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Data on the IL-10R binding sites (obtained from Josephson [8]), were in line with the receptor binding sites reported by Reineke [9].
The number of total COUP-TF HMM hits in the entire mouse genome is several orders of magnitude higher than the number of binding sites reported by ChIP-based location analyses [2].
We compared the distribution of the strength of nonoverlapping binding sites reported by MAST (as p-values).
Promoter analysis of IGFBP-3 indicated that the NaB-RE sequence is essential for the sodium butyrate (NaB) induced IGFBP-3 expression [ 15], but the importance of the eleven upstream p53 binding sites reported by Bourdon et al. were not confirmed until now [ 16].
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Our results confirmed the GBM binding site reported by another group recently (PDB: 6BAA, EMD-7073) (Martin et al., 2017a).
This site is not a Pc-G binding site reported by Negre et al. We found that the colocalizations of tGgDId on one side, and tGgIdas on the other, with Pc-G bodies are statistically different, 19 versus 29%, respectively (P < 0.02; Fig. 4D).
Nuclear protein concentration was determined using the BCA™ Protein Assay kit (Pierce Biotechnology, Inc .. Oligonucleotide sequences of the Egr-1 consensus-binding site, reported by Santa Cruz Biotechnology, Inc. (Santa Cruz, CA, USA) and synthesized by TibMolBiol (Berlin, Germany), were 5′-GGA TCC AGC GGG GGC GAG CGG GGG CGA-3′ and 3′-CCT AGG TCG CCC CCG CTC GCC CCC GCT-5′.
In this study, the TF binding site reported to be violated by the rSNP is bound by OCT4.
An extensive genomic analysis of the IL-10 gene and flanking regions of 94 Ulcerative colitis and 94 Crohn disease patients revealed polymorphisms in the IL-10 coding gene, of which one (R159) was in the receptor binding site, as reported by Josephson [8], [43].
Conservation score was sampled every 100 bp from the summit of each AR binding site (as reported by MACS) to 10 kb in both directions.
Using RIsearch as a pre-filter in genome-wide screens reduces the number of binding site candidates reported by miRNA target prediction programs, such as TargetScanS and miRanda, by up to 70%.
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