Cited by 36Gene expression and cancer classificationBioinformatics and Genomic NetworksGenomics and Chromatin Dynamics

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

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Kluger, Yuval, Yu, Haiyuan, Qian, Jiang, Gerstein, Mark·2003·BMC Genomics

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 (approximately 42 Kb), and the shorter periodicity is 2 genes (approximately 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.

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  • Positional effects (edge effects, row/column dependencies, or gradient artifacts) are a persistent factor in multi-well assays and microarray experiments.

    “First, positional effects (edge effects, row/column dependencies, or gradient artifacts) are a persistent factor in multi-well assays and microarray experiments30,31,52.”

    From A statistical framework for high-content phenotypic profiling using cellular feature distributions (2022) · cites this paper as [52]

    The Discussion and Conclusions reports spatial artifacts affecting measured co-expression and says the artifact is present in a wide variety of microarray experiments. The Results also describes a systematic artifact linked to probe positions across microarray blocks. Our copy does not address multi-well assays or establish the listed edge, row/column, and gradient effects as a group. (LLM, conf=0.86)

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Authors
Kluger, Y., Yu, H., Qian, J., & Gerstein, M.
Affiliations
  • Yale University (US)
  • Johns Hopkins University (US)
Corresponding author
Gerstein, Mark
Venue
BMC Genomics
Published
2003-12-10
Volume
4
Issue
1
Pages
49-49
ISSN
1471-2164 (ISSN-L)
OpenAlex
W2119504746
Cited by
36
References
19
Citations by year
2022: 1 · 2020: 1 · 2017: 1 · 2016: 1 · 2015: 1 · 2012: 2
FWCI
1.73
Type
journal article
Language
en
Open access
Locations
  • BMC Genomics (publishedVersion)
  • PubMed Central (publishedVersion, other-oa)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
gene co-expression, spatial artifacts, gene clustering, yeast, Caenorhabditis elegans, Drosophila melanogaster, gene expression profiling, periodicity
MeSH terms
Animals, Chromosome Mapping, Drosophila melanogaster, Escherichia coli, Saccharomyces cerevisiae, Oligonucleotide Probes, Artifacts, Caenorhabditis elegans, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Gene Order

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