ArticleBMC bioinformatics2004
CLOE: identification of putative functional relationships among genes by comparison of expression profiles between two species.
Article in BMC bioinformatics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 24 citations in OpenAlex.
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- Drug repositioning for orphan genetic diseases through Conserved Anticoexpressed Gene Clusters (CAGCs).BMC bioinformatics · 2013Article
- An atlas of tissue-specific conserved coexpression for functional annotation and disease gene prediction.European journal of human genetics : EJHG · 2011Article
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- A symphony of regulations centered on p63 to control development of ectoderm-derived structures.Journal of biomedicine & biotechnology · 2011Review
- The MeCP2/YY1 interaction regulates ANT1 expression at 4q35: novel hints for Rett syndrome pathogenesis.Human molecular genetics · 2010Article
- ORTom: a multi-species approach based on conserved co-expression to identify putative functional relationships among genes in tomato.Plant molecular biology · 2010Article
- The RhoU/Wrch1 Rho GTPase gene is a common transcriptional target of both the gp130/STAT3 and Wnt-1 pathways.The Biochemical journal · 2009Article
- Prediction of human disease genes by human-mouse conserved coexpression analysis.PLoS computational biology · 2008Article
- Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata.Genome biology · 2008Article
- Negative feedback regulation of Rac in leukocytes from mice expressing a constitutively active phosphatidylinositol 3-kinase gamma.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- A new computational approach to analyze human protein complexes and predict novel protein interactions.Genome biology · 2007Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPublic repositories of microarray data contain an incredible amount of information that is potentially relevant to explore functional relationships among genes by meta-analysis of expression profiles. However, the widespread use of this resource by the scientific community is at the moment limited by the limited availability of effective tools of analysis. We here describe CLOE, a simple cDNA microarray data mining strategy based on meta-analysis of datasets from pairs of species. The method consists in ranking EST probes in the datasets of the two species according to the similarity of their expression profiles with that of two EST probes from orthologous genes, and extracting orthologous EST pairs from a given top interval of the ranked lists. The Gene Ontology annotation of the obtained candidate partners is then analyzed for keywords overrepresentation.
resultsWe demonstrate the capabilities of the approach by testing its predictive power on three proteomically-defined mammalian protein complexes, in comparison with single and multiple species meta-analysis approaches. Our results show that CLOE can find candidate partners for a greater number of genes, if compared to multiple species co-expression analysis, but retains a comparable specificity even when applied to species as close as mouse and human. On the other hand, it is much more specific than single organisms co-expression analysis, strongly reducing the number of potential candidate partners for a given gene of interest.
conclusionsCLOE represents a simple and effective data mining approach that can be easily used for meta-analysis of cDNA microarray experiments characterized by very heterogeneous coverage. Importantly, it produces for genes of interest an average number of high confidence putative partners that is in the range of standard experimental validation techniques.
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