Confirmation of Organized Modularity in the Yeast Interactome

A recent PLoS Biology article [1] rejected the conclusions of two previous publications [2,3] that two categories of highly connected “hub” proteins—“date” and “party” hubs—have distinct properties in the Saccharomyces cerevisiae interactome network. Currently available protein–protein interaction datasets are vastly incomplete, even for yeast [4]. Therefore, it is reasonable to rigorously re-scrutinize global properties of interactome networks as new datasets become available. Here we show that distinctions between date and party hubs [2], previously shown in a high-quality filtered yeast interactome (FYI) dataset [2,3], are in fact confirmed in an updated literature-curated yeast interactome network.

• Publication year

  2007

• Venue

  PLoS Biology

• Publication date

  2007-06-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1371/JOURNAL.PBIO.0050153PMID 17564493PMCID 1892830
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Stratus Not Altocumulus: A New View of the Yeast Protein Interaction Network

  2006cited by this paper
• Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae

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

  2006cited by this paper
• Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise

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

  2006cited by this paper
• Transcriptome profiling of Saccharomyces cerevisiae during a transition from fermentative to glycerol-based respiratory growth reveals extensive metabolic and structural remodeling

  2006cited by this paper
• Metabolic-State-Dependent Remodeling of the Transcriptome in Response to Anoxia and Subsequent Reoxygenation in Saccharomyces cerevisiae

  2006cited by this paper
• Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights

  2006cited by this paper
• Evolutionary and Physiological Importance of Hub Proteins

  2006cited by this paper
• Modularity and evolutionary constraint on proteins

  2005influential reference
• Adjusting for selection on synonymous sites in estimates of evolutionary distance.

  2005cited by this paper
• Why highly expressed proteins evolve slowly.

  2005cited by this paper
• Effect of sampling on topology predictions of protein-protein interaction networks

  2005cited by this paper
• High-definition macromolecular composition of yeast RNA-processing complexes.

  2004cited by this paper
• Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips.

  2004cited by this paper
• Integrating phenotypic and expression profiles to map arsenic-response networks

  2004cited by this paper
• Evidence for dynamically organized modularity in the yeast protein–protein interaction network

  2004influential reference
• Exploration of essential gene functions via titratable promoter alleles.

  2004cited by this paper
• Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data

  2003cited by this paper
• Global architecture of genetic interactions on the protein network

  2003cited by this paper
• Genome-wide Analysis of Gene Expression Regulated by the Calcineurin/Crz1p Signaling Pathway in Saccharomyces cerevisiae *

  2002cited by this paper
• Interplay of TBP inhibitors in global transcriptional control.

  2002cited by this paper
• Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

  2002cited by this paper
• Functional organization of the yeast proteome by systematic analysis of protein complexes

  2002cited by this paper
• Transcriptome profiling to identify genes involved in peroxisome assembly and function

  2002cited by this paper
• MIPS: a database for genomes and protein sequences.

  2002cited by this paper
• 90S pre-ribosomes include the 35S pre-rRNA, the U3 snoRNP, and 40S subunit processing factors but predominantly lack 60S synthesis factors.

  2002cited by this paper
• Evolutionary Rate in the Protein Interaction Network

  2002cited by this paper
• Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p.

  2001cited by this paper
• A comprehensive two-hybrid analysis to explore the yeast protein interactome

  2001cited by this paper
• Functional and Genomic Analyses Reveal an Essential Coordination between the Unfolded Protein Response and ER-Associated Degradation

  2000cited by this paper
• A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae

  2000cited by this paper
• Arrest, adaptation, and recovery following a chromosome double-strand break in Saccharomyces cerevisiae.

  2000cited by this paper
• Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles.

  2000cited by this paper
• New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis.

  2000cited by this paper
• Genomic expression programs in the response of yeast cells to environmental changes.

  2000cited by this paper
• Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation.

  2000cited by this paper
• Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast

  1999cited by this paper
• Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.

  1998cited by this paper
• The transcriptional program of sporulation in budding yeast.

  1998cited by this paper
• The Dip Test of Unimodality

  1985cited by this paper
• Computation of the Dip Statistic to Test for Unimodality

  1985cited by this paper

• Hubs and Bottlenecks in Protein-Protein Interaction Networks.

  2024cites this paper
• Yeast-Based Solutions in Controlling Plant Pathogens

  2024cites this paper
• Prediction, Analysis, Visualization, and Storage of Protein–Protein Interactions Using Computational Approaches

  2021cites this paper
• A large accessory protein interactome is rewired across environments

  2020cites this paper
• Identification of Essential Proteins by Detecting Topological and Functional Clusters in Protein Interaction Network of Saccharomyces Cerevisiae

  2019cites this paper
• Investigating the Network Basis of Negative Genetic Interactions in Saccharomyces cerevisiae with Integrated Biological Networks and Triplet Motif Analysis.

  2018cites this paper
• Integrating molecular networks with genetic variant interpretation for precision medicine

  2018cites this paper
• Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions

  2017cites this paper
• A preferential attachment approach to community structure and the structure of communities

  2016cites this paper
• GIT2 Acts as a Systems-Level Coordinator of Neurometabolic Activity and Pathophysiological Aging

  2016cites this paper
• Interaction and localization diversities of global and local hubs in human protein-protein interaction networks.

  2016cites this paper
• Deciphering the cross-talking of human competitive endogenous RNAs in K562 chronic myelogenous leukemia cell line.

  2016cites this paper
• Collective Graph Identification

  2016cites this paper
• Compartmentalization and Functionality of Nuclear Disorder: Intrinsic Disorder and Protein-Protein Interactions in Intra-Nuclear Compartments

  2015cites this paper
• Proteome mining for drug target identification in Listeria monocytogenes strain EGD-e and structure-based virtual screening of a candidate drug target penicillin binding protein 4.

  2015cites this paper
• The terminal enzymes of cholesterol synthesis, DHCR24 and DHCR7, interact physically and functionally[S]

  2015cites this paper
• Respiratory particle deposition probability due to sedimentation with variable gravity and electrostatic forces.

  2014cites this paper
• Protein-protein interaction networks (PPI) and complex diseases

  2014cites this paper
• Dynamic Modularity of Host Protein Interaction Networks in Salmonella Typhi Infection

  2014cites this paper
• Co-expression and co-localization of hub proteins and their partners are encoded in protein sequence.

  2014cites this paper
• Prediction of Essential Proteins Based on Overlapping Essential Modules

  2014cites this paper
• Mining the Modular Structure of Protein Interaction Networks

  2014cites this paper
• Classifications of protein roles in the functional organization of the cell

  2014cites this paper
• Análisis de redes complejas en sistemas biomoleculares

  2014cites this paper
• Protein-protein interactions and genetic diseases: The interactome.

  2014cites this paper
• Discovering meaning from biological sequences: focus on predicting misannotated proteins, binding patterns, and g4-quadruplex secondary structures

  2013cites this paper
• On the functional and structural characterization of hubs in protein-protein interaction networks.

  2013cites this paper
• Protein-Protein Interaction Networks

  2013cites this paper
• Predicting the Binding Patterns of Hub Proteins: A Study Using Yeast Protein Interaction Networks

  2013cites this paper
• Global versus local hubs in human protein-protein interaction network.

  2013cites this paper
• Bioinformatics analysis of protein interaction networks: Statistics, topologies, and meeting the standards of experimental biologists

  2013cites this paper
• Dynamic Structures of Protein Interaction Networks Predict Complex Phenotypes of Biological Systems

  2013cites this paper
• Simple Topological Features Reflect Dynamics and Modularity in Protein Interaction Networks

  2013cites this paper
• Nodes Having a Major Influence to Break Cooperation Define a Novel Centrality Measure: Game Centrality

  2013influential citation
• Dynamic modular architecture of protein-protein interaction networks beyond the dichotomy of ‘date' and ‘party' hubs

  2013influential citation
• Tutorial on biological networks

  2012cites this paper
• The methylproteome and the intracellular methylation network

  2012cites this paper
• Sic1 as a timer of Clb cyclin waves in the yeast cell cycle – design principle of not just an inhibitor

  2012cites this paper
• HINT: High-quality protein interactomes and their applications in understanding human disease

  2012cites this paper
• Time-Course Proteome Analysis Reveals the Dynamic Response of Cryptococcus gattii Cells to Fluconazole

  2012cites this paper
• Proteome-Wide Discovery of Evolutionary Conserved Sequences in Disordered Regions

  2012influential citation
• Topological Characteristics of Molecular Networks

  2012cites this paper
• A multidimensional matrix for systems biology research and its application to interaction networks.

  2012cites this paper
• A Survey on Evolutionary Analysis in PPI Networks

  2012cites this paper
• Characterization and evolutionary analysis of protein-protein interaction networks.

  2012cites this paper
• Combinatorial network of transcriptional regulation and microRNA regulation in human cancer

  2012influential citation
• Interactome mapping for analysis of complex phenotypes: Insights from benchmarking binary interaction assays

  2012cites this paper
• Protein interaction networks in medicine and disease

  2012cites this paper
• Correlation of Genomic Features With Dynamic Modularity in the Yeast Interactome: A View From the Structural Perspective

  2012cites this paper
• Identifying Graphs from Noisy Observational Data

  2012cites this paper
• Understanding centrality-lethality rule from the distinction of essential party/date hub proteins in yeast protein-protein interaction networks

  2012cites this paper
• Knowledge derivation and data mining strategies for probabilistic functional integrated networks

  2012cites this paper
• Visualization of the interactome: What are we looking at?

  2012cites this paper
• Molecular systems biology of Sic1 in yeast cell cycle regulation through multiscale modeling.

  2012cites this paper
• I STITUTO DI A NALISI DEI S ISTEMI ED I NFORMATICA

  2012cites this paper
• Networks in nature : dynamics, evolution, and modularity

  2012cites this paper
• Discovery and analysis of patterns in molecular networks: Link prediction, network analysis, and applications to novel drug target discovery

  2012cites this paper
• Dynamic Hubs Show Competitive and Static Hubs Non-Competitive Regulation of Their Interaction Partners

  2012cites this paper
• I STITUTO DI A NALISI DEI S ISTEMI ED I NFORMATICA “ Antonio Ruberti

  2012cites this paper
• Interactome networks and human disease.

  2011cites this paper
• Correlation of genomics features with the date and party hub distinction: A view from three dimensional protein structures

  2011influential citation
• Heat Shock Partially Dissociates the Overlapping Modules of the Yeast Protein-Protein Interaction Network: A Systems Level Model of Adaptation

  2011cites this paper
• The Dichotomy in Degree Correlation of Biological Networks

  2011cites this paper
• Detection of functional modules from protein interaction networks with an enhanced random walk based algorithm

  2011influential citation
• Four‐dimensional visualisation and analysis of protein–protein interaction networks

  2011cites this paper
• Protein‐protein interactions: Making sense of networks via graph‐theoretic modeling

  2011cites this paper
• Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs

  2011cites this paper
• Coupling protein complex analysis to peptide based proteomics.

  2010cites this paper
• Hub Promiscuity in Protein-Protein Interaction Networks

  2010cites this paper
• Investigating the validity of current network analysis on static conglomerate networks by protein network stratification

  2010cites this paper
• Understanding protein evolutionary rate by integrating gene co-expression with protein interactions

  2010influential citation
• Modeling Virus-Host Networks

  2010cites this paper
• Computational modeling in systems biology.

  2010cites this paper
• Low-complexity regions within protein sequences have position-dependent roles

  2010cites this paper
• Structural properties of hub proteins

  2010cites this paper
• From evidence to inference: Probing the evolution of protein interaction networks

  2009cites this paper
• Hares and tortoises: The high‐ versus low‐throughput proteomic race

  2009cites this paper
• The properties of hub proteins in a yeast‐aggregated cell cycle network and its phase sub‐networks

  2009cites this paper
• Identifying Hubs in Protein Interaction Networks

  2009cites this paper
• Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks

  2009influential citation
• The Interactorium: Visualising proteins, complexes and interaction networks in a virtual 3‐D cell

  2009cites this paper
• Module Finding Approaches for Protein Interaction Networks

  2009cites this paper
• Fine-Scale Dissection of Functional Protein Network Organization by Statistical Network Analysis

  2009cites this paper
• Progress in The Evolutionary Analysis of Protein Interaction Networks*: Progress in The Evolutionary Analysis of Protein Interaction Networks*

  2009cites this paper
• Understanding the functional significance of intrinsically disordered regions in proteins using computational methods

  2009cites this paper
• Dynamic modularity in protein interaction networks predicts breast cancer outcome

  2009cites this paper
• Challenges and Rewards of Interaction Proteomics *

  2009cites this paper
• Exploring the evolutionary rate differences of party hub and date hub proteins in Saccharomyces cerevisiae protein-protein interaction network.

  2009cites this paper
• RETRACTED: Why proteins evolve at different rates: The functional hypothesis versus the mistranslation‐induced protein misfolding hypothesis

  2009cites this paper
• Sticking together? Falling apart? Exploring the dynamics of the interactome.

  2008cites this paper
• Protein-protein interaction networks and biology—what's the connection?

  2008cites this paper
• Selection to minimise noise in living systems and its implications for the evolution of gene expression

  2008cites this paper
• Systems Biology in Molecular Psychiatry

  2008cites this paper
• The role of disorder in interaction networks: a structural analysis

  2008influential citation
• Understanding biological functions through molecular networks

  2008cites this paper
• Evolutionary analysis in PPI networks and applications

  2008cites this paper
• Current awareness on yeast

  2008cites this paper
• Evolution and dynamics of protein interactions and networks.

  2008cites this paper
• High throughput protein-protein interaction data: clues for the architecture of protein complexes

  2008cites this paper
• Chaperones as integrators of cellular networks: Changes of cellular integrity in stress and diseases

  2007cites this paper