PINA v2.0: mining interactome modules.

scientific article published on 8 November 2011

PINA v2.0: mining interactome modules. is …
instance of (P31):
scholarly articleQ13442814

External links are
P8978DBLP publication IDjournals/nar/CowleyPKWPGBHW12
P356DOI10.1093/NAR/GKR967
P932PMC publication ID3244997
P698PubMed publication ID22067443
P5875ResearchGate publication ID51783414

P50authorAndrew BiankinQ38802580
Mark PineseQ55167830
Nicola J WaddellQ60503046
Sampsa HautaniemiQ30347472
Mark J. CowleyQ38802512
Sean GrimmondQ38802553
P2093author name stringJohn V Pearson
Karin S Kassahn
Jianmin Wu
P2860cites workA graph-based approach to systematically reconstruct human transcriptional regulatory modulesQ42626909
Integrated network analysis platform for protein-protein interactionsQ43961965
CFinder: locating cliques and overlapping modules in biological networksQ82534265
Large-scale data integration framework provides a comprehensive view on glioblastoma multiformeQ21183973
An automated method for finding molecular complexes in large protein interaction networksQ21284295
Gene ontology: tool for the unification of biologyQ23781406
MPact: the MIPS protein interaction resource on yeastQ24538008
International network of cancer genome projectsQ24611474
KEGG for representation and analysis of molecular networks involving diseases and drugsQ24644514
The Pfam protein families databaseQ24644670
An efficient algorithm for large-scale detection of protein familiesQ28131838
Specificity and stability in topology of protein networksQ28216450
The Database of Interacting Proteins: 2004 updateQ28234998
The BioGRID Interaction Database: 2011 updateQ28298160
The IntAct molecular interaction database in 2010Q28749230
Network motifs: simple building blocks of complex networksQ29547340
Human Protein Reference Database--2009 updateQ29547392
Cytoscape 2.8: new features for data integration and network visualizationQ29547471
Using GOstats to test gene lists for GO term associationQ29615168
MINT, the molecular interaction database: 2009 updateQ29617595
Evaluation of clustering algorithms for protein-protein interaction networksQ33262820
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactionsQ33302066
SPICi: a fast clustering algorithm for large biological networksQ33785547
MINE: Module Identification in NetworksQ33909439
Assessing the functional coherence of modules found in multiple-evidence networks from ArabidopsisQ33911818
Modular organization of cellular networksQ34329388
Molecular signatures database (MSigDB) 3.0.Q35019708
Interactome: gateway into systems biologyQ36257382
P275copyright licenseCreative Commons Attribution-NonCommercial 3.0 UnportedQ18810331
P6216copyright statuscopyrightedQ50423863
P4510describes a project that usesCytoscapeQ3699942
P433issueDatabase issue
P407language of work or nameEnglishQ1860
P304page(s)D862-5
P577publication date2011-11-08
P1433published inNucleic Acids ResearchQ135122
P1476titlePINA v2.0: mining interactome modules
P478volume40

Reverse relations

cites work (P2860)
Q28547803A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types
Q35477305A comparative study of disease genes and drug targets in the human protein interactome
Q92376994A genome-wide positioning systems network algorithm for in silico drug repurposing
Q34388604A network synthesis model for generating protein interaction network families
Q38833493A new locus regulating MICALL2 expression was identified for association with executive inhibition in children with attention deficit hyperactivity disorder
Q34530287A probabilistic coevolutionary biclustering algorithm for discovering coherent patterns in gene expression dataset
Q39149150A scored human protein-protein interaction network to catalyze genomic interpretation.
Q36529860A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics.
Q35671408A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case
Q34635119AIM: a comprehensive Arabidopsis interactome module database and related interologs in plants.
Q34524369APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks.
Q36088348ASEB: a web server for KAT-specific acetylation site prediction.
Q37096363Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes
Q36111466An integrative genomics approach for identifying novel functional consequences of PBRM1 truncated mutations in clear cell renal cell carcinoma (ccRCC).
Q42144725Analysis of Protein-protein Interaction Interface between Yeast Mitochondrial Proteins Rim1 and Pif1 Using Chemical Cross-linking Mass Spectrometry.
Q33608642Analyzing the genes related to Alzheimer's disease via a network and pathway-based approach
Q49870570Analyzing the genes related to nicotine addiction or schizophrenia via a pathway and network based approach
Q49487202Ancestry-specific and sex-specific risk alleles identified in a genome-wide gene-by-alcohol dependence interaction study of risky sexual behaviors
Q58599240Assembly of the β4-integrin interactome based on proximal biotinylation in the presence and absence of heterodimerization
Q37620950BambooGDB: a bamboo genome database with functional annotation and an analysis platform
Q30008764Bioinformatics analysis of the proteins interacting with LASP-1 and their association with HBV-related hepatocellular carcinoma
Q35804009Bioinformatics analysis of the target gene of fibroblast growth factor receptor 3 in bladder cancer and associated molecular mechanisms
Q48921064Characterization of a Protein Interactome by Co-Immunoprecipitation and Shotgun Mass Spectrometry
Q35221224Colorectal cancer drug target prediction using ontology-based inference and network analysis
Q35907078Common Variants in CLDN2 and MORC4 Genes Confer Disease Susceptibility in Patients with Chronic Pancreatitis
Q58766236Comprehensive analysis of multi Ewing sarcoma microarray datasets identifies several prognosis biomarkers
Q45943481Computational systems biology approaches for Parkinson's disease.
Q45943371Computer-aided biomarker discovery for precision medicine: data resources, models and applications.
Q35621416Concordant dysregulation of miR-5p and miR-3p arms of the same precursor microRNA may be a mechanism in inducing cell proliferation and tumorigenesis: a lung cancer study
Q41612701Construction and analysis of a protein-protein interaction network related to self-renewal of mouse spermatogonial stem cells
Q57809415Context-specific interactions in literature-curated protein interaction databases
Q42777346Controllability of protein-protein interaction phosphorylation-based networks: Participation of the hub 14-3-3 protein family
Q64095371Cross-species alcohol dependence-associated gene networks: Co-analysis of mouse brain gene expression and human genome-wide association data
Q47095768Decoding critical long non-coding RNA in ovarian cancer epithelial-to-mesenchymal transition
Q47817283Detecting pathway relationship in the context of human protein-protein interaction network and its application to Parkinson's disease.
Q36224331Determining the Significance of Protein Network Features and Attributes Using Permutation Testing.
Q58743435Differential expression of NF-κB heterodimer RelA/p50 in human urothelial carcinoma
Q89636883Discovering the genes mediating the interactions between chronic respiratory diseases in the human interactome
Q38760518Discovery Proteomics Identifies a Molecular Link between the Coatomer Protein Complex I and Androgen Receptor-dependent Transcription
Q36088452DroPNet: a web portal for integrated analysis of Drosophila protein-protein interaction networks
Q47205411Drug knowledge bases and their applications in biomedical informatics research.
Q30651571Drug repositioning: a machine-learning approach through data integration
Q33644419Dynamic protein interaction modules in human hepatocellular carcinoma progression
Q27308038E2F4 Promotes Neuronal Regeneration and Functional Recovery after Spinal Cord Injury in Zebrafish
Q38446688EP300 Protects from Light-Induced Retinopathy in Zebrafish.
Q35380551Efficient prediction of progesterone receptor interactome using a support vector machine model
Q39092838Epigenetic targets in hepatocellular carcinoma cells: identification of chaperone protein complexes with histone deacetylases
Q41745576Epstein-Barr virus encoded microRNAs target SUMO-regulated cellular functions
Q36106939Evidence of Polygenic Adaptation in the Systems Genetics of Anthropometric Traits
Q58697064Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery
Q55001949FunGeneNet: a web tool to estimate enrichment of functional interactions in experimental gene sets.
Q30844756Functional and genomic context in pathway analysis of GWAS data
Q34423170Functional consequences of somatic mutations in cancer using protein pocket-based prioritization approach
Q37697834Functional genomics evidence unearths new moonlighting roles of outer ring coat nucleoporins
Q30000781Fusion of large-scale genomic knowledge and frequency data computationally prioritizes variants in epilepsy
Q36259023GSAR: Bioconductor package for Gene Set analysis in R
Q36276884GWAS for serum galactose-deficient IgA1 implicates critical genes of the O-glycosylation pathway
Q90243389Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems
Q57315819Gene expression signatures, pathways and networks in carotid atherosclerosis
Q38522741Gene set analysis: A step-by-step guide
Q28596201Gene-gene Interaction Analyses for Atrial Fibrillation
Q30574645GeneSense: a new approach for human gene annotation integrated with protein-protein interaction networks
Q64945982Generalized gene co-expression analysis via subspace clustering using low-rank representation.
Q41232551Genome-wide association study of body mass index in subjects with alcohol dependence
Q57454614Genomic data integration systematically biases interactome mapping
Q34857146Global characterization of signalling networks associated with tamoxifen resistance in breast cancer.
Q38823733Global profiling of protein complexes: current approaches and their perspective in biomedical research.
Q57797467Heterogeneous network embedding for identifying symptom candidate genes
Q38398015HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species.
Q46683592Human genes with a greater number of transcript variants tend to show biological features of housekeeping and essential genes
Q35583547Identification of sample-specific regulations using integrative network level analysis
Q92976721Identifying Hepatocellular Carcinoma Driver Genes by Integrative Pathway Crosstalk and Protein Interaction Network
Q38379632Individualized network-based drug repositioning infrastructure for precision oncology in the panomics era.
Q61798981Inhibition of histone methyltransferase DOT1L silences ERα gene and blocks proliferation of antiestrogen-resistant breast cancer cells
Q31147704Integrative Analysis of Genetic, Genomic, and Phenotypic Data for Ethanol Behaviors: A Network-Based Pipeline for Identifying Mechanisms and Potential Drug Targets
Q36961276Integrin endosomal signalling suppresses anoikis
Q47668612Interactions Between Genetics, Lifestyle, and Environmental Factors for Healthcare
Q34714652Interfacing cellular networks of S. cerevisiae and E. coli: connecting dynamic and genetic information
Q35872307LENS: web-based lens for enrichment and network studies of human proteins
Q42563914Label-free mass spectrometry proteome quantification of human embryonic kidney cells following 24 hours of sialic acid overproduction
Q91670973Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets
Q37715771Leveraging blood serotonin as an endophenotype to identify de novo and rare variants involved in autism
Q36109610MGDB: a comprehensive database of genes involved in melanoma.
Q92994623Maximizing binary interactome mapping with a minimal number of assays
Q92860321Mechanical forces induce an asthma gene signature in healthy airway epithelial cells
Q58356277Microproteomics by liquid extraction surface analysis: Application to FFPE tissue to study the fimbria region of tubo-ovarian cancer
Q35843886Mining for novel candidate clock genes in the circadian regulatory network
Q47738114Molecular mechanisms underlying gliomas and glioblastoma pathogenesis revealed by bioinformatics analysis of microarray data
Q64981749Molecular subtyping of cancer and nomination of kinase candidates for inhibition with phosphoproteomics: Reanalysis of CPTAC ovarian cancer.
Q38754181Multiplex matrix network analysis of protein complexes in the human TCR signalosome
Q37458692Mutation screening and array comparative genomic hybridization using a 180K oligonucleotide array in VACTERL association
Q35674545NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases
Q62666877Network Analysis of Depression-Related Transcriptomic Profiles
Q31167575Network Biomarkers Constructed from Gene Expression and Protein-Protein Interaction Data for Accurate Prediction of Leukemia
Q31148972Network Tools for the Analysis of Proteomic Data
Q35836735Network analysis of an in vitro model of androgen-resistance in prostate cancer.
Q48184416Network and Pathway-Based Analyses of Genes Associated with Parkinson's Disease.
Q38093187Network pharmacology strategies toward multi-target anticancer therapies: from computational models to experimental design principles
Q31140600Network-Based Biomedical Data Analysis
Q37169490Network-Informed Gene Ranking Tackles Genetic Heterogeneity in Exome-Sequencing Studies of Monogenic Disease
Q39218459Network-assisted prediction of potential drugs for addiction
Q55643995Network-based approach to prediction and population-based validation of in silico drug repurposing.
Q35671030Oncogenes and tumor suppressor genes: comparative genomics and network perspectives
Q42515895Phosphodiesterase 1: A Unique Drug Target for Degenerative Diseases and Cognitive Dysfunction.
Q37480414Phosphoproteomic analysis of anaplastic lymphoma kinase (ALK) downstream signaling pathways identifies signal transducer and activator of transcription 3 as a functional target of activated ALK in neuroblastoma cells.
Q38199642Plant systems biology: insights, advances and challenges.
Q28078131Prediction of Protein-Protein Interactions by Evidence Combining Methods
Q59876271Prioritization of Candidate Genes for Congenital Diaphragmatic Hernia in a Critical Region on Chromosome 4p16 using a Machine-Learning Algorithm
Q35000261Profiling the tyrosine phosphoproteome of different mouse mammary tumour models reveals distinct, model-specific signalling networks and conserved oncogenic pathways.
Q45945654Protein complexes, big data, machine learning and integrative proteomics: lessons learned over a decade of systematic analysis of protein interaction networks.
Q38811108Protein-protein interaction analysis for functional characterization of helicases.
Q38201472Protein-protein interaction detection: methods and analysis
Q37575496Proteome-Scale Investigation of Protein Allosteric Regulation Perturbed by Somatic Mutations in 7,000 Cancer Genomes
Q45810074Quantitative modeling of degree-degree correlation in complex networks.
Q33977022Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy
Q30570202Reconstructing dynamic gene regulatory networks from sample-based transcriptional data
Q28077351Reconstruction and Application of Protein-Protein Interaction Network
Q35006921Reconstruction of the experimentally supported human protein interactome: what can we learn?
Q53180121Regulatory feedback loops bridge the human gene regulatory network and regulate carcinogenesis.
Q38766765Resolution of Novel Pancreatic Ductal Adenocarcinoma Subtypes by Global Phosphotyrosine Profiling
Q38470599Revealing the Strong Functional Association of adipor2 and cdh13 with adipoq: A Gene Network Study.
Q37142800Reversal of dendritic phenotypes in 16p11.2 microduplication mouse model neurons by pharmacological targeting of a network hub.
Q36765345SoftPanel: a website for grouping diseases and related disorders for generation of customized panels.
Q35610049Stimulus-dependent differences in signalling regulate epithelial-mesenchymal plasticity and change the effects of drugs in breast cancer cell lines.
Q27008867Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review
Q33923533Studying tumorigenesis through network evolution and somatic mutational perturbations in the cancer interactome
Q35722850Systematic Analysis of the Molecular Mechanism Underlying Decidualization Using a Text Mining Approach
Q36133996Systematic Determination of Human Cyclin Dependent Kinase (CDK)-9 Interactome Identifies Novel Functions in RNA Splicing Mediated by the DEAD Box (DDX)-5/17 RNA Helicases
Q36960706Systematic analysis of the molecular mechanism underlying atherosclerosis using a text mining approach
Q48905013Targeted activation of CREB in reactive astrocytes is neuroprotective in focal acute cortical injury
Q33913372The common ground of genomics and systems biology
Q42374136The nuclear receptor ERβ engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading.
Q24338785The protein interaction landscape of the human CMGC kinase group
Q38447214The protein interactome of collapsin response mediator protein-2 (CRMP2/DPYSL2) reveals novel partner proteins in brain tissue
Q35132978The protein-protein interaction network of eyestalk, Y-organ and hepatopancreas in Chinese mitten crab Eriocheir sinensis
Q57174048Tissue-specific Network Analysis of Genetic Variants Associated with Coronary Artery Disease
Q47113354Transcriptome-wide association study of inflammatory biologic age.
Q55093434Two independent proteomic approaches provide a comprehensive analysis of the synovial fluid proteome response to Autologous Chondrocyte Implantation.
Q47146443Two missense mutations in KCNQ1 cause pituitary hormone deficiency and maternally inherited gingival fibromatosis.
Q41430377Type 1 Diabetes: Urinary Proteomics and Protein Network Analysis Support Perturbation of Lysosomal Function
Q28544942Use of genome-wide association studies for cancer research and drug repositioning
Q36178385Virtual interactomics of proteins from biochemical standpoint
Q42345749What Signatures Dominantly Associate with Gene Age?
Q57176054Whole Blood Gene Expression Associated with Clinical Biological Age
Q33578278Whole blood gene expression and atrial fibrillation: the Framingham Heart Study
Q41716416Whole blood gene expression and white matter Hyperintensities.
Q37730204X chromosome inactivation: new players in the initiation of gene silencing
Q34346335atBioNet--an integrated network analysis tool for genomics and biomarker discovery
Q35092833cisPath: an R/Bioconductor package for cloud users for visualization and management of functional protein interaction networks.
Q37437305dbCPG: A web resource for cancer predisposition genes
Q33902260m(6)A RNA methylation promotes XIST-mediated transcriptional repression
Q92581331vulcanSpot: a tool to prioritize therapeutic vulnerabilities in cancer

Search more.