title: An empirical framework for binary interactome mapping.
abstract: Several attempts have been made to systematically map protein-protein interaction, or 'interactome', networks. However, it remains difficult to assess the quality and coverage of existing data sets. Here we describe a framework that uses an empirically-based approach to rigorously dissect quality parameters of currently available human interactome maps. Our results indicate that high-throughput yeast two-hybrid (HT-Y2H) interactions for human proteins are more precise than literature-curated interactions supported by a single publication, suggesting that HT-Y2H is suitable to map a significant portion of the human interactome. We estimate that the human interactome contains approximately 130,000 binary interactions, most of which remain to be mapped. Similar to estimates of DNA sequence data quality and genome size early in the Human Genome Project, estimates of protein interaction data quality and interactome size are crucial to establish the magnitude of the task of comprehensive human interactome mapping and to elucidate a path toward this goal.
authors.affiliation: Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA.
authors.forename: Kavitha
authors.initials: K
authors.lastname: Venkatesan
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Rual
authors.forename: Alexei
authors.initials: A
authors.lastname: Vazquez
authors.forename: Ulrich
authors.initials: U
authors.lastname: Stelzl
authors.forename: Irma
authors.initials: I
authors.lastname: Lemmens
authors.forename: Tomoko
authors.initials: T
authors.lastname: Hirozane-Kishikawa
authors.forename: Tong
authors.initials: T
authors.lastname: Hao
authors.forename: Martina
authors.initials: M
authors.lastname: Zenkner
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Xin
authors.forename: Kwang-Il
authors.initials: KI
authors.lastname: Goh
authors.forename: Muhammed A
authors.initials: MA
authors.lastname: Yildirim
authors.forename: Nicolas
authors.initials: N
authors.lastname: Simonis
authors.forename: Kathrin
authors.initials: K
authors.lastname: Heinzmann
authors.forename: Fana
authors.initials: F
authors.lastname: Gebreab
authors.forename: Julie M
authors.initials: JM
authors.lastname: Sahalie
authors.forename: Sebiha
authors.initials: S
authors.lastname: Cevik
authors.forename: Christophe
authors.initials: C
authors.lastname: Simon
authors.forename: Anne-Sophie
authors.initials: AS
authors.lastname: de Smet
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Dann
authors.forename: Alex
authors.initials: A
authors.lastname: Smolyar
authors.forename: Arunachalam
authors.initials: A
authors.lastname: Vinayagam
authors.forename: Haiyuan
authors.initials: H
authors.lastname: Yu
authors.forename: David
authors.initials: D
authors.lastname: Szeto
authors.forename: Heather
authors.initials: H
authors.lastname: Borick
authors.forename: Amélie
authors.initials: A
authors.lastname: Dricot
authors.forename: Niels
authors.initials: N
authors.lastname: Klitgord
authors.forename: Ryan R
authors.initials: RR
authors.lastname: Murray
authors.forename: Chenwei
authors.initials: C
authors.lastname: Lin
authors.forename: Maciej
authors.initials: M
authors.lastname: Lalowski
authors.forename: Jan
authors.initials: J
authors.lastname: Timm
authors.forename: Kirstin
authors.initials: K
authors.lastname: Rau
authors.forename: Charles
authors.initials: C
authors.lastname: Boone
authors.forename: Pascal
authors.initials: P
authors.lastname: Braun
authors.forename: Michael E
authors.initials: ME
authors.lastname: Cusick
authors.forename: Frederick P
authors.initials: FP
authors.lastname: Roth
authors.forename: David E
authors.initials: DE
authors.lastname: Hill
authors.forename: Jan
authors.initials: J
authors.lastname: Tavernier
authors.forename: Erich E
authors.initials: EE
authors.lastname: Wanker
authors.forename: Albert-László
authors.initials: AL
authors.lastname: Barabási
authors.forename: Marc
authors.initials: M
authors.lastname: Vidal
mesh_terms: D030562:Databases, Protein; D006801:Humans; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000032:analysis* / Q000235:genetics / Q000378:metabolism*; D012680:Sensitivity and Specificity
chemical_list: D011506:Proteins