As expected from previous multi-species ChIP study of CEBPA and HNF4A (Schmidt et al., 2010), the known binding motifs for the four TFs was virtually identical between species and occurred close to the ChIP-seq binding summit.
As our previously published (and of course unpublished) primary data is in ArrayExpress, our multi-species ChIP-seq data had not been subject to this QC.
The heatmap shows the −log10 of Bonferroni corrected p-values for the enrichments of CRMs and singletons broken down into categories related to their degree of conservation determined by our multi-species ChIP-seq comparisons.
In particular, recent cross-species ChiP-seq analysis of transcription factor binding (Schmidt et al. 2010) suggests a way to explicitly test our predictions at the level of actual binding affinities of hybrid TF TFBS combinations for recently diverged species, such as in the Drosophila family.
For the retrieval of promoter sequences from the Ensemble database, the following settings were used: Get_Seq from Ensembl/Biomart, comma separated, rat species, AFFY_Rat230_2 chip, 5'Upstreatm Exon 1, 1,000 base pairs (bp) upstream, 200 bp downstream, add to current list, Rev Compl automatically.
The woody species are chipped; the forbs and grasses are cut into small pieces.
Model species Affymetrix chips were purposely not included in the repository as there already exist extensive functional annotation projects.
In fact, SNPchiMp v.3 includes a notable growth in the amount of data regarding new species and chips (e.g. nearly two-fold increase from version 2).
Schmidt et al. (2010), focusing on two transcription factors in liver tissues of five vertebrate species for ChIP-seq analysis, reported that very few regulatory elements are shared by all the species used.
Here we present SNPchiMp, a MySQL database linked to an open access web-based interface to manage bovine and eventually multi-species SNP chip data in a straightforward, flexible, consistent and user-friendly manner.
