A gene-coexpression network for global discovery of conserved genetic modules.
To elucidate gene function on a global scale, we identified pairs of genes that are coexpressed over 3182 DNA microarrays from humans, flies, worms, and yeast. We found 22,163 such coexpression relationships, each of which has been conserved across evolution. This conservation implies that the coexpression of these gene pairs confers a selective advantage and therefore that these genes are functionally related. Many of these relationships provide strong evidence for the involvement of new genes in core biological functions such as the cell cycle, secretion, and protein expression. We experimentally confirmed the predictions implied by some of these links and identified cell proliferation functions for several genes. By assembling these links into a gene-coexpression network, we found several components that were animal-specific as well as interrelationships between newly evolved and ancient modules.
Stuart
Joshua M
JM
Stanford Medical Informatics, 251 Campus Drive, Medical School Office Building X-215, Stanford, CA 94305-5329, USA.
Segal
Eran
E
Koller
Daphne
D
Kim
Stuart K
SK
D000818:Animals; D005075:Biological Evolution; D017173:Caenorhabditis elegans / Q000235:genetics; D002453:Cell Cycle / Q000235:genetics; D002455:Cell Division / Q000235:genetics; D019295:Computational Biology; D017124:Conserved Sequence; D030541:Databases, Genetic; D004331:Drosophila melanogaster / Q000235:genetics; D015870:Gene Expression; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D005800:Genes, Fungal; D017238:Genes, Helminth; D017344:Genes, Insect; D006801:Humans; D015233:Models, Statistical; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D011506:Proteins / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics; D015398:Signal Transduction / Q000235:genetics; D013045:Species Specificity; D014407:Tumor Cells, Cultured
D011506:Proteins