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Information about the method is here: wikipedia:ChIP-on-chip
Programs used to analyze ChIP-CHIP data
- SignalMap (Nimblegene) uses gff format; useful mostly for visualization
- TiMAT2 is a collection of command line java tools used for for both low and high level tiling microarray data analysis using the Affymetrix, Nimblegen, and Agilent platforms. TiMAT2 is designed for processing chIP-chip, RNA difference, and comparative genomic hybridization experiments from both single and multi chip data sets. Options exist for distributed computing on a cluster via PBS.
- TAMALPAIS: Web-based online analysis of ChIP-chip data (gff format); emails results to user
- Promoter Array Analysis Server: simple list comparison for NimbleGen summary files for Minimum Promoter Designs; displays in browser
- ChIPOTle Microsoft Excel: Microsoft Excel macros. Restriction on maximum number of rows accepted by Excel (ca 64k).
- TileHGMM: R package, requires replicates from chips, plus probe location file. For computational reasons data sould be separated for each chromosome.
- Zheng M, Barrera LO, Ren B, and Wu YN. ChIP-chip: Data, Model, and Analysis. University of California, Los Angeles, 2005. PDF
- Ji H and Wong WH. . pmid:16046496.
- Gibbons FD, Proft M, Struhl K, and Roth FP. . pmid:16277751.
- Eden E, Lipson D, Yogev S, Yakhini Z (2007) Discovering Motifs in Ranked Lists of DNA Sequences. PLoS Comput Biol 3(3): e39 doi:10.1371/journal.pcbi.0030039