|  |  |  |  | Comparison to previous 200bp region | Comparison to shuffled sequences | Conservation tests |  | |||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
MatBase matrix family | MatBase family description | Consensus of arbitrarily chosen PWM | Number of predicted sites in 200bp promoter region | Number of 200bp promoters containing > = 1 site | Number of sites expected | Enrichment compared to expected number | Enrichment p-value | Number of sites expected | Enrichment compared to expected number | Enrichment p-value | p-value: whether whole sites are more conserved than local backgrounc | p-vaiue: whether core nucleotides are more conserved than local background | Significance levels of three tests |
Before masking O/E and VTBP sites, default Matlnspector parameters, selected matrices | |||||||||||||
V$NOLF | Neuron-specific-olfactory factor | nncdabTCCCyngrgarbnkgn | 167 | 137 | 24 | 6.96 | 7.4E-28 | 27.4 | 6.1 | <0.0001 | 5.2E-22 | 2.6E-54 | X X X |
O$VTBP | Vertebrate TATA binding protein factor | staTAAAwrnn | 391 | 211 | 494 | 0.79 | 1 | 311 | 1.26 | <0.0001 | 1 | 0.65 | . X . |
V$IKRS | Ikaros zinc finger family | yyTGGGagr | 123 | 104 | 69 | 1.78 | 5.9E-5 | 65.6 | 1.88 | <0.0001 | 2.2E-4 | 4.9E-14 | X X X |
Before masking O/E and VTBP sites, less stringent Matlnspector parameters (opt-0.10), selected matrices | |||||||||||||
V$NOLF | Neuron-specific-olfactory factor | nncdabTCCCyngrgarbnkgn | 653 | 265 | 198 | 3.3 | 9.6E-58 | 239.6 | 2.73 | <0.0001 | 2.7E-64 | 3.4E-130 | X X X |
O$VTBP | Vertebrate TATA binding protein factor | staTAAAwrnn | 2388 | 309 | 2972 | 0.8 | 1 | 2119.1 | 1.13 | <0.0001 | 1 | 0.99 | . X . |
V$IKRS | Ikaros zinc finger family | yyTGGGagr | 963 | 297 | 622 | 1.55 | 5E-18 | 710.3 | 1.36 | <0.0001 | 1.6E-29 | 1.7E-73 | X X X |
After masking O/E and VTBP sites, default Matlnspector parameters, matrices significant in all three tests | |||||||||||||
V$ARID | AT rich interactive domain factor | AATAccvm | 140 | 94 | 89 | 1.57 | 4.6E-4 | 71.9 | 1.95 | <0.0001 | 0.53 | 0.0021 | + X + |
V$ATBF | AT-binding TF | hhwkrttantAATTahh | 101 | 69 | 68 | 1.49 | 0.0068 | 56.3 | 1.8 | <0.0001 | 0.069 | 7.4E-08 | + X X |
V$BCDF | Bicoid-like homeodomain TFs | abnyTAATcmnv | 152 | 119 | 102 | 1.49 | 0.001 | 131.5 | 1.16 | 0.0401 | 4.7E-17 | 4.1E-20 | + + X |
V$BRN5 | Brn-5 POU domain factors | gCATAawttat | 327 | 165 | 282 | 1.16 | 0.037 | 217.5 | 1.5 | <0.0001 | 0.015 | 5.3E-09 | + X X |
V$CART | Cart-1 cartilage homeoprotein 1 | cTAATtrnsynattan | 452 | 183 | 331 | 1.37 | 8.7E-6 | 318.7 | 1.42 | <0.0001 | 2.7E-17 | 2.1E-30 | X X X |
V$DLXF | Distal-less homeodomain TFs | nntAATTan | 274 | 129 | 173 | 1.58 | 1.0E-6 | 141.8 | 1.93 | <0.0001 | 1.9E-20 | 2.7E-35 | X X X |
V$HBOX | Homeobox TFs | raaTTTAattgaa | 510 | 192 | 327 | 1.56 | 1.3E-10 | 317.9 | 1.6 | <0.0001 | 4.3E-17 | 2.7E-30 | X X X |
V$HOMF | Homeodomain TFs | mCTAAttnn | 646 | 214 | 449 | 1.44 | 1.4E-09 | 463.2 | 1.39 | <0.0001 | 8.6E-4 | 1.4E-13 | X X X |
V$HOXF | Paralog hox genes 1-8, clusters A, B, C, D | nnamTAATgrggrwnn | 583 | 204 | 404 | 1.44 | 6.7E-09 | 385.2 | 1.51 | <0.0001 | 2.3E-09 | 9.3E-26 | X X X |
V$LHXF | Lim homeodomain factors | nntwwttAATTaatnn | 557 | 187 | 396 | 1.41 | 1.0E-7 | 350.4 | 1.59 | <0.0001 | 1.8E-08 | 2.8E-28 | X X X |
V$MYOD | Myoblast determining factors | mrgCARCwgswg | 30 | 20 | 13 | 2.31 | 0.0069 | 16.3 | 1.84 | 0.0042 | 0.017 | 0.51 | + + + |
V$NKX1 | NK1 homeobox TFs | wgnrcyAATTrgygsnn | 140 | 75 | 89 | 1.57 | 4.6E-4 | 70.2 | 1.99 | <0.0001 | 1.2E-13 | 9.9E-21 | + X X |
V$NKX6 | NK6 homeobox TFs | TTAAttac | 263 | 151 | 178 | 1.48 | 3.0E-5 | 155.1 | 1.7 | <0.0001 | 1.3E-07 | 6.1E-13 | X X X |
V$PAXH | PAX homeodomain binding sites | aawaATTAnn | 152 | 68 | 95 | 1.6 | 1.7E-4 | 77.5 | 1.96 | <0.0001 | 0.0015 | 2.5E-10 | X X X |
V$PDX1 | Pancreatic and intestinal homeodomain TF | rnTAATtagync | 193 | 96 | 131 | 1.47 | 3.4E-4 | 108.4 | 1.78 | <0.0001 | 1.4E-6 | 8.2E-16 | + X X |
After masking O/E and VTBP sites, less stringent Matlnspector parameters (opt-0.10), matrices significant in all three tests | |||||||||||||
V$AP4R | AP4and related proteins | wgaryCAGCtgyggnc | 121 | 74 | 61 | 1.98 | 5.1E-6 | 99 | 1.22 | 0.0321 | 7.7E-08 | 0.061 | X + X |
V$DICE | Downstream Immunoglobulin Control Element | kgtySTCTccacag | 186 | 134 | 135 | 1.38 | 0.0026 | 138.1 | 1.35 | <0.0001 | 0.0026 | 0.2 | + X + |
V$DLXF | Distal-less homeodomain TFs | nntAATTan | 1252 | 274 | 1149 | 1.09 | 0.019 | 1041.7 | 1.2 | <0.0001 | 0.0004 | 1.3E-18 | + X X |
V$HAND | Twist subfamily of class B bHLH TFs | ccagaTGGCcccccn | 696 | 252 | 537 | 1.3 | 3.3E-6 | 619.8 | 1.12 | 0.0048 | 0.0067 | 0.0019 | X + + |
V$NKX1 | NK1 homeobox TFs | wgnrcyAATTrgygsnn | 783 | 236 | 619 | 1.26 | 6.6E-6 | 634.4 | 1.23 | <0.0001 | 9.9E-12 | 1E-21 | X X X |
V$PAX5 | PAX-5 B-cell-specific activator protein | bcnnnrNKCAnbgnwgnrkrgc | 227 | 139 | 180 | 1.26 | 0.011 | 192.2 | 1.18 | 0.0085 | 0.09 | 0.025 | + + + |
V$PAX6 | PAX-4/PAX-6 paired domain binding sites | GCASbswtgmgtgmn | 664 | 249 | 555 | 1.2 | 9.8E-4 | 617 | 1.08 | 0.0354 | 0.011 | 0.0022 | + + + |
V$PAXH | PAX homeodomain binding sites | aawaATTAnn | 999 | 247 | 889 | 1.12 | 0.0061 | 767.1 | 1.3 | <0.0001 | 4.5E-09 | 2E-20 | + X X |
V$PDX1 | Pancreatic and intestinal homeodomain TF | rnTAATtagync | 1013 | 257 | 828 | 1.22 | 8.9E-6 | 743.9 | 1.36 | <0.0001 | 2.6E-5 | 3.7E-25 | X X X |
V$PTF1 | Pancreas TF 1, heterotrimeric TF | bmcaCCTGyvktkttycccrw | 125 | 95 | 93 | 1.34 | 0.018 | 100.9 | 1.24 | 0.0102 | 0.015 | 0.17 | + + + |
V$SIX3 | Sine oculis homeobox homolog 3 | nnrhnknTAATswcwncnstv | 647 | 254 | 574 | 1.13 | 0.02 | 515.5 | 1.26 | <0.0001 | 1.8E-07 | 6.6E-28 | + X X |