Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network

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Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network is …
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scholarly articleQ13442814

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P6179Dimensions Publication ID1049564858
P356DOI10.1038/NMETH.1279
P2888exact matchhttps://scigraph.springernature.com/pub.10.1038/nmeth.1279
P8608Fatcat IDrelease_ruiibsl2vjhz7fjrq5i4xf5uve
P932PMC publication ID3057923
P698PubMed publication ID19123269
P5875ResearchGate publication ID23720945

P50authorTomoko Hirozane-KishikawaQ28914653
Amélie DricotQ28914655
Sebiha CevikQ28914657
Julie SahalieQ28914660
Jean VandenhauteQ28914664
Jan TavernierQ29998792
Anne-Sophie de SmetQ29998796
Pascal BraunQ37379763
Frederick P. RothQ37393390
Nicolas BertinQ40584212
Mike BoxemQ43964820
Nono Ayivi-GuedehoussouQ43965345
Anne-Ruxandra CarvunisQ43965360
Muhammed A YildirimQ57321035
David E HillQ57644845
Matija DrezeQ81273126
Marc VidalQ81911349
Michael C CusickQ85308684
Muneesh TewariQ86570396
Jean-Christophe SimonQ88301590
Kristin C GunsalusQ96810742
Changyu FanQ114398428
Stuart MilsteinQ114418289
Nicolas SimonisQ115136762
Huey-Ling KaoQ117267122
Kavitha VenkatesanQ117267125
Fana GebreabQ117267126
Alex SmolyarQ117267127
Murat TasanQ117267130
Jin Sook AhnQ117267131
P2093author name stringNing Li
Tong Hao
Haiyuan Yu
Chenwei Lin
Niels Klitgord
Jean-François Rual
Elizabeth Dann
Irma Lemmens
David Szeto
P2860cites workThe COG database: an updated version includes eukaryotesQ21284294
Towards a proteome-scale map of the human protein–protein interaction networkQ21735930
Design and application of a cytokine-receptor-based interaction trapQ24292116
A protein domain-based interactome network for C. elegans early embryogenesisQ24322661
An empirical framework for binary interactome mappingQ24322723
A human protein-protein interaction network: a resource for annotating the proteomeQ24324450
VisANT: an online visualization and analysis tool for biological interaction dataQ24800519
High-throughput in vivo analysis of gene expression in Caenorhabditis elegansQ27334278
A protein interaction map of Drosophila melanogasterQ28131783
Protein interaction mapping in C. elegans using proteins involved in vulval developmentQ28141447
Functional genomic analysis of RNA interference in C. elegansQ28241721
The C. elegans RSA complex localizes protein phosphatase 2A to centrosomes and regulates mitotic spindle assemblyQ28748241
A map of the interactome network of the metazoan C. elegansQ29547482
Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germlineQ30747991
Browsing multidimensional molecular networks with the generic network browser (N-Browse)Q33372165
A protein-protein interaction map of the Caenorhabditis elegans 26S proteasomeQ33757687
An experimentally derived confidence score for binary protein-protein interactionsQ34292333
WormBase: new content and better accessQ34581089
Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs".Q35037874
RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projectsQ38449530
Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling networkQ40583898
Combined functional genomic maps of the C. elegans DNA damage responseQ44069172
vab-8 is a key regulator of posteriorly directed migrations in C. elegans and encodes a novel protein with kinesin motor similarityQ44825556
Mechanisms controlling sex myoblast migration in Caenorhabditis elegans hermaphroditesQ47068697
Two phases of astral microtubule activity during cytokinesis in C. elegans embryosQ47069370
Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans.Q47575778
Reverse MAPPIT detects disruptors of protein-protein interactions in human cells.Q49057103
A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans.Q51896048
Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis.Q51966659
Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.Q52577050
C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression.Q53864505
P433issue1
P407language of work or nameEnglishQ1860
P921main subjectCaenorhabditis elegansQ91703
interactomeQ841382
protein-protein interactionQ896177
P5008on focus list of Wikimedia projectScienceSourceQ55439927
P304page(s)47-54
P577publication date2009-01-01
P1433published inNature MethodsQ680640
P1476titleEmpirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network
P478volume6

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cites work (P2860)
Q34220929"Guilt by association" is the exception rather than the rule in gene networks
Q64107553A Comprehensive Drosophila melanogaster Transcription Factor Interactome
Q36619401A combined binary interaction and phenotypic map of C. elegans cell polarity proteins
Q30580503A computational framework for boosting confidence in high-throughput protein-protein interaction datasets
Q33658615A genome-wide gene function prediction resource for Drosophila melanogaster
Q34018339A genome-wide map of human genetic interactions inferred from radiation hybrid genotypes
Q33756741A genome-wide study of PDZ-domain interactions in C. elegans reveals a high frequency of non-canonical binding.
Q30500031A high-resolution C. elegans essential gene network based on phenotypic profiling of a complex tissue
Q34877875A highly efficient approach to protein interactome mapping based on collaborative filtering framework
Q41843924A membrane protein/signaling protein interaction network for Arabidopsis version AMPv2.
Q33729821A miniaturized sandwich immunoassay platform for the detection of protein-protein interactions
Q33891584A protein network-guided screen for cell cycle regulators in Drosophila
Q42643666A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE).
Q33775510A scalable approach for discovering conserved active subnetworks across species
Q35976800A streamlined tethered chromosome conformation capture protocol.
Q58763274Alteration of the cutaneous microbiome in psoriasis and potential role in Th17 polarization
Q90695918An abscisic acid-responsive protein interaction network for sucrose non-fermenting related kinase1 in abiotic stress response
Q36543809An evolutionarily conserved innate immunity protein interaction network
Q38455090An integrative C. elegans protein-protein interaction network with reliability assessment based on a probabilistic graphical model
Q33807573Antagonistic Smad transcription factors control the dauer/non-dauer switch in C. elegans
Q38014268Applications of stable isotope dimethyl labeling in quantitative proteomics
Q33851535Assembling a protein-protein interaction map of the SSU processome from existing datasets
Q35779549Atypical Transcriptional Activation by TCF via a Zic Transcription Factor in C. elegans Neuronal Precursors
Q33412935Auditory proteomics: methods, accomplishments and challenges
Q29140764Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported
Q34308163Beyond hairballs: The use of quantitative mass spectrometry data to understand protein-protein interactions
Q35834321Big Data in Caenorhabditis elegans: quo vadis?
Q45847143Biological function through network topology: a survey of the human diseasome
Q49966513Bridges in complex networks.
Q52652834Caenorhabditis elegans sperm membrane protein interactome.
Q52700423Comparison of the interactomic networks of different species in terms of accessibility.
Q41850322Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources
Q37090487Counting motifs in the human interactome.
Q37184407Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways
Q92702737Deciphering GRINA/Lifeguard1: Nuclear Location, Ca2+ Homeostasis and Vesicle Transport
Q41578167Deconstruction of the beaten Path-Sidestep interaction network provides insights into neuromuscular system development
Q24307459Development and application of a DNA microarray-based yeast two-hybrid system
Q33978412Dissection of genetic pathways in C. elegans
Q34280594Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system
Q28476723Dominating biological networks
Q38167225Edgotype: a fundamental link between genotype and phenotype
Q34572221Effects of early life exposure to ultraviolet C radiation on mitochondrial DNA content, transcription, ATP production, and oxygen consumption in developing Caenorhabditis elegans
Q38367823Evidence for network evolution in an Arabidopsis interactome map.
Q30914058Exploiting amino acid composition for predicting protein-protein interactions
Q37224364Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network
Q31033753Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches.
Q33716007From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase
Q56889474Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant
Q91742198Functional Proteomics of Nuclear Proteins in Tetrahymena thermophila: A Review
Q26774978Fundamentals of protein interaction network mapping
Q47774070Gibbs free energy as a measure of complexity correlates with time within C. elegans embryonic development
Q27312103Global functional analyses of cellular responses to pore-forming toxins
Q30823934Glucose or Altered Ceramide Biosynthesis Mediate Oxygen Deprivation Sensitivity Through Novel Pathways Revealed by Transcriptome Analysis in Caenorhabditis elegans.
Q34564378GraphCrunch 2: Software tool for network modeling, alignment and clustering
Q36218018Graphlet-based edge clustering reveals pathogen-interacting proteins
Q46226848Graphlet-based measures are suitable for biological network comparison
Q42858941High-quality binary interactome mapping
Q33623110High-resolution network biology: connecting sequence with function
Q38019869History of protein-protein interactions: from egg-white to complex networks
Q27684827Homodimerization of RBPMS2 through a new RRM-interaction motif is necessary to control smooth muscle plasticity
Q21245042Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses
Q37975999How advancement in biological network analysis methods empowers proteomics
Q42584215Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence
Q44518986Identifying functional links between genes by evolutionary transcriptomics.
Q37412756Implicating SCF complexes in organogenesis in Caenorhabditis elegans
Q36876110In Vivo Interaction Proteomics in Caenorhabditis elegans Embryos Provides New Insights into P Granule Dynamics
Q59813654Insect Transcription Factors: A Landscape of Their Structures and Biological Functions in and beyond
Q28301622Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
Q43467712Integrative network alignment reveals large regions of global network similarity in yeast and human
Q38010411Interactome mapping for analysis of complex phenotypes: insights from benchmarking binary interaction assays
Q29615773Interactome networks and human disease
Q37773558It's the machine that matters: Predicting gene function and phenotype from protein networks
Q37802870Large-scale protein interactome mapping: strategies and opportunities
Q30850866Large-scale protein-protein interactions detection by integrating big biosensing data with computational model
Q28482688Linking proteins to signaling pathways for experiment design and evaluation
Q37196237Literature-curated protein interaction datasets.
Q33909439MINE: Module Identification in Networks
Q37604636Mammalian two-hybrids come of age.
Q50903302Mapping Protein-Protein Interaction Using High-Throughput Yeast 2-Hybrid.
Q40749005Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities.
Q26778582Methods for biological data integration: perspectives and challenges
Q34061238Native capillary isoelectric focusing for the separation of protein complex isoforms and subcomplexes
Q30759763Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration
Q43892490Negative protein-protein interaction datasets derived from large-scale two-hybrid experiments.
Q21560992Network compression as a quality measure for protein interaction networks
Q36378788Next-Generation Sequencing for Binary Protein-Protein Interactions
Q26991938Non-transcriptional interactions of Hox proteins: inventory, facts, and future directions
Q92557035Omics Driven Understanding of the Intestines of Parasitic Nematodes
Q42735175Optimal network alignment with graphlet degree vectors
Q34523885PTIR: Predicted Tomato Interactome Resource
Q28114947Pooled-matrix protein interaction screens using Barcode Fusion Genetics
Q34018348Predicting genetic modifier loci using functional gene networks
Q50225769Preventing Illegitimate Extrasynaptic Acetylcholine Receptor Clustering Requires the RSU-1 Protein.
Q36677901Protein determinants of meiotic DNA break hot spots
Q38010662Protein interaction networks in medicine and disease
Q33678711Protein networks reveal detection bias and species consistency when analysed by information-theoretic methods
Q37824310Protein-protein interactions: making sense of networks via graph-theoretic modeling
Q42149240Quantifying noise in mass spectrometry and yeast two-hybrid protein interaction detection experiments
Q29140766Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions
Q34412223Random mutagenesis MAPPIT analysis identifies binding sites for Vif and Gag in both cytidine deaminase domains of Apobec3G.
Q34975931Regulation of RNA granule dynamics by phosphorylation of serine-rich, intrinsically disordered proteins in C. elegans
Q35110916Revealing missing parts of the interactome via link prediction
Q30009888SH3 interactome conserves general function over specific form.
Q38306700SUMV-1 antagonizes the activity of synthetic multivulva genes in Caenorhabditis elegans
Q36051128Seed selection strategy in global network alignment without destroying the entire structures of functional modules
Q27001247Seeing elegance in gene regulatory networks of the worm
Q34554087SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks
Q28478034Signalogs: orthology-based identification of novel signaling pathway components in three metazoans
Q94948286Split Intein-Mediated Protein Ligation for detecting protein-protein interactions and their inhibition
Q33957649Struct2Net: a web service to predict protein-protein interactions using a structure-based approach
Q37630764Systems biology from a yeast omics perspective
Q34992536Systems biology: Untangling the protein web.
Q34123813Tailored graph ensembles as proxies or null models for real networks I: tools for quantifying structure
Q39967137Targeting historically refractory interfaces: a partnership model that accelerates drug discovery within an expanded haystack
Q42373230Taxonomically Restricted Genes with Essential Functions Frequently Play Roles in Chromosome Segregation in Caenorhabditis elegans and Saccharomyces cerevisiae
Q39845045The Bait Compatibility Index: Computational Bait Selection for Interaction Proteomics Experiments
Q44195411The Core Diseasome
Q37107161The Golgi puppet master: COG complex at center stage of membrane trafficking interactions.
Q37395221The human protein coevolution network.
Q38473775The integrated disease network
Q33821575The living microarray: a high-throughput platform for measuring transcription dynamics in single cells
Q38385900The power of the yeast two-hybrid system in the identification of novel drug targets: building and modulating PPP1 interactomes
Q94544437The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma
Q41592105Topological network alignment uncovers biological function and phylogeny
Q48355416Two functionally distinct E2/E3 pairs coordinate sequential ubiquitination of a common substrate in Caenorhabditis elegans development.
Q42211716Unbiased identification of substrates of protein tyrosine phosphatase ptp-3 in C. elegans
Q40538760What you see is not what you get: how sampling affects macroscopic features of biological networks
Q37197823Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development
Q46261914X exceptionalism in Caenorhabditis speciation.
Q27939848Yeast homologues of three BLOC-1 subunits highlight KxDL proteins as conserved interactors of BLOC-1.

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