Table 1 Twenty five binding motifs whose scores pass T1. Those that pass FDR of Q = 0.20 on at least one major Alu subfamily sequence are in bold. The consensus sites of the PSSMs (from the IUPAC convention [33]) is in the second column and the target sequences with the highest scores among all the major Alu consensus sequences – in the third, with nucleotides that agree with the consensus denoted by capital letters. The fourth column contains the locations of the putative target sites on the Alu sequences of the subfamily with the highest score (in case the same sequence appears on several Alu elements, we choose the one with the highest number of copies in the 5 kb upstream regions). Two Alu subsequences serve as putative target sites of several TFs (designated by*, and **). The fifth column contains the p-values (see text and methods) and the number of subfamilies on which the BSs of the third column resides is listed in column 6.
BM name | Consensus | Binding site | location | p-val | n. fam |
|---|---|---|---|---|---|
V$OTX2.01 | NNGGATTAANNN | TGGGATTAcAGG | AluSx (-22:-33)* | 4.00E-03 | 8 |
V$GSC.01 | ANGRGATTASMN | cTGGGATTACAG | AluSx (-23:-34)* | 2.60E-03 | 8 |
V$GFI1.01 | NNAAATCNNAGNN | TGtAATCCCAGCA | AluSx (24:36)* | 2.00E-03 | 8 |
V$PITX2_Q2 | WNTAATCCCAR | TGTAATCCCAG | AluSx (24:34)* | 1.00E-05 | 8 |
V$LUN1_01 | TCCCAGCTACTTTGGGA | TCCCAGCactTTgGGa | AluSx (29:45) | 1.00E-05 | 8 |
V$LYF1.01 | TTTGGGARR | TTTGGGAGG | AluSx (38:46) | 1.70E-03 | 8 |
V$LXRE.01 | NGNTYACTNNMGKTCA | GGATCACcTGAGGTCA | AluSx (58:73) | 1.00E-04 | 2 |
V$SREBP.03 | NATCACGTGAN | GATCACcTGAG | AluSx (59:69) | 1.60E-03 | 3 |
V$RORA1.01 | NNWWNNAGGTCAN | ATcACGAGGTCAA | AluSc (60:72) | 8.50E-03 | 1 |
V$NKX25.01 | TYAAGTG | TCAAGTG | AluJb (-62:-68) | 1.00E-05 | 1 |
V$HNF4.02 | NNGGNCNAAAGNTCN | GAGGTCAAgAGATCG | AluSc (65:79) | 6.60E-03 | 1 |
V$ER.02 | NNAGGTCANNGTGACCT | GTtGGTCAGGcTGgtCT | AluSp (-82:-98) | 4.90E-03 | 1 |
V$CHREBP _MLX_01 | CAYGNGNNANNSNNGTG | CACGGtGAAACCCCGTc | AluY (96:112) | 6.50E-03 | 1 |
V$AARE.01 | RTTKCATCA | GTTTCAcCA | AluSx (-100:-108) | 3.60E-03 | 5 |
V$MEF2.04 | TGTTACTAAAAATAGAAM | ctcTACTAAAAATAcAAA | AluSx (114:131)** | 4.00E-04 | 6 |
V$MEF2.03 | NNKWKCTAWAAATAGMNN | CTcTaCTAAAAATAcAAA | AluSx (114:131)** | 3.50E-03 | 6 |
V$MEF2.02 | NNNCTAWAAATAGMNN | CTACTAAAAATAcAAA | AluSx (116:131)** | 2.60E-03 | 6 |
V$RSRFC4.01 | NWKCTAWAAATAGMNN | CTaCTAAAAATAcAAA | AluSx (116:131)** | 3.30E-03 | 6 |
V$RSRFC4.02 | ANKCTAWAAATAGMWNN | cTaCTAAAAATAcAAAA | AluSx (116:132)** | 3.00E-03 | 6 |
V$OC2.01 | NNANANAATCMANANNT | ACAAAAAATaCAAAAAT | AluJo (118:134)** | 4.00E-04 | 2 |
V$BRN2.03 | NNMTWNATTWNMWTN | ACAaAAATTAGCTgG | AluSc (125:139)** | 8.30E-03 | 1 |
V$HNF1.01 | GGTTAATNWTTAMM | GGcTAATTTTTgtA | AluSx (-126:-139)** | 8.80E-03 | 6 |
V$HNF1.03 | GGTTAATNWTTRNC | GGcTAATTTTTGTa | AluSx (-126:-139)** | 6.60E-03 | 6 |
V$PAX4.01 | NAMWAATTASS | AAAAAATTAGC | AluY (127:137)** | 4.00E-04 | 1 |
V$IRF1.01 | SNAAAGYGAAACY | CAAgAGCGAAACT | AluSp (264:276) | 3.60E-03 | 2 |