A gene recommender algorithm to identify coexpressed genes in C. elegans.
One of the most important uses of whole-genome expression data is for the discovery of new genes with similar function to a given list of genes (the query) already known to have closely related function. We have developed an algorithm, called the gene recommender, that ranks genes according to how strongly they correlate with a set of query genes in those experiments for which the query genes are most strongly coregulated. We used the gene recommender to find other genes coexpressed with several sets of query genes, including genes known to function in the retinoblastoma complex. Genetic experiments confirmed that one gene (JC8.6) identified by the gene recommender acts with lin-35 Rb to regulate vulval cell fates, and that another gene (wrm-1) acts antagonistically. We find that the gene recommender returns lists of genes with better precision, for fixed levels of recall, than lists generated using the C. elegans expression topomap.
Owen
Art B
AB
Department of Statistics, Stanford University, Stanford, California 94305, USA. art@stat.stanford.edu
Stuart
Josh
J
Mach
Kathy
K
Villeneuve
Anne M
AM
Kim
Stuart
S
D000465:Algorithms; D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics*; D019295:Computational Biology; D018509:DNA, Helminth / Q000032:analysis; D030541:Databases, Genetic / Q000706:statistics & numerical data; D020869:Gene Expression Profiling / Q000379:methods* / Q000706:statistics & numerical data; D005786:Gene Expression Regulation / Q000235:genetics*; D017238:Genes, Helminth / Q000235:genetics*; D016161:Genes, Retinoblastoma / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods / Q000706:statistics & numerical data; D034622:RNA Interference; D012984:Software
D018509:DNA, Helminth