# 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 GRGGTCAGRGGTCARV MEME-2 GRGGTCAGRGGTCARV 4.9e-004 6.5e-007 -14.24 0.0 155 485 186 403 0.31959 2.7e-009 242 1 ACACACRCACACACACRCACAC MEME-6 ACACACRCACACACACRCACAC 8.0e0000 1.1e-002 -4.54 0.0 165 479 27 42 0.34447 4.5e-005 239 2 GWGGTCA DREME-1 GAGGTCA 7.9e-010 1.1e-012 -27.58 0.0 164 494 99 154 0.33198 4.3e-015 246 2 TTTATKR DREME-2 TTTATKR 4.9e0000 6.6e-003 -5.02 0.0 120 494 54 135 0.24291 2.7e-005 246 2 GGTSAC DREME-4 GGTSAC 7.7e-008 1.0e-010 -23.00 0.0 257 495 221 307 0.51919 4.2e-013 247 3 M1432_1.02 NR2E1 NYTGACCTCD 2.7e-010 3.6e-013 -28.67 0.0 135 491 240 554 0.27495 1.5e-015 245 3 M1458_1.02 (RORB)_(Tetraodon_nigroviridis)_(DBD_1.00) NNTGACCTCN 1.7e-013 2.2e-016 -36.04 0.0 135 491 251 559 0.27495 9.1e-019 245 3 M2286_1.02 HNF4G TGRMCTTTGNHCYYN 4.3e-002 5.7e-005 -9.76 0.0 224 486 314 552 0.46091 2.4e-007 242 3 M2303_1.02 NR2C2 TGACCTYTGACCYCB 5.6e-005 7.5e-008 -16.41 0.0 242 486 342 542 0.49794 3.1e-010 242 3 M4451_1.02 ATF3 GGTCACGTGRS 7.5e0000 1.0e-002 -4.59 0.0 332 490 336 439 0.67755 4.2e-005 244 3 M4511_1.02 RXRA TGACCYYW 9.2e-008 1.2e-010 -22.81 0.0 189 493 311 588 0.38337 5.0e-013 246 3 M4698_1.02 HNF4A BTGRMCTTTGVMCYB 2.9e-001 3.9e-004 -7.86 0.0 144 486 212 541 0.29630 1.6e-006 242 3 M4702_1.02 NR2F2 TGACCTTT 1.0e-006 1.4e-009 -20.42 0.0 189 493 309 591 0.38337 5.5e-012 246 3 M5965_1.02 ZIC4 DCDCMGCGGGGGGYC 1.1e0000 1.4e-003 -6.54 0.0 164 486 236 550 0.33745 6.0e-006 242 3 M6176_1.02 NR2F1 TGACCTTTGVMC 3.6e-004 4.9e-007 -14.54 0.0 173 489 275 581 0.35378 2.0e-009 244 3 M6180_1.02 CREB1 RTGACGTMA 2.7e0000 3.6e-003 -5.64 0.0 174 492 239 540 0.35366 1.5e-005 245 3 M6181_1.02 CREM CRVTGACGTCA 3.0e0000 4.0e-003 -5.51 0.0 286 490 333 493 0.58367 1.7e-005 244 3 M6215_1.02 ESRRB TGACCTTGR 1.5e-002 2.0e-005 -10.80 0.0 230 492 318 549 0.46748 8.3e-008 245 3 M6216_1.02 ESRRG TGACCTTGA 8.5e0000 1.1e-002 -4.48 0.0 150 492 207 537 0.30488 4.7e-005 245 3 M6276_1.02 HINFP DMSNHMGCGGACGTTV 3.4e-002 4.6e-005 -10.00 0.0 297 485 287 390 0.61237 1.9e-007 242 3 M6383_1.02 NR1H2 MGTTGACCTTTGACCTTTA 5.3e-007 7.2e-010 -21.06 0.0 226 482 103 135 0.46888 3.0e-012 240 3 M6384_1.02 NR1H4 AGGTCANTGACCYY 4.6e-002 6.2e-005 -9.70 0.0 165 487 227 506 0.33881 2.5e-007 243 3 M6389_1.02 NR2C1 VTGACCTCYBRSC 9.1e-009 1.2e-011 -25.13 0.0 252 488 369 548 0.51639 5.0e-014 243 3 M6393_1.02 NR4A1 STGACCTTB 9.7e-006 1.3e-008 -18.16 0.0 274 492 382 552 0.55691 5.3e-011 245 3 M6394_1.02 NR4A2 STGACCTTT 1.2e-011 1.5e-014 -31.80 0.0 272 492 415 575 0.55285 6.3e-017 245 3 M6395_1.02 NR4A3 STGACCTTTG 3.4e-006 4.5e-009 -19.22 0.0 273 491 361 517 0.55601 1.8e-011 245 3 M6430_1.02 PPARA TGACCTY 3.9e-010 5.2e-013 -28.29 0.0 148 494 268 591 0.29960 2.1e-015 246 3 M6432_1.02 PPARD TGACCTTTVNCCTR 1.5e-002 2.0e-005 -10.80 0.0 155 487 243 574 0.31828 8.4e-008 243 3 M6433_1.02 PPARG GKGMMCTTTGACCYASWT 2.3e0000 3.1e-003 -5.77 0.0 283 483 389 579 0.58592 1.3e-005 241 3 M6443_1.02 RARA TGACCTB 4.2e-004 5.6e-007 -14.40 0.0 188 494 296 592 0.38057 2.3e-009 246 3 M6445_1.02 RARB BBBBTGACCTS 4.4e-008 5.9e-011 -23.55 0.0 184 490 305 582 0.37551 2.4e-013 244 3 M6446_1.02 RARG BTGACCTBYNGBYGAMCYCC 4.7e-004 6.3e-007 -14.27 0.0 205 481 310 565 0.42620 2.6e-009 240 3 M6461_1.02 RXRB YSTGACCTSA 1.0e-006 1.3e-009 -20.43 0.0 277 491 413 589 0.56415 5.5e-012 245 3 M6462_1.02 RXRG DTGACCTTTGACC 8.6e-004 1.2e-006 -13.67 0.0 294 488 317 431 0.60246 4.7e-009 243 3 M6521_1.02 THRA STGACCTSAV 7.8e-007 1.0e-009 -20.69 0.0 235 491 363 585 0.47862 4.2e-012 245 3 M6523_1.02 THRB TGACCTSABSTSRSSYC 1.3e-002 1.7e-005 -10.96 0.0 188 484 275 550 0.38843 7.2e-008 241 3 M6532_1.02 VDR TGAMCYC 6.6e-005 8.8e-008 -16.24 0.0 136 494 234 595 0.27530 3.6e-010 246 ## # 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).