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, Bhubaneswar Mishra

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Pages (from-to)314-320
Number of pages7
JournalBioinformatics
Volume23
Issue number3
DOIs
StatePublished - Feb 1 2007

Fingerprint

Functional Genomics
Multiscale Analysis
Gene Expression Profiling
Microarrays
Genomics
Adaptive algorithms
Oligonucleotide Array Sequence Analysis
Gene expression
Gene Expression
DNA
Chip
Genes
DNA Microarray
Target
Microarray Data
Profiling
Normalization
Proportion
Experimental Data
Vary

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

Functional genomics via multiscale analysis : Application to gene expression and ChIP-on-chip data. / Lerman, Gilad; McQuown, Joseph; Blais, Alexandre; Dynlacht, Brian D.; Chen, Guangliang; Mishra, Bhubaneswar.

In: Bioinformatics, Vol. 23, No. 3, 01.02.2007, p. 314-320.

Research output: Contribution to journalArticle

Lerman, Gilad ; McQuown, Joseph ; Blais, Alexandre ; Dynlacht, Brian D. ; Chen, Guangliang ; Mishra, Bhubaneswar. / Functional genomics via multiscale analysis : Application to gene expression and ChIP-on-chip data. In: Bioinformatics. 2007 ; Vol. 23, No. 3. pp. 314-320.
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