title: Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline.
abstract: By integrating functional genomic and proteomic mapping approaches, biological hypotheses should be formulated with increasing levels of confidence. For example, yeast interactome and transcriptome data can be correlated in biologically meaningful ways. Here, we combine interactome mapping data generated for a multicellular organism with data from both large-scale phenotypic analysis ("phenome mapping") and transcriptome profiling. First, we generated a two-hybrid interactome map of the Caenorhabditis elegans germline by using 600 transcripts enriched in this tissue. We compared this map to a phenome map of the germline obtained by RNA interference (RNAi) and to a transcriptome map obtained by clustering worm genes across 553 expression profiling experiments. In this dataset, we find that essential proteins have a tendency to interact with each other, that pairs of genes encoding interacting proteins tend to exhibit similar expression profiles, and that, for approximately 24% of germline interactions, both partners show overlapping embryonic lethal or high incidence of males RNAi phenotypes and similar expression profiles. We propose that these interactions are most likely to be relevant to germline biology. Similar integration of interactome, phenome, and transcriptome data should be possible for other biological processes in the nematode and for other organisms, including humans.
authors.affiliation: Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Albertha J M
authors.initials: AJ
authors.lastname: Walhout
authors.forename: Jérôme
authors.initials: J
authors.lastname: Reboul
authors.forename: Olena
authors.initials: O
authors.lastname: Shtanko
authors.forename: Nicolas
authors.initials: N
authors.lastname: Bertin
authors.forename: Philippe
authors.initials: P
authors.lastname: Vaglio
authors.forename: Hui
authors.initials: H
authors.lastname: Ge
authors.forename: Hongmei
authors.initials: H
authors.lastname: Lee
authors.forename: Lynn
authors.initials: L
authors.lastname: Doucette-Stamm
authors.forename: Kristin C
authors.initials: KC
authors.lastname: Gunsalus
authors.forename: Aaron J
authors.initials: AJ
authors.lastname: Schetter
authors.forename: Diane G
authors.initials: DG
authors.lastname: Morton
authors.forename: Kenneth J
authors.initials: KJ
authors.lastname: Kemphues
authors.forename: Valerie
authors.initials: V
authors.lastname: Reinke
authors.forename: Stuart K
authors.initials: SK
authors.lastname: Kim
authors.forename: Fabio
authors.initials: F
authors.lastname: Piano
authors.forename: Marc
authors.initials: M
authors.lastname: Vidal
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics*; D029742:Caenorhabditis elegans Proteins / Q000235:genetics*; D002874:Chromosome Mapping; D005821:Genetic Techniques; D016678:Genome; D016366:Open Reading Frames; D020543:Proteome; D014158:Transcription, Genetic
chemical_list: D029742:Caenorhabditis elegans Proteins; D020543:Proteome