High-Quality Binary Protein Interaction Map of the Yeast Interactome Network
- Haiyuan Yu1,2,*,
- Pascal Braun1,2,*,
- Muhammed A. Yıldırım1,2,3,*,
- Irma Lemmens4,
- Kavitha Venkatesan1,2,
- Julie Sahalie1,2,
- Tomoko Hirozane-Kishikawa1,2,
- Fana Gebreab1,2,
- Na Li1,2,
- Nicolas Simonis1,2,
- Tong Hao1,2,
- Jean-François Rual1,2,
- Amélie Dricot1,2,
- Alexei Vazquez5,
- Ryan R. Murray1,2,
- Christophe Simon1,2,
- Leah Tardivo1,2,
- Stanley Tam1,2,
- Nenad Svrzikapa1,2,
- Changyu Fan1,2,
- Anne-Sophie de Smet4,
- Adriana Motyl6,
- Michael E. Hudson6,
- Juyong Park1,7,
- Xiaofeng Xin8,
- Michael E. Cusick1,2,
- Troy Moore9,
- Charlie Boone8,
- Michael Snyder6,
- Frederick P. Roth1,10,
- Albert-László Barabási1,7,
- Jan Tavernier4,
- David E. Hill1,2,
- Marc Vidal1,2,†
+ Author Affiliations
- ↵† To whom correspondence should be addressed. E-mail: marc_vidal@dfci.harvard.edu
-
↵* These authors contributed equally to this work.
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.
- Received for publication 4 April 2008.
- Accepted for publication 1 August 2008.
