# 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 RGRBNRRGGTCAGRGGTCAGGGKBMVGGGS MEME-1 RGRBNRRGGTCAGRGGTCAGGGKBMVGGGS 1.5e-007 2.1e-010 -22.30 0.0 143 471 193 409 0.30361 8.8e-013 235 1 GRGGTCAGRGG MEME-4 GRGGTCAGRGG 2.4e-017 3.2e-020 -44.89 0.0 184 490 217 341 0.37551 1.3e-022 244 1 ACCCTGACCCNDAMCC MEME-7 ACCCTGACCCNDAMCC 2.3e0000 3.1e-003 -5.77 0.0 239 485 68 95 0.49278 1.3e-005 242 2 GAGGTYA DREME-1 GAGGTCA 9.4e-015 1.3e-017 -38.91 0.0 136 494 113 191 0.27530 5.1e-020 246 2 AAGGTCR DREME-2 AAGGTCA 1.3e-004 1.8e-007 -15.55 0.0 124 494 60 117 0.25101 7.2e-010 246 2 TGACCCYW DREME-4 TGACCCYW 8.2e-006 1.1e-008 -18.33 0.0 217 493 100 140 0.44016 4.4e-011 246 3 M1432_1.02 NR2E1 NYTGACCTCD 5.4e-014 7.2e-017 -37.17 0.0 187 491 318 560 0.38086 2.9e-019 245 3 M1458_1.02 (RORB)_(Tetraodon_nigroviridis)_(DBD_1.00) NNTGACCTCN 1.2e-022 1.6e-025 -57.07 0.0 187 491 340 557 0.38086 6.7e-028 245 3 M2286_1.02 HNF4G TGRMCTTTGNHCYYN 5.3e-006 7.1e-009 -18.76 0.0 278 486 391 553 0.57202 3.0e-011 242 3 M2303_1.02 NR2C2 TGACCTYTGACCYCB 3.7e-009 5.0e-012 -26.02 0.0 120 486 216 549 0.24691 2.1e-014 242 3 M4511_1.02 RXRA TGACCYYW 4.5e-013 6.1e-016 -35.04 0.0 189 493 329 586 0.38337 2.5e-018 246 3 M4698_1.02 HNF4A BTGRMCTTTGVMCYB 3.2e-004 4.3e-007 -14.67 0.0 112 486 188 550 0.23045 1.8e-009 242 3 M4702_1.02 NR2F2 TGACCTTT 1.7e-009 2.3e-012 -26.81 0.0 189 493 319 591 0.38337 9.2e-015 246 3 M5323_1.02 CREB3 KGRTGACGTCAYNV 3.5e0000 4.6e-003 -5.37 0.0 409 487 258 279 0.83984 1.9e-005 243 3 M6152_1.02 ATF1 VTGACGTCAV 7.3e0000 9.8e-003 -4.63 0.0 383 491 426 501 0.78004 4.0e-005 245 3 M6176_1.02 NR2F1 TGACCTTTGVMC 2.6e-006 3.5e-009 -19.47 0.0 213 489 336 586 0.43558 1.4e-011 244 3 M6180_1.02 CREB1 RTGACGTMA 7.9e0000 1.1e-002 -4.55 0.0 188 492 248 532 0.38211 4.3e-005 245 3 M6181_1.02 CREM CRVTGACGTCA 1.2e-001 1.5e-004 -8.77 0.0 286 490 346 502 0.58367 6.3e-007 244 3 M6197_1.02 E4F1 YGTKACGTC 3.0e0000 4.0e-003 -5.53 0.0 276 492 308 470 0.56098 1.6e-005 245 3 M6215_1.02 ESRRB TGACCTTGR 9.0e-005 1.2e-007 -15.93 0.0 196 492 293 555 0.39837 4.9e-010 245 3 M6216_1.02 ESRRG TGACCTTGA 5.8e-002 7.7e-005 -9.47 0.0 156 492 225 536 0.31707 3.2e-007 245 3 M6276_1.02 HINFP DMSNHMGCGGACGTTV 1.2e0000 1.7e-003 -6.41 0.0 215 485 207 371 0.44330 6.8e-006 242 3 M6306_1.02 INSM1 TGTMAGGGGGCR 1.8e-001 2.4e-004 -8.33 0.0 239 489 280 467 0.48875 9.9e-007 244 3 M6383_1.02 NR1H2 MGTTGACCTTTGACCTTTA 2.8e-013 3.7e-016 -35.54 0.0 194 482 139 194 0.40249 1.5e-018 240 3 M6384_1.02 NR1H4 AGGTCANTGACCYY 3.8e-007 5.1e-010 -21.40 0.0 191 487 283 520 0.39220 2.1e-012 243 3 M6389_1.02 NR2C1 VTGACCTCYBRSC 8.2e-010 1.1e-012 -27.54 0.0 212 488 332 554 0.43443 4.5e-015 243 3 M6393_1.02 NR4A1 STGACCTTB 3.9e-006 5.3e-009 -19.06 0.0 200 492 306 561 0.40650 2.2e-011 245 3 M6394_1.02 NR4A2 STGACCTTT 4.8e-013 6.4e-016 -34.99 0.0 200 492 335 571 0.40650 2.6e-018 245 3 M6395_1.02 NR4A3 STGACCTTTG 2.4e-008 3.3e-011 -24.15 0.0 175 491 263 510 0.35642 1.3e-013 245 3 M6397_1.02 NR6A1 TGAMCTTGAMCTT 3.6e-001 4.8e-004 -7.65 0.0 130 488 156 420 0.26639 2.0e-006 243 3 M6430_1.02 PPARA TGACCTY 3.4e-015 4.6e-018 -39.92 0.0 156 494 294 588 0.31579 1.9e-020 246 3 M6432_1.02 PPARD TGACCTTTVNCCTR 9.5e-004 1.3e-006 -13.57 0.0 151 487 243 572 0.31006 5.3e-009 243 3 M6433_1.02 PPARG GKGMMCTTTGACCYASWT 2.6e-004 3.5e-007 -14.86 0.0 115 483 202 579 0.23810 1.5e-009 241 3 M6443_1.02 RARA TGACCTB 7.5e-008 1.0e-010 -23.03 0.0 188 494 309 586 0.38057 4.1e-013 246 3 M6445_1.02 RARB BBBBTGACCTS 5.6e-013 7.5e-016 -34.82 0.0 184 490 321 580 0.37551 3.1e-018 244 3 M6446_1.02 RARG BTGACCTBYNGBYGAMCYCC 3.5e-005 4.7e-008 -16.88 0.0 125 481 216 569 0.25988 1.9e-010 240 3 M6454_1.02 RORA TGACCTAVWTWH 1.3e-002 1.8e-005 -10.95 0.0 141 489 174 427 0.28834 7.2e-008 244 3 M6461_1.02 RXRB YSTGACCTSA 1.1e-007 1.5e-010 -22.63 0.0 191 491 316 591 0.38900 6.1e-013 245 3 M6462_1.02 RXRG DTGACCTTTGACC 5.6e-006 7.5e-009 -18.70 0.0 100 488 149 438 0.20492 3.1e-011 243 3 M6521_1.02 THRA STGACCTSAV 8.2e-007 1.1e-009 -20.63 0.0 137 491 238 578 0.27902 4.5e-012 245 3 M6523_1.02 THRB TGACCTSABSTSRSSYC 1.3e-002 1.7e-005 -10.96 0.0 226 484 319 550 0.46694 7.2e-008 241 3 M6532_1.02 VDR TGAMCYC 5.2e-009 6.9e-012 -25.69 0.0 142 494 257 593 0.28745 2.8e-014 246 ## # 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).