Protein Interaction Network Analysis platform
Names
More detailed information about this field from each metasource.
Protein Interaction Network Analysis platform
metasource: Fairsharing.org
version: FAIRsharing.org: PINA; Protein Interaction Network Analysis platform; DOI: https://doi.org/10.25504/FAIRsharing.7q4gsz; Last edited: Nov. 9, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
PINA
metasource: Fairsharing.org
version: FAIRsharing.org: PINA; Protein Interaction Network Analysis platform; DOI: https://doi.org/10.25504/FAIRsharing.7q4gsz; Last edited: Nov. 9, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.429369
pina
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.429369
Names
More detailed information about this field from each metasource.
Protein Interaction Network Analysis platform
metasource: Fairsharing.orgversion: FAIRsharing.org: PINA; Protein Interaction Network Analysis platform; DOI: https://doi.org/10.25504/FAIRsharing.7q4gsz; Last edited: Nov. 9, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
PINA
metasource: Fairsharing.orgversion: FAIRsharing.org: PINA; Protein Interaction Network Analysis platform; DOI: https://doi.org/10.25504/FAIRsharing.7q4gsz; Last edited: Nov. 9, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.429369
pina
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:52.429369
Names
More detailed information about this field from each metasource.
Protein Interaction Network Analysis platform
metasource: Fairsharing.orgversion: FAIRsharing.org: PINA; Protein Interaction Network Analysis platform; DOI: https://doi.org/10.25504/FAIRsharing.7q4gsz; Last edited: Nov. 9, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
PINA
metasource: Fairsharing.orgversion: FAIRsharing.org: PINA; Protein Interaction Network Analysis platform; DOI: https://doi.org/10.25504/FAIRsharing.7q4gsz; Last edited: Nov. 9, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.429369
pina
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:52.429369
Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization, and management. It integrates protein-protein interaction (PPI) data from public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms. In particular, it provides a variety of built-in tools to filter and analyze the networks for gaining biological and functional insights into the network.
Description
More detailed information about this field from each metasource.
Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization, and management. It integrates protein-protein interaction (PPI) data from public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms. In particular, it provides a variety of built-in tools to filter and analyze the networks for gaining biological and functional insights into the network.
metasource: Fairsharing.orgversion: FAIRsharing.org: PINA; Protein Interaction Network Analysis platform; DOI: https://doi.org/10.25504/FAIRsharing.7q4gsz; Last edited: Nov. 9, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms. In version 2.0, it provides multiple collections of annotated interaction modules identified from interactomes by different clustering approaches. In version 3.0, it integrated PPI data with TCGA and CPTAC datasets to help characterize cancer context for a PPI network, which includes inferring proteins with expression specificity and identifying candidate prognosis biomarkers, putative cancer drivers, therapeutic targets, and pairs of co-expressing interacting proteins. PINA is freely available at https://omics.bjcancer.org/pina/.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms. Moreover, it provides a variety of built-in tools to filter and analyze the network for gaining insight into the network.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:52.429369
Webpage:
http://omics.bjcancer.org/pina/Webpage
More detailed information about this field from each metasource.
http://omics.bjcancer.org/pina/
metasource: Fairsharing.orgversion: FAIRsharing.org: PINA; Protein Interaction Network Analysis platform; DOI: https://doi.org/10.25504/FAIRsharing.7q4gsz; Last edited: Nov. 9, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.429369
https://omics.bjcancer.org/pina/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Publications:
Publications
More detailed information about this field from each metasource.
PINA v2.0: mining interactome modules
PMID: 22067443
metasource: Fairsharing.org
version: FAIRsharing.org: PINA; Protein Interaction Network Analysis platform; DOI: https://doi.org/10.25504/FAIRsharing.7q4gsz; Last edited: Nov. 9, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.429369
Integrated network analysis platform for protein-protein interactions
PMID: 19079255
metasource: Fairsharing.org
version: FAIRsharing.org: PINA; Protein Interaction Network Analysis platform; DOI: https://doi.org/10.25504/FAIRsharing.7q4gsz; Last edited: Nov. 9, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gkaa1075
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
PINA v2.0: mining interactome modules
PMID: 22067443
metasource: Fairsharing.org
version: FAIRsharing.org: PINA; Protein Interaction Network Analysis platform; DOI: https://doi.org/10.25504/FAIRsharing.7q4gsz; Last edited: Nov. 9, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.429369
Integrated network analysis platform for protein-protein interactions
PMID: 19079255
metasource: Fairsharing.org
version: FAIRsharing.org: PINA; Protein Interaction Network Analysis platform; DOI: https://doi.org/10.25504/FAIRsharing.7q4gsz; Last edited: Nov. 9, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gkaa1075
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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PINA v2.0: mining interactome modules
PubMed citations: 167.
167 articles citing: PINA v2.0: mining interactome modules
Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer's disease. PMID:35849618
Identifying Candidate Flavonoids for Non-Alcoholic Fatty Liver Disease by Network-Based Strategy. PMID:35721123
A comprehensive SARS-CoV-2-human protein-protein interactome network identifies pathobiology and host-targeting therapies for COVID-19. PMID:35677070
Transcriptomic analysis reveals pathophysiological relationship between chronic obstructive pulmonary disease (COPD) and periodontitis. PMID:35676670
Physical and functional interactome atlas of human receptor tyrosine kinases. PMID:35384245
Human transcription factor protein interaction networks. PMID:35140242
A Systematic Analysis on the Genes and Their Interaction Underlying the Comorbidity of Alzheimer's Disease and Major Depressive Disorder. PMID:35126089
Shared Molecular Mechanisms between Atherosclerosis and Periodontitis by Analyzing the Transcriptomic Alterations of Peripheral Blood Monocytes. PMID:34899963
Metabolic endophenotype associated with right ventricular glucose uptake in pulmonary hypertension. PMID:34888034
SARS-CoV-2-host proteome interactions for antiviral drug discovery. PMID:34709727
Regulation of ER Composition and Extent, and Putative Action in Protein Networks by ER/NE Protein TMEM147. PMID:34638576
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Mechanism-Centric Approaches for Biomarker Detection and Precision Therapeutics in Cancer. PMID:34408770
Multimodal single-cell omics analysis identifies epithelium-immune cell interactions and immune vulnerability associated with sex differences in COVID-19. PMID:34330889
A heat shock-responsive lncRNA Heat acts as a HSF1-directed transcriptional brake via m6A modification. PMID:34131081
Target identification among known drugs by deep learning from heterogeneous networks. PMID:34123272
Measuring pathway database coverage of the phosphoproteome. PMID:34113485
Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment. PMID:34108016
Model-based analysis uncovers mutations altering autophagy selectivity in human cancer. PMID:34059679
An integrative drug repositioning framework discovered a potential therapeutic agent targeting COVID-19. PMID:33895786
Shared Molecular Mechanisms between Alzheimer's Disease and Periodontitis Revealed by Transcriptomic Analysis. PMID:33869630
Network-based modeling of herb combinations in traditional Chinese medicine. PMID:33834186
Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment. PMID:33791705
A systems-based method to repurpose marketed therapeutics for antiviral use: a SARS-CoV-2 case study. PMID:33593923
A network-based deep learning methodology for stratification of tumor mutations. PMID:33416857
PINA 3.0: mining cancer interactome. PMID:33231689
Biological network analysis with deep learning. PMID:33169146
A network medicine approach to investigation and population-based validation of disease manifestations and drug repurposing for COVID-19. PMID:33156843
IHP-PING-generating integrated human protein-protein interaction networks on-the-fly. PMID:33129201
Plasma Proteomics Identify Biomarkers and Pathogenesis of COVID-19. PMID:33128875
Analyzing IDPs in Interactomes. PMID:32696395
Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19. PMID:32550253
Dynamic rewiring of the human interactome by interferon signaling. PMID:32539747
Novel Comprehensive Bioinformatics Approaches to Determine the Molecular Genetic Susceptibility Profile of Moderate and Severe Asthma. PMID:32512817
NetConfer: a web application for comparative analysis of multiple biological networks. PMID:32430035
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
Discovering the genes mediating the interactions between chronic respiratory diseases in the human interactome. PMID:32041952
Mechanical forces induce an asthma gene signature in healthy airway epithelial cells. PMID:31969610
Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets. PMID:31798629
Genome-wide Network-assisted Association and Enrichment Study of Amyloid Imaging Phenotype in Alzheimer's Disease. PMID:31755389
Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems. PMID:31548717
Maximizing binary interactome mapping with a minimal number of assays. PMID:31467278
Identifying Hepatocellular Carcinoma Driver Genes by Integrative Pathway Crosstalk and Protein Interaction Network. PMID:31464520
A genome-wide positioning systems network algorithm for in silico drug repurposing. PMID:31375661
Identification of important invasion and proliferation related genes in adrenocortical carcinoma. PMID:31321566
Healthy diet is associated with gene expression in blood: the Framingham Heart Study. PMID:31187853
vulcanSpot: a tool to prioritize therapeutic vulnerabilities in cancer. PMID:31173067
Generalized gene co-expression analysis via subspace clustering using low-rank representation. PMID:31074376
Cross-species alcohol dependence-associated gene networks: Co-analysis of mouse brain gene expression and human genome-wide association data. PMID:31017905
Identification of Important Invasion-Related Genes in Non-functional Pituitary Adenomas. PMID:30982163
Network Analysis of Depression-Related Transcriptomic Profiles. PMID:30825116
Inhibition of histone methyltransferase DOT1L silences ERα gene and blocks proliferation of antiestrogen-resistant breast cancer cells. PMID:30775443
Molecular subtyping of cancer and nomination of kinase candidates for inhibition with phosphoproteomics: Reanalysis of CPTAC ovarian cancer. PMID:30594550
Prioritization of Candidate Genes for Congenital Diaphragmatic Hernia in a Critical Region on Chromosome 4p16 using a Machine-Learning Algorithm. PMID:30430034
Assembly of the β4-Integrin Interactome Based on Proximal Biotinylation in the Presence and Absence of Heterodimerization. PMID:30404858
Heterogeneous network embedding for identifying symptom candidate genes. PMID:30357378
Context-specific interactions in literature-curated protein interaction databases. PMID:30340458
Genomic data integration systematically biases interactome mapping. PMID:30332399
Differential expression of NF-κB heterodimer RelA/p50 in human urothelial carcinoma. PMID:30225173
Comprehensive analysis of multi Ewing sarcoma microarray datasets identifies several prognosis biomarkers. PMID:30221671
Analyzing the disease module associated with osteosarcoma via a network- and pathway-based approach. PMID:30210606
Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. PMID:30082644
Tissue-specific Network Analysis of Genetic Variants Associated with Coronary Artery Disease. PMID:30065343
Whole Blood Gene Expression Associated With Clinical Biological Age. PMID:30010802
Network-based approach to prediction and population-based validation of in silico drug repurposing. PMID:30002366
Two independent proteomic approaches provide a comprehensive analysis of the synovial fluid proteome response to Autologous Chondrocyte Implantation. PMID:29720234
FunGeneNet: a web tool to estimate enrichment of functional interactions in experimental gene sets. PMID:29504895
Analyzing the genes related to nicotine addiction or schizophrenia via a pathway and network based approach. PMID:29440730
Decoding critical long non-coding RNA in ovarian cancer epithelial-to-mesenchymal transition. PMID:29150601
Transcriptome-wide association study of inflammatory biologic age. PMID:29135455
Two missense mutations in KCNQ1 cause pituitary hormone deficiency and maternally inherited gingival fibromatosis. PMID:29097701
The nuclear receptor ERβ engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading. PMID:29017520
Ancestry-specific and sex-specific risk alleles identified in a genome-wide gene-by-alcohol dependence interaction study of risky sexual behaviors. PMID:28990359
Molecular mechanisms underlying gliomas and glioblastoma pathogenesis revealed by bioinformatics analysis of microarray data. PMID:28952134
Whole blood gene expression and white matter Hyperintensities. PMID:28923099
Type 1 Diabetes: Urinary Proteomics and Protein Network Analysis Support Perturbation of Lysosomal Function. PMID:28819457
Analyzing the genes related to Alzheimer's disease via a network and pathway-based approach. PMID:28446202
A new locus regulating MICALL2 expression was identified for association with executive inhibition in children with attention deficit hyperactivity disorder. PMID:28416812
X chromosome inactivation: new players in the initiation of gene silencing. PMID:28408975
Leveraging blood serotonin as an endophenotype to identify de novo and rare variants involved in autism. PMID:28344757
Bioinformatics analysis of the proteins interacting with LASP-1 and their association with HBV-related hepatocellular carcinoma. PMID:28266596
Network Biomarkers Constructed from Gene Expression and Protein-Protein Interaction Data for Accurate Prediction of Leukemia. PMID:28243332
GWAS for serum galactose-deficient IgA1 implicates critical genes of the O-glycosylation pathway. PMID:28187132
GSAR: Bioconductor package for Gene Set analysis in R. PMID:28118818
Proteome-Scale Investigation of Protein Allosteric Regulation Perturbed by Somatic Mutations in 7,000 Cancer Genomes. PMID:27939638
Integrative Analysis of Genetic, Genomic, and Phenotypic Data for Ethanol Behaviors: A Network-Based Pipeline for Identifying Mechanisms and Potential Drug Targets. PMID:27933543
A scored human protein-protein interaction network to catalyze genomic interpretation. PMID:27892958
Prediction of Protein-Protein Interactions by Evidence Combining Methods. PMID:27879651
Gene-gene Interaction Analyses for Atrial Fibrillation. PMID:27824142
What Signatures Dominantly Associate with Gene Age? PMID:27609935
m(6)A RNA methylation promotes XIST-mediated transcriptional repression. PMID:27602518
An integrative genomics approach for identifying novel functional consequences of PBRM1 truncated mutations in clear cell renal cell carcinoma (ccRCC). PMID:27556922
Evidence of Polygenic Adaptation in the Systems Genetics of Anthropometric Traits. PMID:27537407
Multiplex matrix network analysis of protein complexes in the human TCR signalosome. PMID:27485017
Reversal of dendritic phenotypes in 16p11.2 microduplication mouse model neurons by pharmacological targeting of a network hub. PMID:27402753
Discovery Proteomics Identifies a Molecular Link between the Coatomer Protein Complex I and Androgen Receptor-dependent Transcription. PMID:27365400
Network and Pathway-Based Analyses of Genes Associated with Parkinson's Disease. PMID:27349437
Reconstruction and Application of Protein-Protein Interaction Network. PMID:27338356
Resolution of Novel Pancreatic Ductal Adenocarcinoma Subtypes by Global Phosphotyrosine Profiling. PMID:27259358
Systematic analysis of the molecular mechanism underlying atherosclerosis using a text mining approach. PMID:27251057
EP300 Protects from Light-Induced Retinopathy in Zebrafish. PMID:27242532
E2F4 Promotes Neuronal Regeneration and Functional Recovery after Spinal Cord Injury in Zebrafish. PMID:27242526
Controllability of protein-protein interaction phosphorylation-based networks: Participation of the hub 14-3-3 protein family. PMID:27195976
dbCPG: A web resource for cancer predisposition genes. PMID:27192119
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. PMID:27131791
Protein-protein interaction analysis for functional characterization of helicases. PMID:27090004
SoftPanel: a website for grouping diseases and related disorders for generation of customized panels. PMID:27044653
A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics. PMID:26838676
Common Variants in CLDN2 and MORC4 Genes Confer Disease Susceptibility in Patients with Chronic Pancreatitis. PMID:26820620
Analysis of Protein-protein Interaction Interface between Yeast Mitochondrial Proteins Rim1 and Pif1 Using Chemical Cross-linking Mass Spectrometry. PMID:26807012
HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species. PMID:26708988
LENS: web-based lens for enrichment and network studies of human proteins. PMID:26680011
Mining for novel candidate clock genes in the circadian regulatory network. PMID:26576534
Network analysis of an in vitro model of androgen-resistance in prostate cancer. PMID:26553226
Genome-wide association study of body mass index in subjects with alcohol dependence. PMID:26458734
Integrin endosomal signalling suppresses anoikis. PMID:26436690
MGDB: a comprehensive database of genes involved in melanoma. PMID:26424083
Network-Informed Gene Ranking Tackles Genetic Heterogeneity in Exome-Sequencing Studies of Monogenic Disease. PMID:26394720
A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types. PMID:26352260
Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. PMID:26307061
Systematic Analysis of the Molecular Mechanism Underlying Decidualization Using a Text Mining Approach. PMID:26222155
Systematic 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. PMID:26209609
Bioinformatics analysis of the target gene of fibroblast growth factor receptor 3 in bladder cancer and associated molecular mechanisms. PMID:26171066
NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases. PMID:26110971
A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case. PMID:26100720
Oncogenes and tumor suppressor genes: comparative genomics and network perspectives. PMID:26099335
Gene set analysis: A step-by-step guide. PMID:26059482
Stimulus-dependent differences in signalling regulate epithelial-mesenchymal plasticity and change the effects of drugs in breast cancer cell lines. PMID:25975820
Identification of sample-specific regulations using integrative network level analysis. PMID:25928379
A comparative study of disease genes and drug targets in the human protein interactome. PMID:25861037
Concordant 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. PMID:25852169
Colorectal cancer drug target prediction using ontology-based inference and network analysis. PMID:25818893
Use of genome-wide association studies for cancer research and drug repositioning. PMID:25803826
Efficient prediction of progesterone receptor interactome using a support vector machine model. PMID:25741764
cisPath: an R/Bioconductor package for cloud users for visualization and management of functional protein interaction networks. PMID:25708840
AIM: a comprehensive Arabidopsis interactome module database and related interologs in plants. PMID:25480687
Functional consequences of somatic mutations in cancer using protein pocket-based prioritization approach. PMID:25360158
Profiling the tyrosine phosphoproteome of different mouse mammary tumour models reveals distinct, model-specific signalling networks and conserved oncogenic pathways. PMID:25200860
Functional and genomic context in pathway analysis of GWAS data. PMID:25154796
The common ground of genomics and systems biology. PMID:25033072
Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy. PMID:25003367
Studying tumorigenesis through network evolution and somatic mutational perturbations in the cancer interactome. PMID:24881052
Whole blood gene expression and atrial fibrillation: the Framingham Heart Study. PMID:24805109
Functional genomics evidence unearths new moonlighting roles of outer ring coat nucleoporins. PMID:24722254
Protein-protein interaction detection: methods and analysis. PMID:24693427
Network-assisted prediction of potential drugs for addiction. PMID:24689033
The protein-protein interaction network of eyestalk, Y-organ and hepatopancreas in Chinese mitten crab Eriocheir sinensis. PMID:24674293
Plant systems biology: insights, advances and challenges. PMID:24671625
GeneSense: a new approach for human gene annotation integrated with protein-protein interaction networks. PMID:24667292
BambooGDB: a bamboo genome database with functional annotation and an analysis platform. PMID:24602877
Dynamic protein interaction modules in human hepatocellular carcinoma progression. PMID:24564909
Mutation screening and array comparative genomic hybridization using a 180K oligonucleotide array in VACTERL association. PMID:24416387
Reconstruction of the experimentally supported human protein interactome: what can we learn? PMID:24088582
Fusion of large-scale genomic knowledge and frequency data computationally prioritizes variants in epilepsy. PMID:24086149
Label-free mass spectrometry proteome quantification of human embryonic kidney cells following 24 hours of sialic acid overproduction. PMID:23915316
Phosphoproteomic 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. PMID:23889739
Drug repositioning: a machine-learning approach through data integration. PMID:23800010
Interfacing cellular networks of S. cerevisiae and E. coli: connecting dynamic and genetic information. PMID:23663484
Network pharmacology strategies toward multi-target anticancer therapies: from computational models to experimental design principles. PMID:23530504
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. PMID:23384594
A probabilistic coevolutionary biclustering algorithm for discovering coherent patterns in gene expression dataset. PMID:23282075
Reconstructing dynamic gene regulatory networks from sample-based transcriptional data. PMID:23002138
Virtual interactomics of proteins from biochemical standpoint. PMID:22928109
A network synthesis model for generating protein interaction network families. PMID:22912671
atBioNet--an integrated network analysis tool for genomics and biomarker discovery. PMID:22817640
DroPNet: a web portal for integrated analysis of Drosophila protein-protein interaction networks. PMID:22641854
ASEB: a web server for KAT-specific acetylation site prediction. PMID:22600735 -
Integrated network analysis platform for protein-protein interactions
PubMed citations: 145.
145 articles citing: Integrated network analysis platform for protein-protein interactions
Dissecting Meta-Analysis in GWAS Era: Bayesian Framework for Gene/Subnetwork-Specific Meta-Analysis. PMID:35664319
Global ubiquitinome profiling identifies NEDD4 as a regulator of Profilin 1 and actin remodelling in neural crest cells. PMID:35440627
Increased Expression of YAP Inhibited the Autophagy Level by Upregulating mTOR Signal in the Eutopic ESCs of Endometriosis. PMID:35173685
Low-Level Laser Therapy Effects on Rat Blood Hemostasis Via Significant Alteration in Fibrinogen and Plasminogen Expression Level. PMID:35155144
Developing an Embedding, Koopman and Autoencoder Technologies-Based Multi-Omics Time Series Predictive Model (EKATP) for Systems Biology research. PMID:34764986
Computational workflow for functional characterization of COVID-19 through secondary data analysis. PMID:34746856
MMS22L Expression as a Predictive Biomarker for the Efficacy of Neoadjuvant Chemoradiotherapy in Oesophageal Squamous Cell Carcinoma. PMID:34660277
Regulation of ER Composition and Extent, and Putative Action in Protein Networks by ER/NE Protein TMEM147. PMID:34638576
Genetic variation in genes regulating skeletal muscle regeneration and tissue remodelling associated with weight loss in chronic obstructive pulmonary disease. PMID:34523824
PPI-MASS: An Interactive Web Server to Identify Protein-Protein Interactions From Mass Spectrometry-Based Proteomics Data. PMID:34277709
Investigations of Kidney Dysfunction-Related Gene Variants in Sickle Cell Disease Patients in Cameroon (Sub-Saharan Africa). PMID:33790942
PINA 3.0: mining cancer interactome. PMID:33231689
Whole exome sequencing reveals pathogenic variants in MYO3A, MYO15A and COL9A3 and differential frequencies in ancestral alleles in hearing impairment genes among individuals from Cameroon. PMID:33078831
Identification, Validation, and Functional Annotations of Genome-Wide Profile Variation between Melanocytic Nevus and Malignant Melanoma. PMID:32934956
Identification and validation of novel metastasis-related signatures of clear cell renal cell carcinoma using gene expression databases. PMID:32913492
Identifying genetic variants and pathways associated with extreme levels of fetal hemoglobin in sickle cell disease in Tanzania. PMID:32503527
Comprehensive gene and pathway analysis of cervical cancer progression. PMID:32256826
Basement membrane ligands initiate distinct signalling networks to direct cell shape. PMID:32147508
MSP-N: Multiple selection procedure with 'N' possible growth mechanisms. PMID:31830048
Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets. PMID:31798629
Biological Network Approaches and Applications in Rare Disease Studies. PMID:31614842
Screening and Identification of Potential Prognostic Biomarkers in Adrenocortical Carcinoma. PMID:31572440
Machine-learning techniques for the prediction of protein-protein interactions. PMID:31502581
Genome-Wide Meta-Analyses of FTND and TTFC Phenotypes. PMID:31294817
Imbalanced testicular metabolism induced by thyroid disorders: New evidences from quantitative proteome. PMID:31256343
Cross-species alcohol dependence-associated gene networks: Co-analysis of mouse brain gene expression and human genome-wide association data. PMID:31017905
Systematic Identification and Evolution Analysis of Sox Genes in Coturnix japonica Based on Comparative Genomics. PMID:31013663
Assembly of the β4-Integrin Interactome Based on Proximal Biotinylation in the Presence and Absence of Heterodimerization. PMID:30404858
Short term optical defocus perturbs normal developmental shifts in retina/RPE protein abundance. PMID:30157773
In silico drug screening by using genome-wide association study data repurposed dabrafenib, an anti-melanoma drug, for Parkinson's disease. PMID:30137437
Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. PMID:30082644
MiRNA-BD: an evidence-based bioinformatics model and software tool for microRNA biomarker discovery. PMID:30081733
Reciprocal Perspective for Improved Protein-Protein Interaction Prediction. PMID:30076341
Tumor endothelial marker 8 promotes cancer progression and metastasis. PMID:30046396
MTGO: PPI Network Analysis Via Topological and Functional Module Identification. PMID:29615773
Nasopharyngeal Carcinoma Protein Interaction Mapping Analysis via Proteomic Approaches. PMID:29582644
Comparison of Echinococcus multilocularis and Echinococcus granulosus hydatid fluid proteome provides molecular strategies for specialized host-parasite interactions. PMID:29228589
Prediction and Validation of Hub Genes Associated with Colorectal Cancer by Integrating PPI Network and Gene Expression Data. PMID:29209625
SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome. PMID:29141584
Identification of candidate genes related to pancreatic cancer based on analysis of gene co-expression and protein-protein interaction network. PMID:29050346
Molecular mechanisms underlying gliomas and glioblastoma pathogenesis revealed by bioinformatics analysis of microarray data. PMID:28952134
Fasciclin-calcareous corpuscle binary complex mediated protein-protein interactions in Taenia solium metacestode. PMID:28931431
Network analyses elucidate the role of SMYD3 in esophageal squamous cell carcinoma. PMID:28781952
The Sharpin interactome reveals a role for Sharpin in lamellipodium formation via the Arp2/3 complex. PMID:28775156
From protein-protein interactions to protein co-expression networks: a new perspective to evaluate large-scale proteomic data. PMID:28477207
Network-assisted analysis of GWAS data identifies a functionally-relevant gene module for childhood-onset asthma. PMID:28428554
A Genomic and Protein-Protein Interaction Analyses of Nonsyndromic Hearing Impairment in Cameroon Using Targeted Genomic Enrichment and Massively Parallel Sequencing. PMID:28075205
Network-based analysis of differentially expressed genes in cerebrospinal fluid (CSF) and blood reveals new candidate genes for multiple sclerosis. PMID:28028462
The integrin adhesome network at a glance. PMID:27799358
Exploring the interactions of the RAS family in the human protein network and their potential implications in RAS-directed therapies. PMID:27713118
Network analysis reveals potential markers for pediatric adrenocortical carcinoma. PMID:27555782
A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks. PMID:27542402
Reversal of dendritic phenotypes in 16p11.2 microduplication mouse model neurons by pharmacological targeting of a network hub. PMID:27402753
NEpiC: a network-assisted algorithm for epigenetic studies using mean and variance combined signals. PMID:27302130
Genetic Relationship between Schizophrenia and Nicotine Dependence. PMID:27164557
Identification of breast cancer candidate genes using gene co-expression and protein-protein interaction information. PMID:27150055
Candidate genes and pathogenesis investigation for sepsis-related acute respiratory distress syndrome based on gene expression profile. PMID:27090785
An Atlas of the Human Kinome Reveals the Mutational Landscape Underlying Dysregulated Phosphorylation Cascades in Cancer. PMID:26921330
Quantitative succinylome analysis in the liver of non-alcoholic fatty liver disease rat model. PMID:26843850
Modulation of FAK and Src adhesion signaling occurs independently of adhesion complex composition. PMID:26833789
Mining for novel candidate clock genes in the circadian regulatory network. PMID:26576534
ancGWAS: a post genome-wide association study method for interaction, pathway and ancestry analysis in homogeneous and admixed populations. PMID:26508762
Relevance Rank Platform (RRP) for Functional Filtering of High Content Protein-Protein Interaction Data. PMID:26499835
Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response. PMID:26485378
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. PMID:26309733
A Systematic Analysis of Candidate Genes Associated with Nicotine Addiction. PMID:26097843
Proteins interaction network and modeling of IGVH mutational status in chronic lymphocytic leukemia. PMID:26088082
De novo deletions and duplications of 17q25.3 cause susceptibility to cardiovascular malformations. PMID:26070612
Pathways and networks-based analysis of candidate genes associated with nicotine addiction. PMID:25965070
Molecular mechanisms in the pathogenesis of sepsis. PMID:25870671
EW_dmGWAS: edge-weighted dense module search for genome-wide association studies and gene expression profiles. PMID:25805723
Coinheritance of COL4A5 and MYO1E mutations accentuate the severity of kidney disease. PMID:25739341
cisPath: an R/Bioconductor package for cloud users for visualization and management of functional protein interaction networks. PMID:25708840
Defining the phospho-adhesome through the phosphoproteomic analysis of integrin signalling. PMID:25677187
A proteomic approach reveals integrin activation state-dependent control of microtubule cortical targeting. PMID:25609142
Microtubule-dependent modulation of adhesion complex composition. PMID:25526367
Discovery of new risk loci for IgA nephropathy implicates genes involved in immunity against intestinal pathogens. PMID:25305756
Identification of possible pathogenic pathways in Behçet's disease using genome-wide association study data from two different populations. PMID:25227143
Profiling the tyrosine phosphoproteome of different mouse mammary tumour models reveals distinct, model-specific signalling networks and conserved oncogenic pathways. PMID:25200860
Beyond GWAS in COPD: probing the landscape between gene-set associations, genome-wide associations and protein-protein interaction networks. PMID:25171373
Transcriptome sequencing and genome-wide association analyses reveal lysosomal function and actin cytoskeleton remodeling in schizophrenia and bipolar disorder. PMID:25113377
Genome-wide association and network analysis of lung function in the Framingham Heart Study. PMID:25044411
Network based analyses of gene expression profile of LCN2 overexpression in esophageal squamous cell carcinoma. PMID:24954627
Identification of microRNA as sepsis biomarker based on miRNAs regulatory network analysis. PMID:24809055
Functional genomics evidence unearths new moonlighting roles of outer ring coat nucleoporins. PMID:24722254
The protein-protein interaction network of eyestalk, Y-organ and hepatopancreas in Chinese mitten crab Eriocheir sinensis. PMID:24674293
GeneSense: a new approach for human gene annotation integrated with protein-protein interaction networks. PMID:24667292
Interactome analysis of AMP-activated protein kinase (AMPK)-α1 and -β1 in INS-1 pancreatic beta-cells by affinity purification-mass spectrometry. PMID:24625528
BambooGDB: a bamboo genome database with functional annotation and an analysis platform. PMID:24602877
Dynamic protein interaction modules in human hepatocellular carcinoma progression. PMID:24564909
Protein intrinsic disorder and network connectivity. The case of 14-3-3 proteins. PMID:24550932
A Network Approach to Wound Healing. PMID:24527361
Computational developments in microRNA-regulated protein-protein interactions. PMID:24507415
Review of biological network data and its applications. PMID:24465231
Interaction proteome of human Hippo signaling: modular control of the co-activator YAP1. PMID:24366813
IQGAP1 is a key node within the small GTPase network. PMID:24355937
Integrating GWASs and human protein interaction networks identifies a gene subnetwork underlying alcohol dependence. PMID:24268660
Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system. PMID:24162925
Multi-dimensional prioritization of dental caries candidate genes and its enriched dense network modules. PMID:24146904
Network.assisted analysis to prioritize GWAS results: principles, methods and perspectives. PMID:24122152
Insulin biosynthetic interaction network component, TMEM24, facilitates insulin reserve pool release. PMID:24012759
Label-free mass spectrometry proteome quantification of human embryonic kidney cells following 24 hours of sialic acid overproduction. PMID:23915316
A kernel regression approach to gene-gene interaction detection for case-control studies. PMID:23868214
Rac1 is deactivated at integrin activation sites through an IQGAP1-filamin-A-RacGAP1 pathway. PMID:23843620
Drug repositioning: a machine-learning approach through data integration. PMID:23800010
Interfacing cellular networks of S. cerevisiae and E. coli: connecting dynamic and genetic information. PMID:23663484
Comparative proteomic analysis of supportive and unsupportive extracellular matrix substrates for human embryonic stem cell maintenance. PMID:23658023
Extracting coordinated patterns of DNA methylation and gene expression in ovarian cancer. PMID:23599224
Network pharmacology strategies toward multi-target anticancer therapies: from computational models to experimental design principles. PMID:23530504
Identification of protein interactions involved in cellular signaling. PMID:23481661
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. PMID:23384594
Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. PMID:23157382
Searching joint association signals in CATIE schizophrenia genome-wide association studies through a refined integrative network approach. PMID:23134571
A simple knowledge-based mining method for exploring hidden key molecules in a human biomolecular network. PMID:22979956
Weighted frequent gene co-expression network mining to identify genes involved in genome stability. PMID:22956898
Distinct and competitive regulatory patterns of tumor suppressor genes and oncogenes in ovarian cancer. PMID:22952919
Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes. PMID:22912585
DTome: a web-based tool for drug-target interactome construction. PMID:22901092
Network-assisted Causal Gene Detection in Genome-wide Association Studies: An Improved Module Search Algorithm. PMID:22898890
Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. PMID:22844098
Network-assisted investigation of combined causal signals from genome-wide association studies in schizophrenia. PMID:22792057
A comprehensive network and pathway analysis of candidate genes in major depressive disorder. PMID:22784618
NetWalker: a contextual network analysis tool for functional genomics. PMID:22732065
DroPNet: a web portal for integrated analysis of Drosophila protein-protein interaction networks. PMID:22641854
An activation force-based affinity measure for analyzing complex networks. PMID:22355630
GenRev: exploring functional relevance of genes in molecular networks. PMID:22227021
PINA v2.0: mining interactome modules. PMID:22067443
Integrative network analysis identifies key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma. PMID:21824427
Quantitative proteomics reveals the basis for the biochemical specificity of the cell-cycle machinery. PMID:21816347
GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data. PMID:21777475
Unraveling regulation and new components of human P-bodies through a protein interaction framework and experimental validation. PMID:21750099
Do cancer proteins really interact strongly in the human protein-protein interaction network? PMID:21666777
Gene set analysis of genome-wide association studies: methodological issues and perspectives. PMID:21565265
Data integration workflow for search of disease driving genes and genetic variants. PMID:21533266
Network analysis of single nucleotide polymorphisms in asthma. PMID:21437052
Virus interactions with human signal transduction pathways. PMID:21330695
dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks. PMID:21045073
Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme. PMID:20822536
Protein kinase target discovery from genome-wide messenger RNA expression profiling. PMID:20687179
Protein-protein interactions essentials: key concepts to building and analyzing interactome networks. PMID:20589078
Profiling of protein interaction networks of protein complexes using affinity purification and quantitative mass spectrometry. PMID:20445003
MYBBP1A: a new Ipr1's binding protein in mice. PMID:20221700
Genome-wide association study identifies five susceptibility loci for glioma. PMID:19578367
DASMIweb: online integration, analysis and assessment of distributed protein interaction data. PMID:19502495
SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. PMID:19454602 - http://dx.doi.org/10.1093/nar/gkaa1075
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More detailed information about this field from each metasource.
gene ontology enrichment
metasource: Fairsharing.org
version: FAIRsharing.org: PINA; Protein Interaction Network Analysis platform; DOI: https://doi.org/10.25504/FAIRsharing.7q4gsz; Last edited: Nov. 9, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
interactome
metasource: Fairsharing.org
version: FAIRsharing.org: PINA; Protein Interaction Network Analysis platform; DOI: https://doi.org/10.25504/FAIRsharing.7q4gsz; Last edited: Nov. 9, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
network model
metasource: Fairsharing.org
version: FAIRsharing.org: PINA; Protein Interaction Network Analysis platform; DOI: https://doi.org/10.25504/FAIRsharing.7q4gsz; Last edited: Nov. 9, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein interaction
metasource: Fairsharing.org
version: FAIRsharing.org: PINA; Protein Interaction Network Analysis platform; DOI: https://doi.org/10.25504/FAIRsharing.7q4gsz; Last edited: Nov. 9, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metabolic and signaling pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
protein-protein interactions
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
protein interactions
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.429369
molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.429369
model organisms
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.429369
proteins
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.429369
database management
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:52.429369
Tags
More detailed information about this field from each metasource.
gene ontology enrichment
metasource: Fairsharing.orgversion: FAIRsharing.org: PINA; Protein Interaction Network Analysis platform; DOI: https://doi.org/10.25504/FAIRsharing.7q4gsz; Last edited: Nov. 9, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
interactome
metasource: Fairsharing.orgversion: FAIRsharing.org: PINA; Protein Interaction Network Analysis platform; DOI: https://doi.org/10.25504/FAIRsharing.7q4gsz; Last edited: Nov. 9, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
network model
metasource: Fairsharing.orgversion: FAIRsharing.org: PINA; Protein Interaction Network Analysis platform; DOI: https://doi.org/10.25504/FAIRsharing.7q4gsz; Last edited: Nov. 9, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: PINA; Protein Interaction Network Analysis platform; DOI: https://doi.org/10.25504/FAIRsharing.7q4gsz; Last edited: Nov. 9, 2020, 3:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metabolic and signaling pathways
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein-protein interactions
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein interactions
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:52.429369
molecular interactions, pathways and networks
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:52.429369
model organisms
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:52.429369
proteins
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:52.429369
database management
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:52.429369
gene ontology enrichment interactome network model protein interaction metabolic and signaling pathways protein-protein interactions protein interaction molecular interactions, pathways and networks model organisms proteins data management
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