# 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 2 CAGGTRA DREME-1 CAGGTGA 2.9e-003 4.0e-006 -12.44 0.0 134 494 80 169 0.27126 1.6e-008 246 2 TGAGTCAB DREME-2 TGAGTCAB 2.0e-010 2.7e-013 -28.95 0.0 207 493 90 115 0.41988 1.1e-015 246 2 CAGGTGK DREME-3 CAGGTGT 8.2e0000 1.1e-002 -4.51 0.0 292 494 132 180 0.59109 4.5e-005 246 3 M0300_1.02 (ATF2)_(Mus_musculus)_(DBD_1.00) NRTKACGTMA 3.5e-003 4.7e-006 -12.27 0.0 289 491 355 501 0.58859 1.9e-008 245 3 M0719_1.02 FOXG1 RTAAACAW 4.2e0000 5.6e-003 -5.18 0.0 111 493 124 392 0.22515 2.3e-005 246 3 M0894_1.02 LBX1 TTAATTAG 5.3e0000 7.2e-003 -4.94 0.0 21 493 37 418 0.04260 2.9e-005 246 3 M1581_1.02 (CIC)_(Mus_musculus)_(DBD_1.00) NNTGCTGACW 3.4e0000 4.6e-003 -5.39 0.0 211 491 279 537 0.42974 1.9e-005 245 3 M2278_1.02 FOS DVTGASTCATB 7.5e-001 1.0e-003 -6.90 0.0 192 490 207 413 0.39184 4.1e-006 244 3 M2289_1.02 JUN DDRATGATGTMAT 5.8e-005 7.9e-008 -16.36 0.0 280 488 298 413 0.57377 3.2e-010 243 3 M2292_1.02 JUND DRTGASTCATS 2.9e-002 3.9e-005 -10.15 0.0 192 490 206 397 0.39184 1.6e-007 244 3 M4526_1.02 SMARCC1 DSRVDGTGASTCABV 2.8e0000 3.7e-003 -5.60 0.0 238 486 264 449 0.48971 1.5e-005 242 3 M4565_1.02 FOSL2 VDGGATGASTCAYH 1.3e0000 1.8e-003 -6.31 0.0 187 487 201 410 0.38398 7.5e-006 243 3 M4619_1.02 FOSL1 BGGTGASTCAK 1.2e-003 1.6e-006 -13.37 0.0 236 490 252 404 0.48163 6.4e-009 244 3 M4623_1.02 JUNB NDRTGASTCATNYHY 1.8e-001 2.4e-004 -8.33 0.0 234 486 249 416 0.48148 1.0e-006 242 3 M4629_1.02 NFE2 VRTGACTCAGCANWWYB 4.6e0000 6.2e-003 -5.09 0.0 216 484 193 348 0.44628 2.6e-005 241 3 M4681_1.02 BACH2 TGCTGAGTCA 2.0e0000 2.7e-003 -5.91 0.0 313 491 296 401 0.63747 1.1e-005 245 3 M5292_1.02 ATF4 GKATGAYGCAATM 2.1e-003 2.8e-006 -12.78 0.0 250 488 257 393 0.51230 1.2e-008 243 3 M5293_1.02 ATF7 NKATGACGTCATHN 4.5e-003 6.0e-006 -12.02 0.0 251 487 189 278 0.51540 2.5e-008 243 3 M5302_1.02 BATF3 TGATGACGTCATCA 7.1e-003 9.6e-006 -11.55 0.0 275 487 117 150 0.56468 4.0e-008 243 3 M5323_1.02 CREB3 KGRTGACGTCAYNV 1.3e-004 1.8e-007 -15.54 0.0 285 487 220 291 0.58522 7.3e-010 243 3 M5446_1.02 FOXD4L2 GTAAACA 6.9e-001 9.3e-004 -6.98 0.0 204 494 271 531 0.41296 3.8e-006 246 3 M5460_1.02 FOXL1 RTAAACA 5.1e0000 6.8e-003 -4.99 0.0 192 494 239 499 0.38866 2.8e-005 246 3 M5587_1.02 JDP2 ATGASTCAT 4.9e-004 6.7e-007 -14.22 0.0 180 492 179 342 0.36585 2.7e-009 245 3 M5998_1.02 (CREB5)_(Mus_musculus)_(DBD_1.00) DRTGACGTCATN 1.3e-001 1.8e-004 -8.64 0.0 251 489 212 328 0.51329 7.3e-007 244 3 M6152_1.02 ATF1 VTGACGTCAV 1.6e-002 2.2e-005 -10.72 0.0 285 491 321 459 0.58045 9.0e-008 245 3 M6180_1.02 CREB1 RTGACGTMA 4.1e-001 5.5e-004 -7.50 0.0 276 492 342 517 0.56098 2.3e-006 245 3 M6228_1.02 FOSB CTGACTCAYV 3.3e-002 4.5e-005 -10.02 0.0 243 491 316 520 0.49491 1.8e-007 245 3 M6235_1.02 FOXC1 CYWAAGTAAACAWHG 3.0e0000 4.1e-003 -5.50 0.0 124 486 129 365 0.25514 1.7e-005 242 3 M6333_1.02 MAFG MATGACT 4.6e0000 6.2e-003 -5.08 0.0 222 494 287 534 0.44939 2.5e-005 246 3 M6343_1.02 MEIS1 CDTWAAVCTGTCA 2.0e0000 2.7e-003 -5.92 0.0 100 488 129 443 0.20492 1.1e-005 243 3 M6360_1.02 NFE2L2 VRTGACTCAGCA 8.5e0000 1.1e-002 -4.47 0.0 289 489 374 557 0.59100 4.7e-005 244 3 M6368_1.02 NFIL3 VKVMVTTACRTAAY 8.9e0000 1.2e-002 -4.42 0.0 203 487 188 361 0.41684 5.0e-005 243 ## # 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).