Here, users have the option to choose the antibody's target name, provide a list of ChIP targets or turn the filter off altogether for broader searching criteria.
The raw ChIP-seq (data accessible at NCBI GEO database [ 17– 19], accession GSE34019) was processed using the TFTargetCaller [settings: Ouyang, TFAS and closestGene methods] package in R [ 20] to produce an annotated list of ChIP-seq peaks.
As before, we processed the raw ChIP-seq data (NCBI GEO database [ 17], accession GSE36375 and GSE26345, respectively) using the TFTargetCaller [settings: Ouyang, TFAS and closestGene methods] package in R [ 20] to produce an annotated list of ChIP-seq peaks.
GREAT links a list of ChIP-Seq peak regions to gene lists with particular functional significance and unlike previous approaches incorporates binding sites not only in the promoter region of a gene.
ChIP-seq library: list of ChIP-seq DNA fragments uniquely mapped onto reference genome m: number of ChIP-seq DNA fragments shearing a unique locus in the genome; m could represent a relative level of binding avidity of a TFBS in a given genome locus.
Koike et al. [ 14] provide time-resolved genome-wide ChIP-seq binding sampled every four hours over one day in mouse liver for the TFs BMAL1, CLOCK, NPAS, CRY1, CRY2, PER1 and PER2 (the list of ChIP-seq peaks and associated genes for each TF were provided in Table S2 of [ 14]).
A DNA fragment encompassing a putative MrpC binding site upstream of MXAN_5802 produced 3 shifted complexes, suggesting the presence of multiple binding sites, which may account for the high rank of this site on the list of ChIP-seq peaks (Additional file 3).
Rey et al. [ 15] similarly performed a detailed study of the genome-wide binding of activator BMAL1 in the mouse liver sampled every four hours over one day (the list of ChIP-seq peaks and associated genes for each TF were provided in Text S2 of [ 15]).
In addition to acting as a universal file format converter, a second major utility of glbase is to act as the 'glue' between up-stream and down-stream analysis tools, for instance to get from a list of ChIP-seq peaks and gene expression values to heatmaps, gene-peak associations and other informative plots.
Again, this gene was not found in the RU gene list.> -wrap-foot> List of RR ChIP-chip putative Sox2 target genes.
