# 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 YYTGACCYCTGACCYC MEME-1 YYTGACCYCTGACCYC 1.0e-008 1.4e-011 -25.00 0.0 145 485 198 418 0.29897 5.7e-014 242 1 RTGACTCAY MEME-3 RTGACTCAY 1.4e-023 1.9e-026 -59.25 0.0 162 492 139 193 0.32927 7.6e-029 245 2 TGACTMA DREME-1 TGACTCA 6.8e-023 9.1e-026 -57.65 0.0 162 494 145 207 0.32794 3.7e-028 246 2 GAKGTCA DREME-2 GAGGTCA 6.5e-014 8.8e-017 -36.97 0.0 118 494 113 216 0.23887 3.6e-019 246 2 AGGTCA DREME-6 AGGTCA 1.6e-015 2.2e-018 -40.67 0.0 117 495 134 267 0.23636 8.8e-021 247 3 M0300_1.02 (ATF2)_(Mus_musculus)_(DBD_1.00) NRTKACGTMA 3.7e-002 5.0e-005 -9.91 0.0 167 491 242 542 0.34012 2.0e-007 245 3 M0718_1.02 FOXK1 NNRTMAACAH 7.9e-002 1.1e-004 -9.14 0.0 151 491 219 536 0.30754 4.4e-007 245 3 M0719_1.02 FOXG1 RTAAACAW 2.4e0000 3.3e-003 -5.73 0.0 179 493 197 425 0.36308 1.3e-005 246 3 M0728_1.02 (FOXJ1)_(Mus_musculus)_(DBD_1.00) NRTAAACAAANN 5.7e0000 7.6e-003 -4.88 0.0 129 489 172 497 0.26380 3.1e-005 244 3 M0736_1.02 (FOXK2)_(Mus_musculus)_(DBD_0.90) RTAAACAA 2.0e-002 2.7e-005 -10.52 0.0 107 493 165 522 0.21704 1.1e-007 246 3 M0756_1.02 (FOXN3)_(Strongylocentrotus_purpuratus)_(DBD_0.44) NNHMACANN 1.1e-001 1.5e-004 -8.79 0.0 140 492 187 481 0.28455 6.2e-007 245 3 M0897_1.02 HOXB13 DTTWAYDRBN 4.9e-001 6.7e-004 -7.31 0.0 179 491 225 483 0.36456 2.7e-006 245 3 M0994_1.02 (SIX4)_(Mus_musculus)_(DBD_1.00) NYKAYMCBN 4.9e-002 6.7e-005 -9.62 0.0 320 492 392 520 0.65041 2.7e-007 245 3 M1007_1.02 (HOXA11)_(Mus_musculus)_(DBD_1.00) TTWAYKDBN 1.9e-003 2.6e-006 -12.85 0.0 174 492 158 308 0.35366 1.1e-008 245 3 M1034_1.02 (DBX2)_(Mus_musculus)_(DBD_0.93) NHVATNA 8.8e0000 1.2e-002 -4.43 0.0 244 494 121 189 0.49393 4.9e-005 246 3 M1432_1.02 NR2E1 NYTGACCTCD 2.9e-014 3.8e-017 -37.80 0.0 211 491 353 572 0.42974 1.6e-019 245 3 M1458_1.02 (RORB)_(Tetraodon_nigroviridis)_(DBD_1.00) NNTGACCTCN 4.0e-012 5.4e-015 -32.85 0.0 247 491 383 565 0.50305 2.2e-017 245 3 M1863_1.02 FOXD1 GTAAACAW 4.0e0000 5.5e-003 -5.21 0.0 161 493 195 467 0.32657 2.2e-005 246 3 M1917_1.02 USF1 GGTCACRTGRB 6.3e-006 8.5e-009 -18.58 0.0 198 490 272 493 0.40408 3.5e-011 244 3 M2065_1.02 ESR2 RGGKCANBSTGACCT 1.0e0001 1.3e-002 -4.31 0.0 126 486 182 543 0.25926 5.6e-005 242 3 M2278_1.02 FOS DVTGASTCATB 1.8e-013 2.4e-016 -35.95 0.0 186 490 277 479 0.37959 1.0e-018 244 3 M2286_1.02 HNF4G TGRMCTTTGNHCYYN 5.5e-001 7.4e-004 -7.21 0.0 328 486 432 566 0.67490 3.1e-006 242 3 M2289_1.02 JUN DDRATGATGTMAT 1.3e-004 1.8e-007 -15.56 0.0 208 488 266 469 0.42623 7.2e-010 243 3 M2292_1.02 JUND DRTGASTCATS 9.7e-012 1.3e-014 -31.97 0.0 206 490 285 465 0.42041 5.3e-017 244 3 M2303_1.02 NR2C2 TGACCTYTGACCYCB 1.0e-002 1.4e-005 -11.19 0.0 326 486 413 532 0.67078 5.7e-008 242 3 M4451_1.02 ATF3 GGTCACGTGRS 1.7e-002 2.3e-005 -10.67 0.0 172 490 217 461 0.35102 9.6e-008 244 3 M4452_1.02 BATF TYYYRDWATGASTCA 1.2e-002 1.6e-005 -11.07 0.0 102 486 157 505 0.20988 6.4e-008 242 3 M4481_1.02 USF2 GGTCACGTGRSSSSV 1.2e0000 1.7e-003 -6.39 0.0 284 486 275 397 0.58436 6.9e-006 242 3 M4511_1.02 RXRA TGACCYYW 2.0e-011 2.7e-014 -31.23 0.0 213 493 356 592 0.43205 1.1e-016 246 3 M4526_1.02 SMARCC1 DSRVDGTGASTCABV 6.7e-008 9.0e-011 -23.13 0.0 160 486 245 505 0.32922 3.7e-013 242 3 M4565_1.02 FOSL2 VDGGATGASTCAYH 6.4e-009 8.6e-012 -25.48 0.0 153 487 222 460 0.31417 3.5e-014 243 3 M4567_1.02 FOXA2 NCWRWGTAAACANNN 4.1e-003 5.5e-006 -12.12 0.0 206 486 281 515 0.42387 2.3e-008 242 3 M4619_1.02 FOSL1 BGGTGASTCAK 2.5e-009 3.3e-012 -26.42 0.0 208 490 277 460 0.42449 1.4e-014 244 3 M4623_1.02 JUNB NDRTGASTCATNYHY 2.1e-010 2.8e-013 -28.91 0.0 208 486 287 470 0.42798 1.1e-015 242 3 M4629_1.02 NFE2 VRTGACTCAGCANWWYB 6.3e-005 8.5e-008 -16.28 0.0 92 484 127 395 0.19008 3.5e-010 241 3 M4680_1.02 BACH1 GTCACGTG 4.4e0000 5.9e-003 -5.13 0.0 197 493 258 528 0.39959 2.4e-005 246 3 M4681_1.02 BACH2 TGCTGAGTCA 3.4e-005 4.6e-008 -16.89 0.0 229 491 287 469 0.46640 1.9e-010 245 3 M4698_1.02 HNF4A BTGRMCTTTGVMCYB 1.8e-001 2.4e-004 -8.33 0.0 202 486 293 568 0.41564 1.0e-006 242 3 M4702_1.02 NR2F2 TGACCTTT 6.5e-008 8.7e-011 -23.17 0.0 229 493 364 595 0.46450 3.5e-013 246 3 M5234_1.02 (SIM1)_(Drosophila_melanogaster)_(DBD_0.89) GGTCACGTAC 6.7e-001 9.0e-004 -7.02 0.0 47 491 64 375 0.09572 3.7e-006 245 3 M5292_1.02 ATF4 GKATGAYGCAATM 1.0e-001 1.3e-004 -8.91 0.0 174 488 201 425 0.35656 5.5e-007 243 3 M5293_1.02 ATF7 NKATGACGTCATHN 4.3e-005 5.7e-008 -16.67 0.0 245 487 193 280 0.50308 2.4e-010 243 3 M5302_1.02 BATF3 TGATGACGTCATCA 1.2e-002 1.6e-005 -11.07 0.0 155 487 77 144 0.31828 6.4e-008 243 3 M5323_1.02 CREB3 KGRTGACGTCAYNV 5.0e-003 6.8e-006 -11.91 0.0 213 487 186 315 0.43737 2.8e-008 243 3 M5349_1.02 DUXA NTRAYYTAATCAN 5.5e-001 7.4e-004 -7.21 0.0 206 488 245 464 0.42213 3.0e-006 243 3 M5446_1.02 FOXD4L2 GTAAACA 1.7e0000 2.3e-003 -6.06 0.0 162 494 223 535 0.32794 9.5e-006 246 3 M5460_1.02 FOXL1 RTAAACA 2.1e-001 2.9e-004 -8.16 0.0 160 494 210 493 0.32389 1.2e-006 246 3 M5480_1.02 GBX1 RSTAATTRGB 9.5e0000 1.3e-002 -4.36 0.0 265 491 285 451 0.53971 5.3e-005 245 3 M5587_1.02 JDP2 ATGASTCAT 1.1e-015 1.5e-018 -41.04 0.0 186 492 261 434 0.37805 6.1e-021 245 3 M5623_1.02 MEOX1 VSTAATTANC 6.0e0000 8.1e-003 -4.81 0.0 151 491 187 473 0.30754 3.3e-005 245 3 M5624_1.02 MEOX2 NSTAATTAWN 4.1e0000 5.5e-003 -5.21 0.0 249 491 296 493 0.50713 2.2e-005 245 3 M5632_1.02 MLX RTCACGTGAT 1.2e-002 1.6e-005 -11.05 0.0 283 491 240 334 0.57637 6.5e-008 245 3 M5689_1.02 NRL DWWNTGCTGAC 1.9e0000 2.5e-003 -5.98 0.0 128 490 200 586 0.26122 1.0e-005 244 3 M5932_1.02 TFEC VTCAYGTGAY 1.3e-001 1.8e-004 -8.64 0.0 211 491 284 530 0.42974 7.2e-007 245 3 M5945_1.02 VAX2 YTAATTAN 3.7e0000 5.0e-003 -5.29 0.0 245 493 288 487 0.49696 2.1e-005 246 3 M5998_1.02 (CREB5)_(Mus_musculus)_(DBD_1.00) DRTGACGTCATN 1.6e-005 2.2e-008 -17.63 0.0 211 489 204 337 0.43149 9.1e-011 244 3 M6114_1.02 FOXA1 WAWGYAAAYA 7.0e0000 9.4e-003 -4.67 0.0 191 491 240 503 0.38900 3.8e-005 245 3 M6152_1.02 ATF1 VTGACGTCAV 1.0e-002 1.4e-005 -11.20 0.0 25 491 57 512 0.05092 5.6e-008 245 3 M6176_1.02 NR2F1 TGACCTTTGVMC 2.6e-008 3.6e-011 -24.06 0.0 253 489 396 595 0.51738 1.5e-013 244 3 M6180_1.02 CREB1 RTGACGTMA 8.0e-006 1.1e-008 -18.35 0.0 148 492 241 557 0.30081 4.4e-011 245 3 M6181_1.02 CREM CRVTGACGTCA 1.3e-002 1.8e-005 -10.95 0.0 140 490 211 537 0.28571 7.2e-008 244 3 M6197_1.02 E4F1 YGTKACGTC 2.5e0000 3.4e-003 -5.68 0.0 230 492 264 467 0.46748 1.4e-005 245 3 M6215_1.02 ESRRB TGACCTTGR 2.8e-008 3.8e-011 -24.00 0.0 136 492 239 569 0.27642 1.5e-013 245 3 M6216_1.02 ESRRG TGACCTTGA 6.6e-005 8.9e-008 -16.23 0.0 124 492 204 548 0.25203 3.6e-010 245 3 M6228_1.02 FOSB CTGACTCAYV 4.5e-007 6.0e-010 -21.23 0.0 207 491 313 550 0.42159 2.5e-012 245 3 M6239_1.02 FOXF2 HWADGTAAACA 8.7e0000 1.2e-002 -4.44 0.0 154 490 188 468 0.31429 4.9e-005 244 3 M6276_1.02 HINFP DMSHHMGCGGACGTTV 4.0e0000 5.4e-003 -5.22 0.0 157 485 138 316 0.32371 2.2e-005 242 3 M6290_1.02 HOXA13 CCAATAAWAHC 1.8e0000 2.4e-003 -6.03 0.0 110 490 151 489 0.22449 9.8e-006 244 3 M6332_1.02 MAF KTGCTGAC 8.2e-003 1.1e-005 -11.41 0.0 107 493 185 594 0.21704 4.5e-008 246 3 M6333_1.02 MAFG MATGACT 2.3e-011 3.1e-014 -31.11 0.0 254 494 393 575 0.51417 1.3e-016 246 3 M6359_1.02 NFE2L1 NATGACD 4.2e-011 5.7e-014 -30.50 0.0 250 494 390 578 0.50607 2.3e-016 246 3 M6360_1.02 NFE2L2 VRTGACTCAGCA 1.4e0000 1.9e-003 -6.29 0.0 75 489 129 580 0.15337 7.6e-006 244 3 M6368_1.02 NFIL3 VKVMRTTACRTAAY 2.4e0000 3.2e-003 -5.74 0.0 165 487 160 358 0.33881 1.3e-005 243 3 M6382_1.02 NR1D1 WYTGACCTAYTTWT 6.1e-001 8.2e-004 -7.11 0.0 99 487 133 453 0.20329 3.4e-006 243 3 M6383_1.02 NR1H2 MGTTGACCTTTGACCTTTA 2.0e-009 2.7e-012 -26.62 0.0 134 482 92 161 0.27801 1.1e-014 240 3 M6384_1.02 NR1H4 AGGTCANTGACCYY 6.1e-006 8.2e-009 -18.62 0.0 277 487 368 520 0.56879 3.4e-011 243 3 M6389_1.02 NR2C1 VTGACCTCYBRSC 1.6e-008 2.1e-011 -24.59 0.0 252 488 370 550 0.51639 8.6e-014 243 3 M6393_1.02 NR4A1 BTGACCTTB 4.9e-004 6.7e-007 -14.22 0.0 210 492 311 566 0.42683 2.7e-009 245 3 M6394_1.02 NR4A2 STGACCTTT 2.2e-004 2.9e-007 -15.05 0.0 210 492 320 580 0.42683 1.2e-009 245 3 M6395_1.02 NR4A3 STGACCTTTG 1.6e-003 2.2e-006 -13.03 0.0 139 491 201 501 0.28310 8.9e-009 245 3 M6397_1.02 NR6A1 TGAMCTTGAMCTT 2.1e-002 2.8e-005 -10.48 0.0 220 488 245 425 0.45082 1.2e-007 243 3 M6411_1.02 PAX8 BTVAYTSRMGYRKR 2.7e-001 3.6e-004 -7.94 0.0 83 487 144 582 0.17043 1.5e-006 243 3 M6415_1.02 PDX1 CTAATTACY 7.3e-001 9.9e-004 -6.92 0.0 318 492 322 430 0.64634 4.0e-006 245 3 M6430_1.02 PPARA TGACCTY 1.8e-012 2.5e-015 -33.63 0.0 140 494 267 595 0.28340 1.0e-017 246 3 M6432_1.02 PPARD TGACCTTTVNCCTR 1.5e0000 2.0e-003 -6.23 0.0 273 487 366 563 0.56057 8.1e-006 243 3 M6433_1.02 PPARG GKKMMCTTTGACCYASWT 1.5e-002 2.0e-005 -10.83 0.0 141 483 230 583 0.29193 8.3e-008 241 3 M6443_1.02 RARA TGACCTB 8.1e-013 1.1e-015 -34.45 0.0 140 494 266 591 0.28340 4.4e-018 246 3 M6445_1.02 RARB BBBBTGACCTS 1.6e-007 2.1e-010 -22.27 0.0 142 490 248 580 0.28980 8.7e-013 244 3 M6446_1.02 RARG BTGACCTBYNGBYGAMCYCC 1.9e-002 2.5e-005 -10.58 0.0 271 481 378 563 0.56341 1.1e-007 240 3 M6454_1.02 RORA TGACCTAVWTWW 1.3e-003 1.8e-006 -13.26 0.0 267 489 317 469 0.54601 7.2e-009 244 3 M6461_1.02 RXRB YSTGACCTSA 8.1e-011 1.1e-013 -29.85 0.0 135 491 253 589 0.27495 4.4e-016 245 3 M6462_1.02 RXRG DTGACCTTTGACC 6.7e-005 9.1e-008 -16.22 0.0 274 488 310 440 0.56148 3.7e-010 243 3 M6472_1.02 SOX15 CWTTGTT 3.1e0000 4.1e-003 -5.49 0.0 130 494 187 542 0.26316 1.7e-005 246 3 M6498_1.02 NR5A1 TGRCCTTGR 2.2e-001 2.9e-004 -8.14 0.0 172 492 259 581 0.34959 1.2e-006 245 3 M6517_1.02 TFE3 RGTCAYGTGV 3.3e-001 4.4e-004 -7.72 0.0 175 491 258 572 0.35642 1.8e-006 245 3 M6518_1.02 TFEB RGTCACGTG 1.6e-001 2.2e-004 -8.41 0.0 300 492 250 341 0.60976 9.1e-007 245 3 M6519_1.02 TGIF1 MWGSTGACACCTSMCA 1.1e0000 1.5e-003 -6.50 0.0 179 485 268 585 0.36907 6.2e-006 242 3 M6521_1.02 THRA STGACCTSAV 9.3e-007 1.2e-009 -20.50 0.0 213 491 336 585 0.43381 5.1e-012 245 3 M6523_1.02 THRB TGACCTSABSTSRSSYC 1.1e-002 1.4e-005 -11.16 0.0 96 484 162 553 0.19835 5.9e-008 241 3 M6532_1.02 VDR TGAMCYC 4.6e-005 6.2e-008 -16.60 0.0 214 494 336 599 0.43320 2.5e-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).