Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins.

By Takashi Ito, K. Tashiro, S. Muta, Ritsuko Ozawa, Tomoko Chiba, Mayumi Nishizawa, Kiyoshi Yamamoto, S. Kuhara, Y. Sakaki. Proceedings of the National Academy of Sciences of the United States of America, 2000

860 citations recorded by the source corpus.

Subfields: Food Science, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ad381f9a49ec6dc0796004ecab181628e0a533a5

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Citations in the corpus

Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D (2009, background): “Here, we describe verification of PPIs from five human-curated sources in I2D: BIND (Bader et al., 2001), DIP (Xenarios et al., 2000), HPRD (Peri et al., 2003), IntAct (Kerrien et al., 2007), and MINT (Zanzoni et al., 2002).”
DIP: The Database of Interacting Proteins: 2001 update (2001, neutral): “DIP was expanded significantly by the addition of data from large-scale yeast twohybrid experiments (4,5).”
A robust toolkit for functional profiling of the yeast genome. (2004, background): “Interestingly, cdc102-1 also exhibited synthetic interactions with both ptc1 and nbp2 , and Ptc1 and Nbp2 physically interact (Ho et al., 2002; Ito et al., 2000; Uetz et al., 2000).”
BIND: the Biomolecular Interaction Network Database (2003, methodology): “Such tools have been written to import information from the DIP database (13) and from recent yeast two-hybrid protein–protein interaction mapping projects (14, 15 ).”
Evolution of networks (2001, background): “, collaboration networks [11, 12, 13, 14, 15], public relations nets [16, 17, 18, 19, 20], citations of scienti®c papers [21, 22, 23, 24, 25, 26, 27], some industrial networks [11, 12, 28], transportation networks [29, 30], nets of relations between enterprises and agents in ®nancial markets [31], t”
Similarity of phylogenetic trees as indicator of protein-protein interaction. (2001, background): “Indeed, the first genome-scale results are already available: between 183 and 280 experimentally determined interactions in yeast (Ito et al., 2000; Uetz et al., 2000) and 261 in Helicobacter pylori (Rain et al., 2001).”
clusterMaker: a multi-algorithm clustering plugin for Cytoscape (2011, methodology): “Experimental sources of protein-protein interaction data include yeast two-hybrid (Y2H) [47,48] and split-ubiquitin [49] approaches, high-throughput mass spectrometric protein complex identification (HMS-PCI) [50] and tandem affinity purification followed by mass spectrometry (TAP-MS) [35,51].”
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. (2004, background): “With recent genome-wide studies on protein–protein and protein–DNA interactions (Ito et al. 2000; Uetz et al. 2000; Iyer et al. 2001; Gavin et al. 2002; Ho et al. 2002; Horak et al. 2002; Lee et al. 2002), it is now possible to examine the degree to which protein–protein and protein–DNA…”
A Model of Large-Scale proteome Evolution (2002, background): “Protein-protein interaction maps have been studied, at different levels, in a variety of organisms including viruses [5, 13, 25], prokaryotes [31], yeast [18] and multicellular organisms such as C.”
Biological network comparison using graphlet degree distribution (2007, positive): “Statistical and theoretical properties of these networks have been extensively studied (15; 20; 30; 22; 36; 41; 27; 34) due to their important biological implications (14; 17).”