243 3 M5593_1.02 KLF16 GGGGGCGTGKC 1.3e-004 1.7e-007 -15.60 0.0 282 490 409 586 0.57551 6.9e-010 244 3 M5856_1.02 SP8 RGKGGGCGTGGY 2.6e-005 3.4e-008 -17.19 0.0 217 489 336 584 0.44376 1.4e-010 244 3 M5998_1.02 (CREB5)_(Mus_musculus)_(DBD_1.00) DRTGACGTCATN 4.8e0000 6.5e-003 -5.04 0.0 227 489 150 252 0.46421 2.7e-005 244 3 M6139_1.02 AHR KCACGCRAH 3.6e0000 4.8e-003 -5.33 0.0 240 492 313 543 0.48780 2.0e-005 245 3 M6200_1.02 EGR3 WGAGTGGGYGT 3.8e-001 5.0e-004 -7.59 0.0 284 490 375 555 0.57959 2.1e-006 244 3 M6204_1.02 ELF2 TDNCAGGAAGTRRVT 7.9e0000 1.1e-002 -4.56 0.0 272 486 350 544 0.55967 4.4e-005 242 3 M6207_1.02 ELK1 RCCGGAAGT 6.3e0000 8.5e-003 -4.77 0.0 22 492 49 583 0.04472 3.5e-005 245 3 M6322_1.02 KLF1 CAGGGTGKGGC 7.1e0000 9.5e-003 -4.66 0.0 218 490 305 579 0.44490 3.9e-005 244 3 M6324_1.02 KLF4 DGGGYGKGGC 1.0e-007 1.3e-010 -22.73 0.0 249 491 386 591 0.50713 5.5e-013 245 3 M6482_1.02 SP3 VGVVGGGGGCGGGGCBRGSS 3.4e-003 4.6e-006 -12.29 0.0 209 481 321 585 0.43451 1.9e-008 240 3 M6553_1.02 ZNF219 GDGGGGGGYGGA 2.9e0000 3.8e-003 -5.56 0.0 135 489 205 576 0.27607 1.6e-005 244 ## # 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).