An empirical framework for binary interactome mapping

By K. Venkatesan, Jean‐François Rual, A. Vázquez, Ulrich Stelzl, I. Lemmens, T. Hirozane-Kishikawa, Tong Hao, Martina Zenkner, Xiaofeng Xin, K.-I. Goh and 30 more. 2008

909 citations recorded by the source corpus.

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 ∼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.

Subfields: Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

A Directed Protein Interaction Network for Investigating Intracellular Signal Transduction (2011, methodology): “This is in good agreement with previous work, where we used independent experimental measures to estimate the precision of Y2H PPI data ( 19 , 42 ).”
A reference map of the human binary protein interactome (2020, methodology): “3c–g, 4, Supplementary Table 16–18, Supplementary Note 1).”
Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases (2011, neutral): “With the availability of the resulting large datasets, the challenge now lies in the generation PPIs within a cell and between cells at any given moment in . i c . oup . o m b i o i human proteome is estimated to encompass 130000–650000 (Stumpf , 2008; Venkatesan , 2009).”
Network Medicine: A Network-based Approach to Human Disease (2011, background): “The number of functionally relevant interactions between the components of this network, representing the links of the interactome, is expected to be much large”
A human functional protein interaction network and its application to cancer data analysis (2010, background): “The low sensitivity may result, in part, from high false negative rates existing in some of the data sets we used for NBC, especially in PPIs [59].”
Selecting causal genes from genome-wide association studies via functionally-coherent subnetworks (2014, background): “AR (androgen receptor), FGF10 (fibroblast growth factor 10), and NKX3-1 (NK3 homeobox 1)—found at Xq12, 5p12 and 8p21, respectively—have all received considerable attention for their probable role in prostate cancer development despite not yet being declared causal in the SCGC 30–32 .”
Three-dimensional reconstruction of protein networks provides insight into human genetic disease (2012, background): “2d ), confirming the coverage and quality of hSIN ( Supplementary Note 7 ).”
Systems biology of stem cell fate and cellular reprogramming (2009, methodology): “Perhaps the most promising way to address this issue is the combination of meticulous experimentation with computational inference, in which computational techniques are used to infer initial interaction networks and experimental techniques are used to validate inferred interactions and refine netwo”
HINT: High-quality protein interactomes and their applications in understanding human disease (2012, background): “, the search space is scanned without a priori expectations [17,19].”
Recent advances in the development of protein–protein interactions modulators: mechanisms and clinical trials (2020, background): “It is estimated that there are about 130,000–650,000 types of PPIs in the human interactome.(4,8,20) Although the number of protein complexes exceeds that of enzymes and receptors, designing a small molecule to bind to a PPI interface is challenging because of the reasons below.”