Functional genomics via multiscale analysis: application to gene expression and ChIP-on-chip data.

Gilad Lerman; Joseph McQuown; Alexandre Blais; Brian D Dynlacht; Guangliang Chen; Bud Mishra

doi:10.1093/bioinformatics/btl606

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Functional genomics via multiscale analysis: application to gene expression and ChIP-on-chip data.

Gilad Lerman·Joseph McQuown·Alexandre Blais·Brian D Dynlacht·Guangliang Chen·Bud Mishra

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Abstract

UNLABELLED: We present a fast, versatile and adaptive-multiscale algorithm for analyzing a wide-variety of DNA microarray data. Its primary application is in normalization of array data as well as subsequent identification of 'enriched targets', e.g. differentially expressed genes in expression profiling arrays and enriched sites in ChIP-on-chip experimental data. We show how to accommodate the unique characteristics of ChIP-on-chip data, where the set of 'enriched targets' is large, asymmetric and whose proportion to the whole data varies locally. SUPPLEMENTARY INFORMATION: Supplementary figures, related preprint, free software as well as our raw DNA microarray data with PCR validations are available at http://www.math.umn.edu/~lerman/supp/bioinfo06 as well as Bioinformatics online.

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Algorithms Chromatin Immunoprecipitation Chromosome Mapping Gene Expression Profiling Multivariate Analysis Oligonucleotide Array Sequence Analysis Proteome Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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Gilad Lerman, Joseph McQuown, Alexandre Blais, Brian D Dynlacht, Guangliang Chen, Bud Mishra. 2006-12-12. Functional genomics via multiscale analysis: application to gene expression and ChIP-on-chip data.. https://doi.org/10.1093/bioinformatics%2Fbtl606

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