Uses of Tiling Arrays

Target                           Application
mRNA                            gene expression changes
                                        transcript validation/discovery
DNA                                sequencing; genotyping
DNA                                CGH: copy number changes
ChIP-enriched DNA     Protein binding sites
                                         transcription factor binding sites
                                         DNA methylation sites
                                         histone modification sites

(Ru-Fang Yeh, Fall 2007, BMI 209 - Statistical Methods in Bioinformatics: Case Studies)

Some tools for tiling array:

CisGenome

An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis

http://biogibbs.stanford.edu/~jihk/CisGenome/index.htm

Tutorial of CisGenome

http://biogibbs.stanford.edu/~jihk/CisGenome/index_files/tutorial.htm

Files of two types are required,  bpmap file and cel file(affymetrix). They are used for intensity normalization.

Then the data are intergrated with genome annotation to retrieve the DNA sequences.

Packages in R/Bioconductor

tilingArray
Transcript mapping with high-density oligonucleotide tiling arrays
http://bioconductor.org/packages/2.6/bioc/html/tilingArray.html

rMAT
R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.
http://bioconductor.org/packages/2.6/bioc/html/rMAT.html

AffyTiling
Easy extraction of individual probes in Affymetrix tiling arrays
http://bioconductor.org/packages/2.6/bioc/html/AffyTiling.html

BayesPeak
Bayesian Analysis of ChIP-seq Data
http://bioconductor.org/packages/2.6/bioc/html/BayesPeak.html

ChIPpeakAnno
Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments.
http://bioconductor.org/packages/2.6/bioc/html/ChIPpeakAnno.html

Starr
Simple tiling array analysis of Affymetrix ChIP-chip data
http://bioconductor.org/packages/2.6/bioc/html/Starr.html

 

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