Building Protein-Protein Interaction Networks with Proteomics and Informatics Tools*

The systematic characterization of the whole interactomes of different model organisms has revealed that the eukaryotic proteome is highly interconnected. Therefore, biological research is progressively shifting away from classical approaches that focus only on a few proteins toward whole protein interaction networks to describe the relationship of proteins in biological processes. In this minireview, we survey the most common methods for the systematic identification of protein interactions and exemplify different strategies for the generation of protein interaction networks. In particular, we will focus on the recent development of protein interaction networks derived from quantitative proteomics data sets.

• Publication year

  2011

• Venue

  Journal of Biological Chemistry

• Publication date

  2011-05-12

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1074/jbc.R110.174052PMID 21566121PMCID PMC3129144
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• Whole-interactome characterization supports a shift from approaches focused on only a few proteins toward network-level descriptions of protein relationships.

  Confidence 0.88

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• Recent development of protein-protein interaction networks is emphasized in the context of quantitative proteomics data sets.

  Confidence 0.91

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• Different strategies for generating protein-protein interaction networks are exemplified.

  Confidence 0.95

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• Common methods for the systematic identification of protein interactions are surveyed.

  Confidence 0.96

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review

• protein-protein interaction network

  network, model

  A network representation in which proteins are nodes and their interactions are edges.

  Aliases: PPI network, protein interaction network

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• quantitative proteomics data set

  dataset, data source

  A proteomics dataset that includes quantitative measurements of protein abundance or interaction-related signals.

  Aliases: quantitative proteomics dataset, proteomics data set

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• systematic identification of protein interactions

  method, process

  An experimental or computational process for detecting protein-protein interactions across many proteins at once.

  Aliases: protein interaction screening, interaction identification

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• whole interactome

  network, system

  The complete set of molecular interactions present in an organism or proteome.

  Aliases: interactome, global interactome

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review

• Streamlined analysis schema for high-throughput identification of endogenous protein complexes

  2010cited by this paper
• Network organization of the human autophagy system

  2010cited by this paper
• Characterization of cell cycle specific protein interaction networks of the yeast 26S proteasome complex by the QTAX strategy.

  2010cited by this paper
• A Global Protein Kinase and Phosphatase Interaction Network in Yeast

  2010cited by this paper
• Systematic Analysis of Human Protein Complexes Identifies Chromosome Segregation Proteins

  2010cited by this paper
• Defining the human deubiquitinating enzyme interaction landscape.

  2009cited by this paper
• Cell fate decisions are specified by the dynamic ERK interactome

  2009cited by this paper
• Quantitative strategies to fuel the merger of discovery and hypothesis-driven shotgun proteomics.

  2009cited by this paper
• Mammalian two-hybrids come of age.

  2009cited by this paper
• Quantitative mass spectrometry of TATA binding protein-containing complexes and subunit phosphorylations during the cell cycle

  2009cited by this paper
• Determining Protein Complex Connectivity Using a Probabilistic Deletion Network Derived from Quantitative Proteomics

  2009cited by this paper
• Quantitative interaction proteomics using mass spectrometry

  2009cited by this paper
• High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

  2008cited by this paper
• Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics

  2008cited by this paper
• An experimentally derived confidence score for binary protein-protein interactions

  2008cited by this paper
• Characterization of the proteasome interaction network using a QTAX-based tag-team strategy and protein interaction network analysis

  2008cited by this paper
• From pull-down data to protein interaction networks and complexes with biological relevance

  2008cited by this paper
• Toward a Comprehensive Atlas of the Physical Interactome of Saccharomyces cerevisiae*S

  2007cited by this paper
• The human disease network

  2007cited by this paper
• Revealing static and dynamic modular architecture of the eukaryotic protein interaction network

  2007cited by this paper
• Network modeling links breast cancer susceptibility and centrosome dysfunction.

  2007cited by this paper
• Drug—target network

  2007cited by this paper
• A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration.

  2006cited by this paper
• Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

  2006cited by this paper
• Proteome survey reveals modularity of the yeast cell machinery

  2006cited by this paper
• How Scale-Free Are Biological Networks

  2006cited by this paper
• Global topological features of cancer proteins in the human interactome

  2006cited by this paper
• An Integrated Mass Spectrometry-based Proteomic Approach

  2006cited by this paper
• Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae.

  2006cited by this paper
• Mass spectrometry‐based proteomic analysis of the epitope‐tag affinity purified protein complexes in eukaryotes

  2006cited by this paper
• Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors

  2006cited by this paper
• Discovering disease-genes by topological features in human protein-protein interaction network

  2006cited by this paper
• A human protein-protein interaction network: a resource for annotating the proteome.

  2005cited by this paper
• Mining Alzheimer Disease Relevant Proteins from Integrated Protein Interactome Data

  2005cited by this paper
• Towards a proteome-scale map of the human protein–protein interaction network

  2005cited by this paper
• Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents*S

  2004cited by this paper
• Genomic analysis of essentiality within protein networks.

  2004cited by this paper
• A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease.

  2004cited by this paper
• A Map of the Interactome Network of the Metazoan C. elegans

  2004cited by this paper
• Cytoscape: a software environment for integrated models of biomolecular interaction networks.

  2003cited by this paper
• Global analysis of protein expression in yeast

  2003cited by this paper
• Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS

  2003cited by this paper
• A Protein Interaction Map of Drosophila melanogaster

  2003cited by this paper
• Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics*

  2002cited by this paper
• A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae

  2000cited by this paper
• A generic protein purification method for protein complex characterization and proteome exploration

  1999cited by this paper
• Quantitative analysis of complex protein mixtures using isotope-coded affinity tags

  1999cited by this paper
• A novel genetic system to detect protein–protein interactions

  1989cited by this paper

• Identification of host proteins interacting with NS3 protein of Bluetongue virus

  2026cites this paper
• PTMs as molecular encoders: reprogramming chaperones into epichaperomes for network control in disease

  2025cites this paper
• Patient-specific Biomolecular Instruction Tuning

  2025cites this paper
• Contextual AI models for single-cell protein biology

  2023cites this paper
• Generation and Utilization of a Monoclonal Antibody against Hepatitis B Virus Core Protein for a Comprehensive Interactome Analysis

  2022cites this paper
• A subnetwork-based framework for prioritizing and evaluating prognostic gene modules from cancer transcriptome data

  2022cites this paper
• A proximity labeling method for protein–protein interactions on cell membrane

  2022cites this paper
• Acetylation-Specific Interference by Anti-Histone H3K9ac Intrabody Results in Precise Modulation of Gene Expression

  2022cites this paper
• Gene expression profile analysis unravelled the systems level association of renal cell carcinoma with diabetic nephropathy and Matrix-metalloproteinase-9 as a potential therapeutic target

  2022cites this paper
• Bioinformatics Analysis Reveals Crosstalk Among Platelets, Immune Cells, and the Glomerulus That May Play an Important Role in the Development of Diabetic Nephropathy

  2021influential citation
• Mapping major SARS-CoV-2 drug targets and assessment of druggability using computational fragment screening: Identification of an allosteric small-molecule binding site on the Nsp13 helicase

  2021cites this paper
• Genome-scale protein interaction network construction and topology analysis of functional hypothetical proteins in Helicobacter pylori divulges novel therapeutic targets.

  2021cites this paper
• MCS+: An Efficient Algorithm for Crawling the Community Structure in Multiplex Networks

  2021cites this paper
• Antisense long non-coding RNA WEE2-AS1 regulates human vascular endothelial cell viability via cell cycle G2/M transition in arteriosclerosis obliterans

  2020cites this paper
• Prediction of a miRNA‐mRNA functional synergistic network for cervical squamous cell carcinoma

  2019cites this paper
• Diversified Application of Barcoded PLATO (PLATO-BC) Platform for Identification of Protein Interactions

  2019cites this paper
• Impact of Symmetries in Graph Clustering

  2019cites this paper
• Genome‐wide profiling of mRNA and lncRNA expression in dengue fever and dengue hemorrhagic fever

  2019cites this paper
• Conceptual Evolution of Cell Signaling

  2019cites this paper
• Protein-Protein Interactions

  2019cites this paper
• Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function.

  2018cites this paper
• Genome-Wide Association Studies and Heritability Estimation in the Functional Genomics Era

  2018cites this paper
• Screening of binding proteins that interact with Chinese sacbrood virus VP3 capsid protein in Apis cerana larvae cDNA library by the yeast two-hybrid method.

  2018cites this paper
• Identification of Essential Proteins Using Induced Stars in Protein-Protein Interaction Networks

  2017cites this paper
• Protein-protein interactions: detection, reliability assessment and applications

  2016cites this paper
• Boolean modeling techniques for protein co-expression networks in systems medicine

  2016cites this paper
• Construction and analysis of protein-protein interaction networks based on proteomics data of prostate cancer

  2016cites this paper
• Construction and characterization of yeast two-hybrid cDNA library derived from LFBK cell line.

  2015cites this paper
• An overview of protein identification studies in cassava.

  2015cites this paper
• Systems Biology: A New Paradigm for Drug Discovery

  2015cites this paper
• Split focal adhesion kinase for probing protein–protein interactions

  2014cites this paper
• The Impact of Mass Spectrometry-Based Proteomics on Fundamental Discoveries in Virology.

  2014cites this paper
• Dysbindin-Associated Proteome in the P2 Synaptosome Fraction of Mouse Brain

  2014cites this paper
• Proteomic Analysis of the SH2 Domain-containing Leukocyte Protein of 76 kDa (SLP76) Interactome in Resting and Activated Primary Mast Cells

  2014cites this paper
• System Biology of Cell Signaling

  2013cites this paper
• Quantifying proteomes and their post-translational modifications by stable isotope label-based mass spectrometry.

  2013cites this paper
• Protein-protein interaction networks: probing disease mechanisms using model systems

  2013cites this paper
• Protein–protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches

  2013cites this paper
• Protein-Protein Interactions as a Strategy towards Protein-Specific Drug Design: The Example of Ataxin-1

  2013cites this paper
• eview daptation and learning of molecular networks as a description of ancer development at the systems-level : Potential use in nti-cancer therapies

  2013cites this paper
• Human diseases through the lens of network biology.

  2013cites this paper
• The Human Eye Proteome Project: Perspectives on an emerging proteome

  2013cites this paper
• Proteomic approaches in circadian biology.

  2013cites this paper
• A proteomics view of the molecular mechanisms and biomarkers of glaucomatous neurodegeneration.

  2013cites this paper
• Proteomic approaches to the study of papillomavirus-host interactions.

  2013cites this paper
• Target Identification and Validation

  2013cites this paper
• Adaptation and learning of molecular networks as a description of cancer development at the systems-level: potential use in anti-cancer therapies.

  2013cites this paper
• Proteomic Analysis of the SH2Domain-containing Leukocyte Protein of 76 kDa (SLP76) Interactome*

  2013cites this paper
• The Protein-Protein Interactome of Saccharomyces cerevisiae ABC Transporters Nft1p, Pdr10p, Pdr18p and Vmr1p

  2012cites this paper
• Comparative protein interactomics of neuroglobin and myoglobin

  2012cites this paper
• ELF3 recruitment to the PRR9 promoter requires other Evening Complex members in the Arabidopsis circadian clock

  2012cites this paper
• System level mechanisms of adaptation, learning, memory formation and evolvability: the role of chaperone and other networks.

  2012cites this paper
• Structure and dynamics of molecular networks: A novel paradigm of drug discovery. A comprehensive review

  2012influential citation
• The proteomic landscape of human disease: construction and evaluation of networks associated to complex traits

  2012influential citation
• Mass Spectrometry on the Frontiers of Molecular Biophysics and Structural Biology: Perspectives and Challenges

  2012cites this paper
• Structure-based algorithms for protein-protein interaction prediction

  2012cites this paper
• Identification of the Structural Features that Mediate Binding Specificity in the Recognition of STAT Proteins by Dual-Specificity Phosphatases

  2012cites this paper
• Proteomics and microRNA profiling in cardiac fibrosis

  2012cites this paper
• Opportunities and challenges for nutritional proteomics in cancer prevention.

  2012cites this paper
• Latest developments in experimental and computational approaches to characterize protein–lipid interactions

  2012cites this paper
• Affinity purification of protein complexes for analysis by multidimensional protein identification technology.

  2012cites this paper
• Virtual Interactomics of Proteins from Biochemical Standpoint

  2012cites this paper
• Identification of aberrant pathways and network activities from high-throughput data

  2012cites this paper
• 2012 Landes Bioscience. Do not distribute. ELF3 recruitment to the PRR9 promoter requires other Evening Complex members in the Arabidopsis circadian clock

  2012cites this paper
• A computational framework for boosting confidence in high-throughput protein-protein interaction datasets

  2012cites this paper
• Integration of Bioinformatics Tools for Proteomics Research

  2011cites this paper
• Integration of Bioinformatics Tools for Proteomics Research

  2011cites this paper