title: Empirically controlled mapping of the Caenorhabditis  elegans protein-protein interactome network.
abstract: To provide accurate biological hypotheses and elucidate global properties of cellular networks, systematic identification of protein-protein interactions must meet high quality standards.We present an expanded C. elegans protein-protein interaction network, or 'interactome' map, derived from testing a matrix of approximately 10,000 x approximately 10,000 proteins using a highly specific, high-throughput yeast two-hybrid system. Through a new empirical quality control framework, we show that the resulting data set (Worm Interactome 2007, or WI-2007) was similar in quality to low-throughput data curated from the literature. We filtered previous interaction data sets and integrated them with WI-2007 to generate a high-confidence consolidated map (Worm Interactome version 8, or WI8). This work allowed us to estimate the size of the worm interactome at approximately 116,000 interactions. Comparison with other types of functional genomic data shows the complementarity of distinct experimental approaches in predicting different functional relationships between genes or proteins
authors.affiliation: Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Simonis
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Rual
authors.forename: Anne-Ruxandra
authors.initials: AR
authors.lastname: Carvunis
authors.forename: Murat
authors.initials: M
authors.lastname: Tasan
authors.forename: Irma
authors.initials: I
authors.lastname: Lemmens
authors.forename: Tomoko
authors.initials: T
authors.lastname: Hirozane-Kishikawa
authors.forename: Tong
authors.initials: T
authors.lastname: Hao
authors.forename: Julie M
authors.initials: JM
authors.lastname: Sahalie
authors.forename: Kavitha
authors.initials: K
authors.lastname: Venkatesan
authors.forename: Fana
authors.initials: F
authors.lastname: Gebreab
authors.forename: Sebiha
authors.initials: S
authors.lastname: Cevik
authors.forename: Niels
authors.initials: N
authors.lastname: Klitgord
authors.forename: Changyu
authors.initials: C
authors.lastname: Fan
authors.forename: Pascal
authors.initials: P
authors.lastname: Braun
authors.forename: Ning
authors.initials: N
authors.lastname: Li
authors.forename: Nono
authors.initials: N
authors.lastname: Ayivi-Guedehoussou
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Dann
authors.forename: Nicolas
authors.initials: N
authors.lastname: Bertin
authors.forename: David
authors.initials: D
authors.lastname: Szeto
authors.forename: Amélie
authors.initials: A
authors.lastname: Dricot
authors.forename: Muhammed A
authors.initials: MA
authors.lastname: Yildirim
authors.forename: Chenwei
authors.initials: C
authors.lastname: Lin
authors.forename: Anne-Sophie
authors.initials: AS
authors.lastname: de Smet
authors.forename: Huey-Ling
authors.initials: HL
authors.lastname: Kao
authors.forename: Christophe
authors.initials: C
authors.lastname: Simon
authors.forename: Alex
authors.initials: A
authors.lastname: Smolyar
authors.forename: Jin Sook
authors.initials: JS
authors.lastname: Ahn
authors.forename: Muneesh
authors.initials: M
authors.lastname: Tewari
authors.forename: Mike
authors.initials: M
authors.lastname: Boxem
authors.forename: Stuart
authors.initials: S
authors.lastname: Milstein
authors.forename: Haiyuan
authors.initials: H
authors.lastname: Yu
authors.forename: Matija
authors.initials: M
authors.lastname: Dreze
authors.forename: Jean
authors.initials: J
authors.lastname: Vandenhaute
authors.forename: Kristin C
authors.initials: KC
authors.lastname: Gunsalus
authors.forename: Michael E
authors.initials: ME
authors.lastname: Cusick
authors.forename: David E
authors.initials: DE
authors.lastname: Hill
authors.forename: Jan
authors.initials: J
authors.lastname: Tavernier
authors.forename: Frederick P
authors.initials: FP
authors.lastname: Roth
authors.forename: Marc
authors.initials: M
authors.lastname: Vidal
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics / Q000378:metabolism*; D029742:Caenorhabditis elegans Proteins / Q000032:analysis* / Q000235:genetics / Q000378:metabolism*; D002460:Cell Line; D006801:Humans; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D012984:Software
chemical_list: D029742:Caenorhabditis elegans Proteins