Relationship between gene co-expression and probe localization on microarray slides

Yuval Kluger, Haiyuan Yu, Jiang Qian, Mark Gerstein

Research output: Contribution to journalArticle

Abstract

Background: Microarray technology allows simultaneous measurement of thousands of genes in a single experiment. This is a potentially useful tool for evaluating co-expression of genes and extraction of useful functional and chromosomal structural information about genes. Results: In this work we studied the association between the co-expression of genes, their location on the chromosome and their location on the microarray slides by analyzing a number of eukaryotic expression datasets, derived from the S. cerevisiae, C. elegans, and D. melanogaster. We find that in several different yeast microarray experiments the distribution of the number of gene pairs with correlated expression profiles as a function of chromosomal spacing is peaked at short separations and has two superimposed periodicities. The longer periodicity has a spacing of 22 genes (∼42 Kb), and the shorter periodicity is 2 genes (∼4 Kb). Conclusion: The relative positioning of DNA probes on microarray slides and source plates introduces subtle but significant correlations between pairs of genes. Careful consideration of this spatial artifact is important for analysis of microarray expression data. It is particularly relevant to recent microarray analyses that suggest that co-expressed genes cluster along chromosomes or are spaced by multiples of a fixed number of genes along the chromosome.

Original languageEnglish (US)
Article number49
JournalBMC Genomics
Volume4
DOIs
StatePublished - Dec 10 2003

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Gene Expression
Genes
Periodicity
Chromosomes
Microarray Analysis
DNA Probes
Multigene Family
Artifacts
Saccharomyces cerevisiae
Yeasts
Technology

ASJC Scopus subject areas

  • Medicine(all)
  • Biotechnology
  • Genetics

Cite this

Relationship between gene co-expression and probe localization on microarray slides. / Kluger, Yuval; Yu, Haiyuan; Qian, Jiang; Gerstein, Mark.

In: BMC Genomics, Vol. 4, 49, 10.12.2003.

Research output: Contribution to journalArticle

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