High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

• Published in: Science (American Association for the Advancement of Science) Vol. 322; no. 5898; pp. 104 - 110
• Main Authors: Yu, Haiyuan, Braun, Pascal, Yıldırım, Muhammed A, Lemmens, Irma, Venkatesan, Kavitha, Sahalie, Julie, Hirozane-Kishikawa, Tomoko, Gebreab, Fana, Li, Na, Simonis, Nicolas, Hao, Tong, Rual, Jean-François, Dricot, Amélie, Vazquez, Alexei, Murray, Ryan R, Simon, Christophe, Tardivo, Leah, Tam, Stanley, Svrzikapa, Nenad, Fan, Changyu, de Smet, Anne-Sophie, Motyl, Adriana, Hudson, Michael E, Park, Juyong, Xin, Xiaofeng, Cusick, Michael E, Moore, Troy, Boone, Charlie, Snyder, Michael, Roth, Frederick P, Barabási, Albert-László, Tavernier, Jan, Hill, David E, Vidal, Marc
• Format: Journal Article
• Language: English
• Published: Washington, DC American Association for the Advancement of Science 03.10.2008; The American Association for the Advancement of Science
• Subjects: Biological and medical sciences; Biological properties; Cellular biology; Computational Biology; Connectivity; Data analysis; data collection; Datasets; Diverse techniques; Drug interactions; Fundamental and applied biological sciences. Psychology; Gene Regulatory Networks; Grants; Mass Spectrometry; Metabolic Networks and Pathways; Molecular and cellular biology; Molecular biology; Molecular interactions; Open reading frames; pleiotropy; Principal components analysis; Protein Array Analysis; Protein Binding; Protein interaction mapping; Protein Interaction Mapping - methods; Protein Interaction Mapping - standards; proteins; Proteome - metabolism; Proteomics; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - isolation & purification; Saccharomyces cerevisiae Proteins - metabolism; screening; Screening tests; Signal Transduction; Spectrum analysis; topology; Transcription Factors - metabolism; Two-Hybrid System Techniques; Yeast; Yeasts; Ascomycota; Fungi; Molecular interaction; Interactome; Saccharomyces cerevisiae; Protein
• ISSN: 0036-8075; 1095-9203; 1095-9203
• DOI: 10.1126/science.1158684

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 ~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.