Towards a proteome-scale map of the human protein–protein interaction network

By Jean‐François Rual, K. Venkatesan, Tong Hao, T. Hirozane-Kishikawa, Amélie Dricot, Ning Li, G. Berriz, Francis D. Gibbons, Matija Dreze, N. Ayivi-Guedehoussou and 28 more. 2005

3,029 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology

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Citations in the corpus

Graph Kernels (2008, positive): “Specifically, a patient’s gene expression profile was transformed into a graph as follows: A node was created for every protein which — according to Rual et al. (2005) — participates in an interaction, and whose corresponding gene expression level was measured on this patient’s microarray.”
A human phenome-interactome network of protein complexes implicated in genetic disorders (2007, background): “Additionally, only a few large-scale protein interaction studies have been finalized for the human proteom”
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization (2009, background): “Recent biotechnological advances such as the high-throughput yeast two-hybrid screen have facilitated building proteome-wide protein–protein interaction networks (PPINs) or ‘interactome’ maps in humans (18,19).”
Biological network comparison using graphlet degree distribution (2007, positive): “Several different data sets are available for yeast and human, so we analyzed five yeast PPI networks obtained from three different high-throughput studies (35; 13; 37) and five human PPI networks obtained from the two recent high-throughput studies (32; 29) and three curated data bases (2; 26; 42).”
The Emerging Paradigm of Network Medicine in the Study of Human Disease (2012, background): “18–22 To date, novel insight of biological function from these PPI networks has resulted largely from analysis of static networks.”
Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes (2006, methodology): “Datasets. The protein–protein interaction datasets for each organism (Table 1) were constructed as follows: (i) The interaction dataset for C. elegans (WORM) corresponds to the ‘‘First-Pass’’ interactions of the worm interactome version 5, or ‘‘WI5’’ [3]; (ii) The interaction dataset for H. sapiens ”
BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions (2016, background): “…attention has been paid to a variety of molecular interaction networks and their potential roles in disease mechanism and drug development [1, 4–7], including transcriptional and post-transcriptional regulatory networks [8–10], functional RNA networks [11–13], protein–protein interaction…”
Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics (2013, background): “While wild-type CDKN1A interacts with CCND2 (76, 77), the interaction is disrupted by R67I mutation (HGMD accession number: CM092604) on CDKN1A (Figure S16).”
Human protein interaction networks across tissues and diseases (2015, background): “…section: This article was submitted to Systems Biology, a section of the journal Frontiers in Genetics Received: 28 May 2015 Accepted: 17 July 2015 Published: Citation: Yeger-Lotem E and Sharan R (2015) Human protein interaction networks across tissues and diseases.”
Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps (2007, background): “This includes one of the two major yeast high-throughput screens [2], a screen for Helicobacter pylori interactions [37], and important recent screens for human protein–protein interactions [6,7].”
Current approaches to gene regulatory network modelling (2007, methodology): “For example, the yeast-2-hybrid technology was used to determine protein-protein interactions between human proteins, yet the yeast cell provides a very different environment from a human cell [41,42].”