# 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 CYBSHCYYTRACCYCTGACCYC MEME-1 CYBSHCYYTRACCYCTGACCYC 8.5e-017 1.1e-019 -43.63 0.0 183 479 299 503 0.38205 4.7e-022 239 1 GTGAAACCCCGTCTCTACTAAAAATACAAAA MEME-2 GTGAAACCCCGTCTCTACTAAAAATACAAAA 2.5e0000 3.4e-003 -5.69 0.0 176 470 44 70 0.37447 1.4e-005 234 1 GKGTKWGKGTSWGKGTKWGKGT MEME-4 GKGTKWGKGTSWGKGTKWGKGT 2.7e-003 3.6e-006 -12.55 0.0 213 479 109 164 0.44468 1.5e-008 239 1 CCTGRCCAACAT MEME-6 CCTGRCCAACAT 5.7e0000 7.6e-003 -4.88 0.0 277 489 94 126 0.56646 3.1e-005 244 1 RRGGTCAGGGK MEME-7 RRGGTCAGGGK 2.8e-026 3.7e-029 -65.47 0.0 192 490 308 467 0.39184 1.5e-031 244 2 RAGGTCA DREME-1 GAGGTCA 1.6e-021 2.2e-024 -54.49 0.0 196 494 192 266 0.39676 8.8e-027 246 2 GGTCA DREME-2 GGTCA 1.1e-015 1.5e-018 -41.06 0.0 196 496 276 449 0.39516 5.9e-021 247 2 GGATTA DREME-3 GGATTA 6.5e0000 8.7e-003 -4.75 0.0 313 495 122 155 0.63232 3.5e-005 247 2 CRAGACCA DREME-7 CRAGACCA 7.9e0000 1.0e-002 -4.56 0.0 149 493 77 171 0.30223 4.3e-005 246 3 M0300_1.02 (ATF2)_(Mus_musculus)_(DBD_1.00) NRTKACGTMA 7.1e0000 9.5e-003 -4.66 0.0 91 491 134 525 0.18534 3.9e-005 245 3 M1157_1.02 (HOXB9)_(PBM_CONSTRUCTS)_(DBD_1.00) WTTWATKRBN 5.5e0000 7.3e-003 -4.92 0.0 15 491 30 428 0.03055 3.0e-005 245 3 M1432_1.02 NR2E1 NYTGACCTCD 4.4e-011 5.9e-014 -30.47 0.0 203 491 323 550 0.41344 2.4e-016 245 3 M1458_1.02 (RORB)_(Tetraodon_nigroviridis)_(DBD_1.00) NNTGACCTCN 8.9e-016 1.2e-018 -41.28 0.0 195 491 328 550 0.39715 4.8e-021 245 3 M1934_1.02 ESR1 RGGTCAGGGTGACCTKGVNB 9.7e-003 1.3e-005 -11.26 0.0 165 481 235 514 0.34304 5.4e-008 240 3 M2065_1.02 ESR2 RGGKCANBSTGACCT 1.1e-006 1.5e-009 -20.33 0.0 162 486 250 524 0.33333 6.1e-012 242 3 M2286_1.02 HNF4G TGRMCTTTGNHCYYN 5.6e-007 7.5e-010 -21.01 0.0 122 486 214 556 0.25103 3.1e-012 242 3 M2303_1.02 NR2C2 TGACCTYTGACCYCB 3.9e-009 5.2e-012 -25.99 0.0 198 486 299 522 0.40741 2.1e-014 242 3 M4438_1.02 ESRRA RGGTCANKSTGACCY 5.4e0000 7.2e-003 -4.93 0.0 52 486 86 518 0.10700 3.0e-005 242 3 M4511_1.02 RXRA TGACCYYW 3.3e-013 4.3e-016 -35.37 0.0 227 493 373 583 0.46045 1.8e-018 246 3 M4698_1.02 HNF4A BTGRMCTTTGVMCYB 4.3e-005 5.7e-008 -16.68 0.0 150 486 241 553 0.30864 2.4e-010 242 3 M4702_1.02 NR2F2 TGACCTTT 4.2e-008 5.6e-011 -23.61 0.0 119 493 222 590 0.24138 2.3e-013 246 3 M5722_1.02 PKNOX2 TGACACCTGTCA 7.4e0000 9.9e-003 -4.62 0.0 133 489 108 284 0.27198 4.1e-005 244 3 M5903_1.02 TCF7L1 AAAGATCAAAGG 7.9e0000 1.1e-002 -4.55 0.0 49 489 71 438 0.10020 4.4e-005 244 3 M6176_1.02 NR2F1 TGACCTTTGVMC 6.7e-009 8.9e-012 -25.45 0.0 201 489 328 578 0.41104 3.6e-014 244 3 M6215_1.02 ESRRB TGACCTTGR 4.6e-007 6.2e-010 -21.21 0.0 198 492 305 555 0.40244 2.5e-012 245 3 M6216_1.02 ESRRG TGACCTTGA 4.1e-005 5.5e-008 -16.72 0.0 224 492 321 544 0.45528 2.2e-010 245 3 M6290_1.02 HOXA13 CCAATAAWAHC 6.5e-001 8.7e-004 -7.04 0.0 120 490 148 434 0.24490 3.6e-006 244 3 M6306_1.02 INSM1 TGTMAGGGGGCR 2.2e-001 2.9e-004 -8.13 0.0 51 489 78 435 0.10429 1.2e-006 244 3 M6382_1.02 NR1D1 WYTGACCTAYTTWT 8.9e-002 1.2e-004 -9.04 0.0 131 487 167 442 0.26899 4.9e-007 243 3 M6383_1.02 NR1H2 MGTTGACCTTTGACCTTTA 9.2e-016 1.2e-018 -41.25 0.0 176 482 127 179 0.36515 5.1e-021 240 3 M6384_1.02 NR1H4 AGGTCANTGACCYY 2.6e-005 3.4e-008 -17.19 0.0 199 487 285 521 0.40862 1.4e-010 243 3 M6389_1.02 NR2C1 VTGACCTCYBRSC 6.1e-010 8.1e-013 -27.84 0.0 204 488 322 552 0.41803 3.3e-015 243 3 M6391_1.02 NR2E3 TGACTTTTGACTTT 1.4e-002 1.9e-005 -10.87 0.0 139 487 202 512 0.28542 7.8e-008 243 3 M6392_1.02 NR2F6 YYMNNTGAMCTTTGWCCY 4.0e-001 5.4e-004 -7.53 0.0 65 483 115 560 0.13458 2.2e-006 241 3 M6393_1.02 NR4A1 BTGACCTTB 2.8e-006 3.8e-009 -19.40 0.0 76 492 152 578 0.15447 1.5e-011 245 3 M6394_1.02 NR4A2 STGACCTTT 2.0e-007 2.6e-010 -22.06 0.0 120 492 218 578 0.24390 1.1e-012 245 3 M6395_1.02 NR4A3 STGACCTTTG 3.7e-004 5.0e-007 -14.52 0.0 77 491 130 501 0.15682 2.0e-009 245 3 M6397_1.02 NR6A1 TGAMCTTGAMCTT 2.0e-001 2.7e-004 -8.21 0.0 264 488 297 456 0.54098 1.1e-006 243 3 M6430_1.02 PPARA TGACCTY 1.1e-010 1.4e-013 -29.59 0.0 214 494 351 587 0.43320 5.7e-016 246 3 M6432_1.02 PPARD TGACCTTTVNCCTR 1.0e-001 1.3e-004 -8.92 0.0 211 487 304 568 0.43326 5.5e-007 243 3 M6433_1.02 PPARG GKKMMCTTTGACCYASWT 1.5e-009 2.0e-012 -26.92 0.0 123 483 230 572 0.25466 8.4e-015 241 3 M6443_1.02 RARA TGACCTB 2.9e-007 3.9e-010 -21.66 0.0 200 494 318 578 0.40486 1.6e-012 246 3 M6445_1.02 RARB BBBBTGACCTS 1.5e-013 2.0e-016 -36.16 0.0 198 490 330 560 0.40408 8.1e-019 244 3 M6446_1.02 RARG BTGACCTBYNGBYGAMCYCC 1.9e-003 2.5e-006 -12.89 0.0 129 481 213 565 0.26819 1.0e-008 240 3 M6454_1.02 RORA TGACCTAVWTWH 2.0e-001 2.6e-004 -8.24 0.0 141 489 180 458 0.28834 1.1e-006 244 3 M6461_1.02 RXRB YSTGACCTSA 2.9e-006 3.8e-009 -19.38 0.0 127 491 224 582 0.25866 1.6e-011 245 3 M6462_1.02 RXRG DTGACCTTTGACC 2.2e-005 3.0e-008 -17.33 0.0 136 488 187 445 0.27869 1.2e-010 243 3 M6498_1.02 NR5A1 TGRCCTTGR 2.1e-002 2.8e-005 -10.49 0.0 68 492 126 578 0.13821 1.1e-007 245 3 M6518_1.02 TFEB RGTCACGTG 5.4e0000 7.3e-003 -4.92 0.0 376 492 276 323 0.76423 3.0e-005 245 3 M6521_1.02 THRA STGACCTSAV 1.3e-006 1.7e-009 -20.21 0.0 139 491 239 574 0.28310 6.9e-012 245 3 M6523_1.02 THRB TGACCTSABSTSRSSYC 1.2e-003 1.6e-006 -13.35 0.0 148 484 229 541 0.30579 6.6e-009 241 3 M6532_1.02 VDR TGAMCYC 4.7e-012 6.3e-015 -32.70 0.0 140 494 264 592 0.28340 2.6e-017 246 ## # 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).