Wikiomics:ChIP-chip

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).

• Mpeak [1] Win only ver.2 ?not working?

• CEAS BED/GFF file format (BED format) so far only human genome?

• HMMTiling

• TileMap [2]

• TileHGMM: R package, requires replicates from chips, plus probe location file. For computational reasons data sould be separated for each chromosome.

• Chipper online and stand-alone R-based software (2006) [3]

• DRIM online and stand alone program (2007) [4]

References

1. Zheng M, Barrera LO, Ren B, and Wu YN. ChIP-chip: Data, Model, and Analysis. University of California, Los Angeles, 2005. PDF

2. Ji H and Wong WH. TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics. 2005 Sep 15;21(18):3629-36. DOI:10.1093/bioinformatics/bti593 |
3. Gibbons FD, Proft M, Struhl K, and Roth FP. Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization. Genome Biol. 2005;6(11):R96. DOI:10.1186/gb-2005-6-11-r96 |

4. 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