Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans

Fabio Piano, Aaron J. Schetter, Diane G. Morton, Kristin C. Gunsalus, Valerie Reinke, Stuart K. Kim, Kenneth J. Kemphues

Research output: Contribution to journalArticle

Abstract

Recently, a set of 766 genes that are enriched in the ovary as compared to the soma was identified by microarray analysis [1]. Here, we report a functional analysis of 98% of these genes by RNA interference (RNAi). Over half the genes tested showed at least one detectable phenotype, most commonly embryonic lethality, consistent with the expectation that ovary transcripts would be enriched for genes that are essential in basic cellular and developmental processes. We find that essential genes are more likely to be conserved and to be highly expressed in the ovary. We extend previous observations [2, 3] and find that fewer than the expected number of ovary-expressed essential genes are present on the X chromosome. We characterized early embryonic defects for 161 genes and used time-lapse microscopy to systematically describe the defects for each gene in terms of 47 RNAi-associated phenotypes. In this paper, we discuss the use of these data to group genes into "phenoclusters"; in the accompanying paper, we use these data as one component in the integration of different types of large-scale functional analyses [4]. We find that phenoclusters correlate well with sequence-based functional predictions and thus may be useful in predicting functions of uncharacterized genes.

Original languageEnglish (US)
Pages (from-to)1959-1964
Number of pages6
JournalCurrent Biology
Volume12
Issue number22
DOIs
StatePublished - Nov 19 2002

Fingerprint

RNA Interference
RNA interference
Cluster Analysis
Ovary
Genes
RNA
Phenotype
phenotype
Essential Genes
genes
X Chromosome
Carisoprodol
Microarray Analysis
X chromosome
Functional analysis
Defects
Microscopy
microscopy
Microarrays
Chromosomes

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)

Cite this

Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans. / Piano, Fabio; Schetter, Aaron J.; Morton, Diane G.; Gunsalus, Kristin C.; Reinke, Valerie; Kim, Stuart K.; Kemphues, Kenneth J.

In: Current Biology, Vol. 12, No. 22, 19.11.2002, p. 1959-1964.

Research output: Contribution to journalArticle

Piano, Fabio ; Schetter, Aaron J. ; Morton, Diane G. ; Gunsalus, Kristin C. ; Reinke, Valerie ; Kim, Stuart K. ; Kemphues, Kenneth J. / Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans. In: Current Biology. 2002 ; Vol. 12, No. 22. pp. 1959-1964.
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