Sentence examples for binding intervals from a from inspiring English sources

Given a set of transcription factor binding intervals from a ChIP-seq experiment in BED format (nfkb.bed), we wish to determine how many binding intervals lie within exons, introns or intergenic sequence using a reference gene set from GENCODE (Harrow et al., 2012), in GTF format (hg19.gtf).

Example: does a set of transcription factor binding site intervals from a ChIP-Seq experiment overlaps more than expected by chance with a set of DNaseI-hypersensitive sites?

Existing ChIP data was obtained from the BDTNP website [ 34], where we used the published binding intervals, and from modENCODE ([ 35]; DCCid modENCODE_2571).

For non- melanogaster species, the annotation was performed on binding intervals called from sequence data that had been translated to the D. melanogaster genome.

For each translated DamID binding interval dataset, the total number of binding intervals overlapping an intron by at least 100 bp, as well as the number of binding intervals overlapping the first intron of a transcript, were counted.

Both binding intervals and reads from non- D. melanogaster species were translated to the D. melanogaster UCSC dm3 reference genome using the LiftOver utility from the UCSC Genome Browser (http://genome.ucsc.edu/cgi-bin/hgLiftOver) [ 123].

The distances from binding intervals to TSSs were calculated and plotted using ChIPpeakAnno [ 125].

The PWMs were also used to scan multiple alignments of both four-way conserved and unique D. melanogaster Dichaete-Dam binding intervals using matrix-scan from RSAT, with the pre-compiled Drosophila background file and with the cutoff for reporting matches set to a PWM weight-score of > = 4 and a p-value of < 0.0001.

Nonetheless, binding intervals associated with annotated CRMs from FlyLight or REDFly display a higher rate of conservation than those located outside of CRMs altogether, which highlights their functional role.

Of particular interest, we found that the Sox motifs identified in the Dichaete binding intervals of each species differed from those found for SoxN.

Integrating in vivo binding data from two species allowed us to identify a set of orthologous binding intervals that are consistently bound by both Dichaete and SoxN across genomes and nuclear environments.