# 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 KGRTGAYGTCAT MEME-3 KGRTGAYGTCAT 2.9e-007 3.8e-010 -21.69 0.0 179 489 162 284 0.36605 1.6e-012 244 1 TGACTCA MEME-4 TGACTCA 3.5e-008 4.7e-011 -23.79 0.0 284 494 187 233 0.57490 1.9e-013 246 1 TTWAWVHAMANWAHAWWANWWA MEME-8 TTWAWVHAMANWAHAWWANWWA 2.6e0000 3.5e-003 -5.66 0.0 81 479 87 334 0.16910 1.5e-005 239 1 ATSACMWCAYMAMWVCMAYBACATCATCA MEME-9 ATSACMWCAYMAMWVCMAYBACATCATCA 8.0e0000 1.1e-002 -4.53 0.0 166 472 16 19 0.35169 4.6e-005 235 2 TGACTCAB DREME-1 TGACTCAB 1.4e-008 1.9e-011 -24.70 0.0 285 493 129 150 0.57809 7.6e-014 246 2 SCGGAAS DREME-2 SCGGAAS 1.1e-004 1.5e-007 -15.73 0.0 234 494 136 197 0.47368 6.0e-010 246 2 TGABGTCA DREME-3 TGATGTCA 8.1e-001 1.1e-003 -6.82 0.0 313 493 105 128 0.63489 4.4e-006 246 2 TTTATGR DREME-4 TTTATGR 9.5e-002 1.3e-004 -8.97 0.0 102 494 51 129 0.20648 5.2e-007 246 3 M0300_1.02 (ATF2)_(Mus_musculus)_(DBD_1.00) NRTKACGTMA 2.5e-008 3.3e-011 -24.14 0.0 175 491 280 549 0.35642 1.3e-013 245 3 M0607_1.02 KDM2B NCGNWNNNN 7.2e0000 9.6e-003 -4.64 0.0 96 492 17 33 0.19512 3.9e-005 245 3 M0608_1.02 MLL NNNRSCGNDN 6.2e0000 8.4e-003 -4.79 0.0 457 491 410 420 0.93075 3.4e-005 245 3 M0887_1.02 HOXA2 NNYRAYBDN 2.8e-001 3.8e-004 -7.87 0.0 164 492 48 81 0.33333 1.6e-006 245 3 M0892_1.02 EMX1 NYTAATKAVB 9.9e-003 1.3e-005 -11.23 0.0 93 491 145 502 0.18941 5.4e-008 245 3 M0896_1.02 VENTX TTAATTAG 2.6e-001 3.5e-004 -7.95 0.0 91 493 124 449 0.18458 1.4e-006 246 3 M0897_1.02 HOXB13 DTTWAYDRBN 2.9e0000 3.9e-003 -5.56 0.0 141 491 194 521 0.28717 1.6e-005 245 3 M0949_1.02 (AC012531.1)_(Mus_musculus)_(DBD_1.00) NTAATDR 7.7e-001 1.0e-003 -6.88 0.0 92 494 123 449 0.18623 4.2e-006 246 3 M1007_1.02 (HOXA11)_(Mus_musculus)_(DBD_1.00) TTWAYKDBN 1.5e-002 2.1e-005 -10.79 0.0 170 492 143 288 0.34553 8.4e-008 245 3 M1027_1.02 (HOXA6)_(Mus_musculus)_(DBD_1.00) WTAATKRBN 2.2e-001 2.9e-004 -8.13 0.0 112 492 162 505 0.22764 1.2e-006 245 3 M1039_1.02 (ENSG00000229544)_(Mus_musculus)_(DBD_1.00) NNTAATDRN 5.3e0000 7.1e-003 -4.94 0.0 86 492 122 493 0.17480 2.9e-005 245 3 M1125_1.02 (NKX1-1)_(Mus_musculus)_(DBD_1.00) NNTAATKRNN 2.4e0000 3.2e-003 -5.76 0.0 85 491 128 518 0.17312 1.3e-005 245 3 M1157_1.02 (HOXB9)_(PBM_CONSTRUCTS)_(DBD_1.00) WTTWATKRBN 2.7e-001 3.6e-004 -7.92 0.0 155 491 218 527 0.31568 1.5e-006 245 3 M1163_1.02 (NKX6-3)_(PBM_CONSTRUCTS)_(DBD_1.00) NWTAATKRN 9.4e0000 1.3e-002 -4.37 0.0 114 492 154 501 0.23171 5.2e-005 245 3 M2267_1.02 CDX2 TTTTATKRCHB 1.5e0000 2.1e-003 -6.18 0.0 150 490 190 476 0.30612 8.5e-006 244 3 M2278_1.02 FOS DVTGASTCATB 3.1e-004 4.2e-007 -14.69 0.0 296 490 329 445 0.60408 1.7e-009 244 3 M2287_1.02 (HOXC9)_(Mus_musculus)_(DBD_0.98) RGCCATAAATCAB 9.4e-001 1.3e-003 -6.68 0.0 126 488 159 451 0.25820 5.2e-006 243 3 M2289_1.02 JUN DDRATGATGTMAT 1.0e-002 1.4e-005 -11.21 0.0 282 488 314 449 0.57787 5.6e-008 243 3 M2292_1.02 JUND DRTGASTCATS 4.2e-007 5.6e-010 -21.31 0.0 130 490 181 429 0.26531 2.3e-012 244 3 M2388_1.02 SREBF2 RTGGGGTGAY 4.3e0000 5.8e-003 -5.15 0.0 215 491 275 522 0.43788 2.4e-005 245 3 M4526_1.02 SMARCC1 DSRVDGTGASTCABV 4.3e-005 5.7e-008 -16.67 0.0 262 486 320 470 0.53909 2.4e-010 242 3 M4565_1.02 FOSL2 VDGGATGASTCAYH 1.9e-005 2.6e-008 -17.47 0.0 273 487 308 433 0.56057 1.1e-010 243 3 M4619_1.02 FOSL1 BGGTGASTCAK 1.3e-006 1.7e-009 -20.17 0.0 212 490 253 424 0.43265 7.1e-012 244 3 M4623_1.02 JUNB NDRTGASTCATNYHY 1.7e-006 2.3e-009 -19.89 0.0 296 486 333 437 0.60905 9.5e-012 242 3 M4629_1.02 NFE2 VRTGACTCAGCANWWYB 1.3e-001 1.8e-004 -8.64 0.0 182 484 188 377 0.37603 7.3e-007 241 3 M4681_1.02 BACH2 TGCTGAGTCA 6.3e-001 8.4e-004 -7.08 0.0 289 491 290 416 0.58859 3.4e-006 245 3 M5234_1.02 (SIM1)_(Drosophila_melanogaster)_(DBD_0.89) GGTCACGTAC 9.3e-002 1.2e-004 -8.99 0.0 379 491 341 392 0.77189 5.1e-007 245 3 M5292_1.02 ATF4 GKATGAYGCAATM 7.3e-002 9.8e-005 -9.23 0.0 232 488 261 440 0.47541 4.0e-007 243 3 M5293_1.02 ATF7 NKATGACGTCATHN 2.4e-005 3.2e-008 -17.25 0.0 179 487 170 311 0.36756 1.3e-010 243 3 M5302_1.02 BATF3 TGATGACGTCATCA 4.1e-005 5.4e-008 -16.73 0.0 171 487 97 164 0.35113 2.2e-010 243 3 M5323_1.02 CREB3 KGRTGACGTCAYNV 2.2e-003 2.9e-006 -12.75 0.0 363 487 281 322 0.74538 1.2e-008 243 3 M5342_1.02 DLX4 NTAATTRB 1.4e0000 1.9e-003 -6.25 0.0 89 493 133 514 0.18053 7.9e-006 246 3 M5349_1.02 DUXA NTRAYYTAATCAN 9.3e0000 1.2e-002 -4.38 0.0 200 488 229 457 0.40984 5.2e-005 243 3 M5377_1.02 ELF4 AACCCGGAAGTR 8.7e0000 1.2e-002 -4.46 0.0 273 489 287 441 0.55828 4.8e-005 244 3 M5388_1.02 EMX2 VYTAATTAVB 3.2e0000 4.3e-003 -5.45 0.0 91 491 122 460 0.18534 1.8e-005 245 3 M5390_1.02 EN1 VBTAATTRSB 7.1e0000 9.6e-003 -4.65 0.0 87 491 127 511 0.17719 3.9e-005 245 3 M5420_1.02 ETV1 ACCGGAAGTD 7.9e0000 1.1e-002 -4.54 0.0 117 491 169 540 0.23829 4.4e-005 245 3 M5421_1.02 ETV2 AACCGGAAATR 1.4e0000 1.8e-003 -6.31 0.0 118 490 166 507 0.24082 7.5e-006 244 3 M5493_1.02 GMEB2 KTRCGTAA 1.1e-001 1.5e-004 -8.83 0.0 361 493 393 475 0.73225 5.9e-007 246 3 M5502_1.02 GSX1 NBTAATKRSN 3.5e0000 4.7e-003 -5.37 0.0 93 491 136 516 0.18941 1.9e-005 245 3 M5518_1.02 HMX1 NNTTAATTGNT 2.7e0000 3.6e-003 -5.62 0.0 70 490 108 510 0.14286 1.5e-005 244 3 M5519_1.02 HMX2 NDTTAAKTGBT 3.0e0000 4.0e-003 -5.53 0.0 70 490 112 534 0.14286 1.6e-005 244 3 M5544_1.02 HOXC10 DTTTWATKDB 1.8e0000 2.4e-003 -6.05 0.0 157 491 212 517 0.31976 9.6e-006 245 3 M5547_1.02 HOXC11 DGTCRTWAAAH 2.6e-001 3.5e-004 -7.95 0.0 92 490 131 474 0.18776 1.4e-006 244 3 M5555_1.02 HOXD11 RTCGTAAAAH 3.1e-002 4.1e-005 -10.10 0.0 93 491 132 456 0.18941 1.7e-007 245 3 M5587_1.02 JDP2 ATGASTCAT 3.2e-007 4.3e-010 -21.56 0.0 214 492 248 408 0.43496 1.8e-012 245 3 M5945_1.02 VAX2 YTAATTAN 1.6e0000 2.1e-003 -6.15 0.0 91 493 133 504 0.18458 8.7e-006 246 3 M5998_1.02 (CREB5)_(Mus_musculus)_(DBD_1.00) DRTGACGTCATN 1.7e-008 2.2e-011 -24.53 0.0 171 489 195 361 0.34969 9.1e-014 244 3 M6152_1.02 ATF1 VTGACGTCAV 6.2e-002 8.2e-005 -9.40 0.0 255 491 306 484 0.51935 3.4e-007 245 3 M6167_1.02 CDX1 HCATAAAD 3.6e-001 4.8e-004 -7.65 0.0 109 493 170 555 0.22110 1.9e-006 246 3 M6180_1.02 CREB1 RTGACGTMA 9.3e-003 1.2e-005 -11.29 0.0 238 492 329 551 0.48374 5.1e-008 245 3 M6181_1.02 CREM CRVTGACGTCA 2.4e-003 3.3e-006 -12.63 0.0 236 490 314 519 0.48163 1.3e-008 244 3 M6186_1.02 DBP BVTTRCATAAB 2.0e0000 2.7e-003 -5.90 0.0 170 490 221 503 0.34694 1.1e-005 244 3 M6197_1.02 E4F1 YGTKACGTC 4.8e-003 6.5e-006 -11.95 0.0 300 492 352 483 0.60976 2.6e-008 245 3 M6224_1.02 ETV7 KCMHCAGGAAGTRACDY 3.1e-002 4.2e-005 -10.08 0.0 324 484 348 446 0.66942 1.7e-007 241 3 M6228_1.02 FOSB CTGACTCAYV 4.8e-003 6.4e-006 -11.96 0.0 125 491 195 539 0.25458 2.6e-008 245 3 M6245_1.02 FOXO1 AAAWWVWAAACAAVHH 5.6e0000 7.5e-003 -4.90 0.0 73 485 111 506 0.15052 3.1e-005 242 3 M6256_1.02 GATA4 RSWGATAAV 2.2e-001 2.9e-004 -8.13 0.0 156 492 235 571 0.31707 1.2e-006 245 3 M6258_1.02 GATA6 NWGATAA 3.7e-001 5.0e-004 -7.60 0.0 160 494 221 526 0.32389 2.0e-006 246 3 M6276_1.02 HINFP DMSHHMGCGGACGTTV 7.3e0000 9.8e-003 -4.63 0.0 291 485 246 350 0.60000 4.1e-005 242 3 M6277_1.02 HLF SKRTTACRYAAYC 3.2e0000 4.3e-003 -5.44 0.0 248 488 267 440 0.50820 1.8e-005 243 3 M6297_1.02 HOXB7 MATYAATCAA 8.7e0000 1.2e-002 -4.46 0.0 143 491 154 402 0.29124 4.8e-005 245 3 M6333_1.02 MAFG MATGACT 5.7e-006 7.6e-009 -18.69 0.0 120 494 209 569 0.24291 3.1e-011 246 3 M6359_1.02 NFE2L1 NATGACD 3.0e-005 4.1e-008 -17.01 0.0 246 494 364 579 0.49798 1.7e-010 246 3 M6368_1.02 NFIL3 VKVMRTTACRTAAY 2.2e-004 3.0e-007 -15.03 0.0 189 487 213 397 0.38809 1.2e-009 243 3 M6380_1.02 NOBOX HTAATTRSY 1.7e0000 2.3e-003 -6.09 0.0 84 492 119 478 0.17073 9.2e-006 245 3 M6413_1.02 PBX2 VMATCAATCAMWTYM 4.6e0000 6.1e-003 -5.10 0.0 132 486 184 520 0.27160 2.5e-005 242 3 M6415_1.02 PDX1 CTAATTACY 2.5e0000 3.3e-003 -5.70 0.0 88 492 117 449 0.17886 1.4e-005 245 3 M6419_1.02 PKNOX1 MATCARTCAABYB 8.7e0000 1.2e-002 -4.46 0.0 228 488 288 520 0.46721 4.8e-005 243 3 M6510_1.02 TEF TGTTTATRTAAMTK 1.1e0000 1.5e-003 -6.53 0.0 293 487 349 501 0.60164 6.0e-006 243 ## # 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).