# 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 DGCTTTCYAGGAAW MEME-1 DGCTTTCYAGGAAW 6.9e-186 9.4e-189 -432.95 0.0 85 487 426 582 0.17454 3.9e-191 243 2 TCYWRGAA DREME-1 TCYWRGAA 1.2e-111 1.6e-114 -262.02 0.0 79 493 250 350 0.16024 6.5e-117 246 2 CTVGAAA DREME-2 CTRGAAA 7.8e-060 1.1e-062 -142.71 0.0 84 494 182 297 0.17004 4.3e-065 246 2 RTAAACA DREME-3 RTAAACA 3.8e-005 5.2e-008 -16.77 0.0 212 494 129 198 0.42915 2.1e-010 246 2 MTGAGTCA DREME-4 MTGAGTCA 6.6e-003 8.9e-006 -11.63 0.0 177 493 78 131 0.35903 3.6e-008 246 2 CRAGGAA DREME-5 CRAGGAA 1.0e-002 1.4e-005 -11.18 0.0 92 494 50 128 0.18623 5.7e-008 246 3 M0718_1.02 FOXK1 DNRTMAACAH 8.4e-002 1.1e-004 -9.08 0.0 167 491 254 578 0.34012 4.7e-007 245 3 M0719_1.02 FOXG1 RTAAACAW 1.8e-003 2.4e-006 -12.93 0.0 125 493 193 529 0.25355 9.8e-009 246 3 M0728_1.02 (FOXJ1)_(Mus_musculus)_(DBD_1.00) NRTAAACAAANN 9.4e0000 1.3e-002 -4.37 0.0 231 489 314 566 0.47239 5.2e-005 244 3 M0736_1.02 (FOXK2)_(Mus_musculus)_(DBD_0.90) RTAAACAA 2.0e0000 2.6e-003 -5.93 0.0 197 493 279 571 0.39959 1.1e-005 246 3 M0737_1.02 (FOXB2)_(Mus_musculus)_(DBD_0.94) WRWGTAAAYA 1.0e-001 1.3e-004 -8.91 0.0 201 491 292 571 0.40937 5.5e-007 245 3 M0747_1.02 (FOXL2)_(Mus_musculus)_(DBD_0.70) WNNRTAAAYA 3.2e0000 4.3e-003 -5.46 0.0 129 491 196 572 0.26273 1.7e-005 245 3 M0756_1.02 (FOXN3)_(Strongylocentrotus_purpuratus)_(DBD_0.44) NNHMACANN 9.4e0000 1.3e-002 -4.37 0.0 152 492 207 531 0.30894 5.2e-005 245 3 M0897_1.02 HOXB13 DTTWAYDRBN 3.6e-001 4.9e-004 -7.63 0.0 173 491 246 548 0.35234 2.0e-006 245 3 M1157_1.02 (HOXB9)_(PBM_CONSTRUCTS)_(DBD_1.00) WTTWATKRBN 6.2e-003 8.4e-006 -11.69 0.0 173 491 253 543 0.35234 3.4e-008 245 3 M1163_1.02 (NKX6-3)_(PBM_CONSTRUCTS)_(DBD_1.00) NWTAATKRN 3.2e-001 4.3e-004 -7.76 0.0 176 492 236 515 0.35772 1.7e-006 245 3 M1583_1.02 (BBX)_(Mus_musculus)_(DBD_0.99) TTCATTGA 5.2e-006 7.1e-009 -18.77 0.0 51 493 98 472 0.10345 2.9e-011 246 3 M1863_1.02 FOXD1 GTAAACAW 7.9e0000 1.1e-002 -4.54 0.0 193 493 253 530 0.39148 4.3e-005 246 3 M1928_1.02 NFKB1 KGGRMTTTCCM 1.9e0000 2.6e-003 -5.94 0.0 36 490 67 528 0.07347 1.1e-005 244 3 M1955_1.02 STAT1 TTTCYRGGAAA 2.9e-101 4.0e-104 -238.09 0.0 68 490 303 575 0.13878 1.6e-106 244 3 M2385_1.02 FOXP2 RWGTAAACAVR 2.8e0000 3.7e-003 -5.59 0.0 166 490 235 553 0.33878 1.5e-005 244 3 M4444_1.02 RELA DGGGRMTTTCCMVN 1.3e0000 1.8e-003 -6.34 0.0 33 487 60 488 0.06776 7.2e-006 243 3 M4478_1.02 STAT3 SHBVTSAYTTCYRGKAAATR 8.8e-043 1.2e-045 -103.45 0.0 61 481 205 551 0.12682 4.9e-048 240 3 M4567_1.02 FOXA2 NMWRWGTAAACANNN 3.4e0000 4.6e-003 -5.37 0.0 268 486 365 572 0.55144 1.9e-005 242 3 M5292_1.02 ATF4 RKATGAYGCAATM 2.1e-001 2.9e-004 -8.15 0.0 136 488 172 448 0.27869 1.2e-006 243 3 M5303_1.02 BCL6B TGCTTTCTAGGAATTCM 1.7e-106 2.3e-109 -250.15 0.0 72 484 223 312 0.14876 9.5e-112 241 3 M5446_1.02 FOXD4L2 RTAAACA 1.2e-005 1.6e-008 -17.94 0.0 168 494 273 581 0.34008 6.6e-011 246 3 M5460_1.02 FOXL1 RTAAACA 1.2e-005 1.6e-008 -17.95 0.0 168 494 268 569 0.34008 6.5e-011 246 3 M5547_1.02 HOXC11 DGTCRTWAAAH 4.4e0000 6.0e-003 -5.12 0.0 116 490 162 512 0.23673 2.4e-005 244 3 M5567_1.02 HSF4 GAANVTTCTAGAA 1.5e0000 2.1e-003 -6.19 0.0 58 488 91 486 0.11885 8.5e-006 243 3 M5568_1.02 HSFY2 TTCGAAHVRTTCGAA 2.3e-001 3.1e-004 -8.07 0.0 56 486 78 393 0.11523 1.3e-006 242 3 M5587_1.02 JDP2 ATGASTCAT 4.7e-001 6.3e-004 -7.37 0.0 174 492 205 446 0.35366 2.6e-006 245 3 M5624_1.02 MEOX2 DSTAATTAWN 4.5e-002 6.1e-005 -9.71 0.0 173 491 252 551 0.35234 2.5e-007 245 3 M5981_1.02 ZSCAN4 TTTTCAGKGTGTGCA 5.0e0000 6.8e-003 -4.99 0.0 256 486 203 317 0.52675 2.8e-005 242 3 M6114_1.02 FOXA1 WAWGYAAAYA 3.6e-001 4.8e-004 -7.64 0.0 123 491 191 563 0.25051 2.0e-006 245 3 M6159_1.02 BCL6 TTCCWRGAAWGYHHWH 4.0e-123 5.4e-126 -288.43 0.0 73 485 346 596 0.15052 2.3e-128 242 3 M6186_1.02 DBP KVTTRCATAAB 9.3e0000 1.3e-002 -4.37 0.0 388 490 469 547 0.79184 5.2e-005 244 3 M6226_1.02 FEV CAGGAARTDA 1.0e0000 1.4e-003 -6.57 0.0 107 491 173 582 0.21792 5.7e-006 245 3 M6235_1.02 FOXC1 CYWAAGTAAACAWHG 3.2e0000 4.4e-003 -5.44 0.0 130 486 171 483 0.26749 1.8e-005 242 3 M6247_1.02 FOXO4 MRTAAACAA 2.1e0000 2.8e-003 -5.89 0.0 128 492 193 567 0.26016 1.1e-005 245 3 M6277_1.02 HLF SKRTTACRYAAYH 2.9e0000 3.9e-003 -5.55 0.0 240 488 262 442 0.49180 1.6e-005 243 3 M6287_1.02 HSF2 VGAABRTTCTAGAA 1.7e-005 2.3e-008 -17.59 0.0 59 487 125 578 0.12115 9.4e-011 243 3 M6290_1.02 HOXA13 CCAATAAWAHC 6.1e0000 8.3e-003 -4.79 0.0 146 490 209 553 0.29796 3.4e-005 244 3 M6302_1.02 HOXD13 TCYCTAATAAA 6.3e0000 8.5e-003 -4.77 0.0 8 490 24 571 0.01633 3.5e-005 244 3 M6333_1.02 MAFG MATGACT 1.4e-003 1.9e-006 -13.19 0.0 172 494 269 581 0.34818 7.6e-009 246 3 M6359_1.02 NFE2L1 NATGACD 3.2e-001 4.4e-004 -7.73 0.0 172 494 260 589 0.34818 1.8e-006 246 3 M6363_1.02 NFATC2 RWTTTTCCA 1.3e-004 1.8e-007 -15.55 0.0 54 492 116 594 0.10976 7.2e-010 245 3 M6364_1.02 NFATC3 RDTTTTCCA 5.2e-002 7.0e-005 -9.57 0.0 50 492 101 593 0.10163 2.8e-007 245 3 M6365_1.02 NFATC4 WADTTTTCCH 2.0e-003 2.7e-006 -12.83 0.0 55 491 113 592 0.11202 1.1e-008 245 3 M6415_1.02 PDX1 CTAATTACY 5.3e0000 7.1e-003 -4.94 0.0 172 492 207 470 0.34959 2.9e-005 245 3 M6491_1.02 STAT5A YTTCYVRGAAWT 1.1e-115 1.5e-118 -271.28 0.0 69 489 326 589 0.14110 6.3e-121 244 3 M6492_1.02 STAT5B DTTTCYDGGAATT 1.4e-097 1.9e-100 -229.61 0.0 68 488 294 560 0.13934 7.9e-103 243 3 M6496_1.02 STAT4 TTTCCMAGAAAAV 1.6e-046 2.2e-049 -112.04 0.0 64 488 224 589 0.13115 9.0e-052 243 3 M6497_1.02 STAT6 TTCYYHGGAAWYY 1.8e-038 2.5e-041 -93.50 0.0 66 488 213 585 0.13525 1.0e-043 243 ## # 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).