Significant Differential Binding Locations Of Two-Color Two Chip-Chip Data

Question

[Shumon]

I have two color (Agilent) ChIP-chip data on two different cell types (lets say IP1 and IP2 for cell type1 and cell type2 respectively). I want to get differential binding locations (probes) with Log ratio.

For example: What I want is to compare:

(IP1/input1 versus IP2/input2)

Q: How can I do that ? Q: Is there any tools/software/package that does this job? There are some tools for such analysis with ChIP-seq data, but I am looking something for two color ChIP-chip data.

thanks,

Answer 1

[Mikael Huss]

I think it might be possible with the Ringo Bioconductor package. This is a package for two-color array ChIP-chip analysis including the differential binding scenario that you describe. However, I think it's primarily geared towards Nimblegen arrays (which I have used it for) although the manual also mentions Agilent several times.

[Shumon]

@Huaa: Thanks....... but giving a quick look to the Ringo manual, I did not find the example of differential binding analysis situation. Could you please explain little more?. Thanks again.

[Mikael Huss]

See this tutorial from PLoS Computational Biology: http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000227 The section "Comparing ChIP-Enrichment between the Tissues" presents an approach which is maybe simpler than what you are looking for but it also points to the supplementary material, where they present "an additional way for comparing H3K4me3 enrichment between the two tissues, an enriched-region–wise comparison considering the actual overlap of the enriched regions".