title: High-quality binary protein interaction map of the yeast interactome network.
abstract: Current yeast interactome network maps contain several hundred molecular complexes with limited and somewhat controversial representation of direct binary interactions. We carried out a comparative quality assessment of current yeast interactome data sets, demonstrating that high-throughput yeast two-hybrid (Y2H) screening provides high-quality binary interaction information. Because a large fraction of the yeast binary interactome remains to be mapped, we developed an empirically controlled mapping framework to produce a "second-generation" high-quality, high-throughput Y2H data set covering approximately 20% of all yeast binary interactions. Both Y2H and affinity purification followed by mass spectrometry (AP/MS) data are of equally high quality but of a fundamentally different and complementary nature, resulting in networks with different topological and biological properties. Compared to co-complex interactome models, this binary map is enriched for transient signaling interactions and intercomplex connections with a highly significant clustering between essential proteins. Rather than correlating with essentiality, protein connectivity correlates with genetic pleiotropy.
authors: Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02115, USA.
authors: Haiyuan
authors: H
authors: Yu
authors: Pascal
authors: P
authors: Braun
authors: Muhammed A
authors: MA
authors: Yildirim
authors: Irma
authors: I
authors: Lemmens
authors: Kavitha
authors: K
authors: Venkatesan
authors: Julie
authors: J
authors: Sahalie
authors: Tomoko
authors: T
authors: Hirozane-Kishikawa
authors: Fana
authors: F
authors: Gebreab
authors: Na
authors: N
authors: Li
authors: Nicolas
authors: N
authors: Simonis
authors: Tong
authors: T
authors: Hao
authors: Jean-François
authors: JF
authors: Rual
authors: Amélie
authors: A
authors: Dricot
authors: Alexei
authors: A
authors: Vazquez
authors: Ryan R
authors: RR
authors: Murray
authors: Christophe
authors: C
authors: Simon
authors: Leah
authors: L
authors: Tardivo
authors: Stanley
authors: S
authors: Tam
authors: Nenad
authors: N
authors: Svrzikapa
authors: Changyu
authors: C
authors: Fan
authors: Anne-Sophie
authors: AS
authors: de Smet
authors: Adriana
authors: A
authors: Motyl
authors: Michael E
authors: ME
authors: Hudson
authors: Juyong
authors: J
authors: Park
authors: Xiaofeng
authors: X
authors: Xin
authors: Michael E
authors: ME
authors: Cusick
authors: Troy
authors: T
authors: Moore
authors: Charlie
authors: C
authors: Boone
authors: Michael
authors: M
authors: Snyder
authors: Frederick P
authors: FP
authors: Roth
authors: Albert-László
authors: AL
authors: Barabási
authors: Jan
authors: J
authors: Tavernier
authors: David E
authors: DE
authors: Hill
authors: Marc
authors: M
authors: Vidal
mesh_terms: D019295:Computational Biology; D053263:Gene Regulatory Networks; D013058:Mass Spectrometry; D053858:Metabolic Networks and Pathways; D040081:Protein Array Analysis; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods / Q000592:standards; D020543:Proteome / Q000378:metabolism; D040901:Proteomics; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D015398:Signal Transduction; D014157:Transcription Factors / Q000378:metabolism; D020798:Two-Hybrid System Techniques
chemical_list: D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors