Sentence examples for binding sites obtained from from inspiring English sources

We mapped ChIP-Seq and ChIP-Chip derived transcription factor binding sites obtained from ENCODE, CISTROME and Kittler et al. to all RefSeq gene promoters in order to calculate in-silico ChIP-Seq binding enrichment.

Data on the IL-10R binding sites (obtained from Josephson [8]), were in line with the receptor binding sites reported by Reineke [9].

SAMPLEX was run to determine the significant changes in the CSP data of the two binding sites obtained from NMR titrations of Josephin constructs with a mutation at either site 1 (I77K-Q78K) or site 2 (W87K).

Notably, the binding sites obtained from Piranha software are not strand-specific because the current Piranha version does not provide strandness information.

To identify PU.1 target genes associated with the preleukemic hypermethylated CGIs, we searched for overlaps between the genomic coordinates of PU.1 binding sites obtained from publicly available PU.1 ChIP-Seq data [ 30] and the coordinates of the preleukemic hypermethylated CGIs.

Sp1, MAZ, and PU.1 binding sites were obtained from FANTOM 4 (http://fantom.gsc.riken.jp/4/download/GenomeBrowser/hg18/TFBS_CAGE/allsites_cage_tfbs_feb09_latest.gff.gz) [ 1].

The loci of the CpGs in regard to CGIs, TSSs, promoters, and CTCF binding sites were obtained from the Infinium Human Methylation450K BeadChip annotation files and from the UCSC genome browser.

Transcription factor binding sites were obtained from the ENCODE transcription factor ChIP track of the UCSC genome browser [ 86] (downloaded December 15 , 2011.

Likewise, enhancers and insulators needed to be colocalized with p300 [ 31] and cohesin [ 32, 33], respectively, the data on p300 and cohesin binding sites were obtained from the ENCODE ChIP-seq dataset [ 17].

The positions of subsequences containing binding sites was obtained from the UCSC browser [ 45] using tracks created for the ENCODE project [ 1] and the tables labeled "peaks":- for three factors from the "HAIB TFBS" data [ 38], (ENCODE November 2008 and February 2009 freezes) and for eleven factors from the "YALE TFBS" data [ 39], (release 2 of October 2009).

Alternatively, if no ligands are available in the crystal structures, known binding site residues obtained from the catalytic site atlas (Porter et al., 2004) and literature were used.