Table 1

Main DNA binding motifs overrepresented in Pax8-dependent peaks
TF Matrices Family information Matches in Input (n) Expected (genome) Overrep. (genome) Z-Score (genome)
O$BRE.01 Transcription factor II B (TFIIB) recognition element 924 88.75 10.41 88.61
O$HMTE.01 Human motif ten element 2481 350.02 7.09 113.88
O$XCPE1.01 X gene core promoter element 1 5454 1531.85 3.56 100.21
O$DMTE.01 Drosophila motif ten element 4415 1442.3 3.06 78.27
O$INR_DPE.01 Initiator (INR) and downstream promoter element (DPE) with strictly maintained spacing 2460 1071.16 2.30 42.42
V$NRF1.01 Nuclear respiratory factor 1 6640 1323.52 5.02 146.13
V$SP1.02 GC-Box factors SP1/GC; Stimulating protein 1, ubiquitous zinc finger transcription factor 5792 1090.23 5.31 142.39
V$SP1.03 GC-Box factors SP1/GC; Stimulating protein 1, ubiquitous zinc finger transcription factor 4802 1129.17 5.14 139.05
V$ZF5.01 Zinc finger / POZ domain transcription factor 5543 1260.88 4.40 120.59
V$CTCF.01 CCCTC-binding factor 4729 1015.47 4.66 116.52

The Overrep. (genome) column represents the fold overrepresentation of these matrices in our IP peaks compared to their presence in the rat genome, and the Z-Score (genome) column indicates association value between the DNA matrices and Pax8-immunoprecipitated DNA.

Ruiz-Llorente et al.

Ruiz-Llorente et al. BMC Genomics 2012 13:147   doi:10.1186/1471-2164-13-147

Open Data