High Quality Binary Protein Interaction Map of the Yeast Interactome Network

By Haiyuan Yu, P. Braun, Muhammed A. Yıldırım, I. Lemmens, K. Venkatesan, Julie M. Sahalie, T. Hirozane-Kishikawa, Fana Gebreab, Na Li, Nicolas Simonis and 24 more. Science, 2008

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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.

Subfields: Food Science, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f520c530fa783ecb36d9ef60e29f2baee40d5751

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Citations in the corpus

HINT: High-quality protein interactomes and their applications in understanding human disease (2012, neutral): “, the search space is scanned without a priori expectations [17,19].”
A proteome-wide fission yeast interactome reveals network evolution principles from yeasts to human (2016, methodology): “Here, we compare the unbiased proteome-wide networks of S. pombe (FissionNet) and S. cerevisiae (CCSB-YI1) (Yu et al., 2008) that we produced using the same Y2H assay to analyze these two types of functional divergence.”
Computed structures of core eukaryotic protein complexes (2021, neutral): “cerevisiae and improved ortholog identification, the statistical method (direct coupling analysis, DCA) we had used in our previous coevolution-guided protein-protein interaction (PPI) screen in prokaryotes (9) [themore accurate GREMLIN (11) method is too slow for this] couldnot effectively distingu”
Fitting Heavy Tailed Distributions: The poweRlaw Package (2014, background): “• The number of interacting partners of proteins in yeast (Yu et al., 2008).”
An atlas of combinatorial transcriptional regulation in mouse and man (2010, neutral): “These figures are consistent with high quality interaction networks published elsewhere recently (Yu et al., 2008).”
An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man (vol 140, pg 744, 2010) (2010, neutral): “Other studies have successfully assembled large networks of protein interactions using technologies such as co-immunoprecipitation and twohybrid screening (Park et al., 2005; Yu et al., 2008), but to date these have not been systematically applied to map networks of transcription factors.”
Universality in network dynamics (2013, neutral): “Hence regardless of whether the underlying network is random (ER), scale-free (SF) or an empirical network (yeast protein-protein interaction (PPI) network [52]; yeast transcriptional regulatory network (TRN) [53]; see Sec S.VII) P ( S ) will be bounded (Fig.”
Link Prediction in Complex Networks: A Survey (2010, neutral): “Our knowledge of these networks is very limited, for example, 80% of the molecular interactions in cells of Yeast [10] and 99.7% of human [11,12] are still unknown.”
Literature-curated protein interaction datasets (2009, methodology): “BioGRID reports the greatest completeness for yeast but is not yet observations explain the poor reliability, relative to high-throughput datasets, of the singly supported literature-curated dataset in both computational and experimental comparative analyses 7 .”