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
https://biogibbs.stanford.edu/~jihk/CisGenome/index.htm
Tutorial of CisGenome
https://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
https://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.
https://bioconductor.org/packages/2.6/bioc/html/rMAT.html
AffyTiling
Easy extraction of individual probes in Affymetrix tiling arrays
https://bioconductor.org/packages/2.6/bioc/html/AffyTiling.html
BayesPeak
Bayesian Analysis of ChIP-seq Data
https://bioconductor.org/packages/2.6/bioc/html/BayesPeak.html
ChIPpeakAnno
Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments.
https://bioconductor.org/packages/2.6/bioc/html/ChIPpeakAnno.html
Starr
Simple tiling array analysis of Affymetrix ChIP-chip data
