Human Protein-Protein Interaction rEference
Names
More detailed information about this field from each metasource.
Human Protein-Protein Interaction rEference
metasource: Fairsharing.org
version: FAIRsharing.org: HIPPIE; Human Protein-Protein Interaction rEference; DOI: https://doi.org/10.25504/FAIRsharing.3pt56w; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
HIPPIE
metasource: Fairsharing.org
version: FAIRsharing.org: HIPPIE; Human Protein-Protein Interaction rEference; DOI: https://doi.org/10.25504/FAIRsharing.3pt56w; Last edited: Jan. 8, 2019, 1:25 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
Names
More detailed information about this field from each metasource.
Human Protein-Protein Interaction rEference
metasource: Fairsharing.orgversion: FAIRsharing.org: HIPPIE; Human Protein-Protein Interaction rEference; DOI: https://doi.org/10.25504/FAIRsharing.3pt56w; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
HIPPIE
metasource: Fairsharing.orgversion: FAIRsharing.org: HIPPIE; Human Protein-Protein Interaction rEference; DOI: https://doi.org/10.25504/FAIRsharing.3pt56w; Last edited: Jan. 8, 2019, 1:25 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
Names
More detailed information about this field from each metasource.
Human Protein-Protein Interaction rEference
metasource: Fairsharing.orgversion: FAIRsharing.org: HIPPIE; Human Protein-Protein Interaction rEference; DOI: https://doi.org/10.25504/FAIRsharing.3pt56w; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
HIPPIE
metasource: Fairsharing.orgversion: FAIRsharing.org: HIPPIE; Human Protein-Protein Interaction rEference; DOI: https://doi.org/10.25504/FAIRsharing.3pt56w; Last edited: Jan. 8, 2019, 1:25 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
HIPPIE integrates human protein-protein interactions from several manually curated source databases. It provides a web tool to query the interaction data, generate highly reliable, context-specific interaction networks and to make sense out of them.
Description
More detailed information about this field from each metasource.
HIPPIE integrates human protein-protein interactions from several manually curated source databases. It provides a web tool to query the interaction data, generate highly reliable, context-specific interaction networks and to make sense out of them.
metasource: Fairsharing.orgversion: FAIRsharing.org: HIPPIE; Human Protein-Protein Interaction rEference; DOI: https://doi.org/10.25504/FAIRsharing.3pt56w; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Human Integrated Protein-Protein Interaction rEference
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://cbdm.uni-mainz.de/hippie/Webpage
More detailed information about this field from each metasource.
http://cbdm.uni-mainz.de/hippie/
metasource: Fairsharing.orgversion: FAIRsharing.org: HIPPIE; Human Protein-Protein Interaction rEference; DOI: https://doi.org/10.25504/FAIRsharing.3pt56w; Last edited: Jan. 8, 2019, 1:25 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
Publications:
Publications
More detailed information about this field from each metasource.
HIPPIE: Integrating protein interaction networks with experiment based quality scores
PMID: 22348130
metasource: Fairsharing.org
version: FAIRsharing.org: HIPPIE; Human Protein-Protein Interaction rEference; DOI: https://doi.org/10.25504/FAIRsharing.3pt56w; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks
PMID: 27794551
metasource: Fairsharing.org
version: FAIRsharing.org: HIPPIE; Human Protein-Protein Interaction rEference; DOI: https://doi.org/10.25504/FAIRsharing.3pt56w; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Adding protein context to the human protein-protein interaction network to reveal meaningful interactions
PMID: 23300433
metasource: Fairsharing.org
version: FAIRsharing.org: HIPPIE; Human Protein-Protein Interaction rEference; DOI: https://doi.org/10.25504/FAIRsharing.3pt56w; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/1942
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.
HIPPIE: Integrating protein interaction networks with experiment based quality scores
PMID: 22348130
metasource: Fairsharing.org
version: FAIRsharing.org: HIPPIE; Human Protein-Protein Interaction rEference; DOI: https://doi.org/10.25504/FAIRsharing.3pt56w; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks
PMID: 27794551
metasource: Fairsharing.org
version: FAIRsharing.org: HIPPIE; Human Protein-Protein Interaction rEference; DOI: https://doi.org/10.25504/FAIRsharing.3pt56w; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Adding protein context to the human protein-protein interaction network to reveal meaningful interactions
PMID: 23300433
metasource: Fairsharing.org
version: FAIRsharing.org: HIPPIE; Human Protein-Protein Interaction rEference; DOI: https://doi.org/10.25504/FAIRsharing.3pt56w; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/1942
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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HIPPIE: Integrating protein interaction networks with experiment based quality scores
PubMed citations: 144.
144 articles citing: HIPPIE: Integrating protein interaction networks with experiment based quality scores
Deep learning frameworks for protein-protein interaction prediction. PMID:35832624
DEMA: a distance-bounded energy-field minimization algorithm to model and layout biomolecular networks with quantitative features. PMID:35758816
Analysis of Huntington's Disease Modifiers Using the Hyperbolic Mapping of the Protein Interaction Network. PMID:35628660
Proteome-wide prediction and analysis of the Cryptosporidium parvum protein-protein interaction network through integrative methods. PMID:35615014
S1P defects cause a new entity of cataract, alopecia, oral mucosal disorder, and psoriasis-like syndrome. PMID:35362222
From complete cross-docking to partners identification and binding sites predictions. PMID:35089918
Computational modeling of human-nCoV protein-protein interaction network. PMID:34902553
Testing biological network motif significance with exponential random graph models. PMID:34841042
In silico Methods for Identification of Potential Therapeutic Targets. PMID:34826045
Tumor relevant protein functional interactions identified using bipartite graph analyses. PMID:34728699
Performance Assessment of the Network Reconstruction Approaches on Various Interactomes. PMID:34676243
Matrix-screening reveals a vast potential for direct protein-protein interactions among RNA binding proteins. PMID:34133714
Predicting Protein-Protein Interactions via Gated Graph Attention Signed Network. PMID:34071437
In silico comparative analysis of LRRK2 interactomes from brain, kidney and lung. PMID:33915162
A network-informed analysis of SARS-CoV-2 and hemophagocytic lymphohistiocytosis genes' interactions points to Neutrophil extracellular traps as mediators of thrombosis in COVID-19. PMID:33684134
Biological network analysis with deep learning. PMID:33169146
MasterPATH: network analysis of functional genomics screening data. PMID:32928103
PINOT: an intuitive resource for integrating protein-protein interactions. PMID:32527260
MIPPIE: the mouse integrated protein-protein interaction reference. PMID:32496562
Prevention of age-associated neuronal hyperexcitability with improved learning and attention upon knockout or antagonism of LPAR2. PMID:32468095
WeiBI (web-based platform): Enriching integrated interaction network with increased coverage and functional proteins from genome-wide experimental OMICS data. PMID:32221380
Systems analysis of RhoGEF and RhoGAP regulatory proteins reveals spatially organized RAC1 signalling from integrin adhesions. PMID:32203420
Triangular correlation (TrC) between cancer aggressiveness, cell uptake capability, and cell deformability. PMID:31998832
OCIAD1 contributes to neurodegeneration in Alzheimer's disease by inducing mitochondria dysfunction, neuronal vulnerability and synaptic damages. PMID:31931285
Integrating protein localization with automated signaling pathway reconstruction. PMID:31787091
Mapping the perturbome network of cellular perturbations. PMID:31723137
HMNPPID-human malignant neoplasm protein-protein interaction database. PMID:31639057
Differential network analysis and protein-protein interaction study reveals active protein modules in glucocorticoid resistance for infant acute lymphoblastic leukemia. PMID:31370801
Beyond Synthetic Lethality: Charting the Landscape of Pairwise Gene Expression States Associated with Survival in Cancer. PMID:31340155
Disease gene prediction for molecularly uncharacterized diseases. PMID:31276496
Augmenting subnetwork inference with information extracted from the scientific literature. PMID:31246951
Prediction of Bone Metastasis in Breast Cancer Based on Minimal Driver Gene Set in Gene Dependency Network. PMID:31213036
Multi-Omic Data Interpretation to Repurpose Subtype Specific Drug Candidates for Breast Cancer. PMID:31134131
Protein interaction disruption in cancer. PMID:31014259
Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy. PMID:30858180
IMMAN: an R/Bioconductor package for Interolog protein network reconstruction, mapping and mining analysis. PMID:30755155
Network-guided prediction of aromatase inhibitor response in breast cancer. PMID:30742607
Network spectra for drug-target identification in complex diseases: new guns against old foes. PMID:30596144
Network-Guided Discovery of Influenza Virus Replication Host Factors. PMID:30563907
Manifold learning and maximum likelihood estimation for hyperbolic network embedding. PMID:30533502
Predicting protein-protein interactions through sequence-based deep learning. PMID:30423091
A Network Pharmacology Approach to Uncover the Molecular Mechanisms of Herbal Formula Ban-Xia-Xie-Xin-Tang. PMID:30410554
Context-dependent prediction of protein complexes by SiComPre. PMID:30245847
The Synergistic Combination of Everolimus and Paroxetine Exerts Post-ischemic Neuroprotection In Vitro. PMID:30062636
ProfPPIdb: Pairs of physical protein-protein interactions predicted for entire proteomes. PMID:30020956
An integrative network-based approach to identify novel disease genes and pathways: a case study in the context of inflammatory bowel disease. PMID:30005591
IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins. PMID:30002402
Identification of drug-target interaction by a random walk with restart method on an interactome network. PMID:29897326
PPI network analyses of human WD40 protein family systematically reveal their tendency to assemble complexes and facilitate the complex predictions. PMID:29745845
ENTPRISE-X: Predicting disease-associated frameshift and nonsense mutations. PMID:29723276
Proteomic analysis defines kinase taxonomies specific for subtypes of breast cancer. PMID:29643987
The latent geometry of the human protein interaction network. PMID:29635317
Quantitative mass spectrometry analysis reveals a panel of nine proteins as diagnostic markers for colon adenocarcinomas. PMID:29568375
Single-Nucleotide Variations of the Human Nuclear Hormone Receptor Genes in 60,000 Individuals. PMID:29379896
The integration of weighted gene association networks based on information entropy. PMID:29272314
Biological Implications of Differential Expression of Mitochondrial-Shaping Proteins in Parkinson's Disease. PMID:29267236
Gene gravity-like algorithm for disease gene prediction based on phenotype-specific network. PMID:29212543
A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer. PMID:29190299
Computational systems biology approaches for Parkinson's disease. PMID:29185073
SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome. PMID:29141584
Biological function integrated prediction of severe radiographic progression in rheumatoid arthritis: a nested case control study. PMID:29065906
Using uncertainty to link and rank evidence from biomedical literature for model curation. PMID:29036627
PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology. PMID:29023571
Synaptic Interactome Mining Reveals p140Cap as a New Hub for PSD Proteins Involved in Psychiatric and Neurological Disorders. PMID:28713243
Strength of functional signature correlates with effect size in autism. PMID:28687074
More Is Better: Recent Progress in Multi-Omics Data Integration Methods. PMID:28670325
Computational analysis of multimorbidity between asthma, eczema and rhinitis. PMID:28598986
Persistence of Innate Immune Pathways in Late Stage Human Bacterial and Fungal Keratitis: Results from a Comparative Transcriptome Analysis. PMID:28573109
Identification of oral cancer related candidate genes by integrating protein-protein interactions, gene ontology, pathway analysis and immunohistochemistry. PMID:28559546
Protease-Inhibitor Interaction Predictions: Lessons on the Complexity of Protein-Protein Interactions. PMID:28385878
A Comprehensive View of the β-Arrestinome. PMID:28321204
Identification of Entry Factors Involved in Hepatitis C Virus Infection Based on Host-Mimicking Short Linear Motifs. PMID:28129350
Genome-wide Analysis of WD40 Protein Family in Human. PMID:27991561
Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery. PMID:27955713
Early age decline in DNA repair capacity in the liver: in depth profile of differential gene expression. PMID:27922819
The TissueNet v.2 database: A quantitative view of protein-protein interactions across human tissues. PMID:27899616
Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences. PMID:27881428
Quantitative GTPase Affinity Purification Identifies Rho Family Protein Interaction Partners. PMID:27852748
Large-scale identification of human protein function using topological features of interaction network. PMID:27849060
A network of epigenetic modifiers and DNA repair genes controls tissue-specific copy number alteration preference. PMID:27831464
From Proteomic Analysis to Potential Therapeutic Targets: Functional Profile of Two Lung Cancer Cell Lines, A549 and SW900, Widely Studied in Pre-Clinical Research. PMID:27814385
HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks. PMID:27794551
Co-regulation of paralog genes in the three-dimensional chromatin architecture. PMID:27634932
Efficient embedding of complex networks to hyperbolic space via their Laplacian. PMID:27445157
Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens. PMID:27403523
Intrinsic Disorder in Transmembrane Proteins: Roles in Signaling and Topology Prediction. PMID:27391701
Evolutionary and Topological Properties of Genes and Community Structures in Human Gene Regulatory Networks. PMID:27359334
An integer programming framework for inferring disease complexes from network data. PMID:27307626
A knowledge-based approach for predicting gene-disease associations. PMID:27283949
Cross-talk between AMPK and EGFR dependent Signaling in Non-Small Cell Lung Cancer. PMID:27279498
Uncovering disease mechanisms through network biology in the era of Next Generation Sequencing. PMID:27080396
ENTPRISE: An Algorithm for Predicting Human Disease-Associated Amino Acid Substitutions from Sequence Entropy and Predicted Protein Structures. PMID:26982818
Mutanome and expression of immune response genes in microsatellite stable colon cancer. PMID:26871478
Lamina Associated Polypeptide 1 (LAP1) Interactome and Its Functional Features. PMID:26784240
Novel insights into human respiratory syncytial virus-host factor interactions through integrated proteomics and transcriptomics analysis. PMID:26760927
Are protein-protein interfaces special regions on a protein's surface? PMID:26723634
HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species. PMID:26708988
Proteomic Profiling in the Brain of CLN1 Disease Model Reveals Affected Functional Modules. PMID:26707855
Prediction of Druggable Proteins Using Machine Learning and Systems Biology: A Mini-Review. PMID:26696900
Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer. PMID:26683094
Proteomic Analysis of Dynein-Interacting Proteins in Amyotrophic Lateral Sclerosis Synaptosomes Reveals Alterations in the RNA-Binding Protein Staufen1. PMID:26598648
Histone H1 couples initiation and amplification of ubiquitin signalling after DNA damage. PMID:26503038
Predicting Pharmacodynamic Drug-Drug Interactions through Signaling Propagation Interference on Protein-Protein Interaction Networks. PMID:26469276
Mining protein interactomes to improve their reliability and support the advancement of network medicine. PMID:26442112
Quo vadis computational analysis of PPI data or why the future isn't here yet. PMID:26442107
New genes drive the evolution of gene interaction networks in the human and mouse genomes. PMID:26424194
Integrative analysis of human protein, function and disease networks. PMID:26399914
Identifying problematic drugs based on the characteristics of their targets. PMID:26388775
Exploring novel mechanistic insights in Alzheimer's disease by assessing reliability of protein interactions. PMID:26346705
Correcting for the study bias associated with protein-protein interaction measurements reveals differences between protein degree distributions from different cancer types. PMID:26300911
Detecting conserved protein complexes using a dividing-and-matching algorithm and unequally lenient criteria for network comparison. PMID:26136815
Evolutionary trends and functional anatomy of the human expanded autophagy network. PMID:26103419
MyProteinNet: build up-to-date protein interaction networks for organisms, tissues and user-defined contexts. PMID:25990735
Involvement of multiple cellular pathways in regulating resistance to tamoxifen in BIK-suppressed MCF-7 cells. PMID:25861752
Mining the modular structure of protein interaction networks. PMID:25856434
A scalable method for molecular network reconstruction identifies properties of targets and mutations in acute myeloid leukemia. PMID:25844667
Amyloid domains in the cell nucleus controlled by nucleoskeletal protein lamin B1 reveal a new pathway of mercury neurotoxicity. PMID:25699204
A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology. PMID:25648416
STRING v10: protein-protein interaction networks, integrated over the tree of life. PMID:25352553
Characterizing protein interactions employing a genome-wide siRNA cellular phenotyping screen. PMID:25255318
Network medicine analysis of COPD multimorbidities. PMID:25248857
A computational model to predict bone metastasis in breast cancer by integrating the dysregulated pathways. PMID:25163697
Protein conservation and variation suggest mechanisms of cell type-specific modulation of signaling pathways. PMID:24922536
Structural bioinformatics of the interactome. PMID:24895853
The palmitoyl acyltransferase HIP14 shares a high proportion of interactors with huntingtin: implications for a role in the pathogenesis of Huntington's disease. PMID:24705354
Inferring gene dependency network specific to phenotypic alteration based on gene expression data and clinical information of breast cancer. PMID:24637666
Integrating systems biology sources illuminates drug action. PMID:24577151
Bias tradeoffs in the creation and analysis of protein-protein interaction networks. PMID:24480284
Functional and genomic analyses of alpha-solenoid proteins. PMID:24278209
UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks. PMID:24214987
Prediction of oncogenic interactions and cancer-related signaling networks based on network topology. PMID:24204854
Reconstruction of the experimentally supported human protein interactome: what can we learn? PMID:24088582
Target essentiality and centrality characterize drug side effects. PMID:23874169
Exploration of binary virus-host interactions using an infectious protein complementation assay. PMID:23816991
Metabolic turnover of synaptic proteins: kinetics, interdependencies and implications for synaptic maintenance. PMID:23658807
Predicting physical interactions between protein complexes. PMID:23438732
Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. PMID:23300433
Assessing identity, redundancy and confounds in Gene Ontology annotations over time. PMID:23297035
Development and application of a DNA microarray-based yeast two-hybrid system. PMID:23275563
Flaws in evaluation schemes for pair-input computational predictions. PMID:23223166
SynSysNet: integration of experimental data on synaptic protein-protein interactions with drug-target relations. PMID:23143269
Cluster-based assessment of protein-protein interaction confidence. PMID:23050565
IntScore: a web tool for confidence scoring of biological interactions. PMID:22649056
Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks. PMID:22287626 -
HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks
PubMed citations: 135.
135 articles citing: HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks
Gene networks under circadian control exhibit diurnal organization in primate organs. PMID:35906476
Construction and contextualization approaches for protein-protein interaction networks. PMID:35832626
Deep learning frameworks for protein-protein interaction prediction. PMID:35832624
RPpocket: An RNA-Protein Intuitive Database with RNA Pocket Topology Resources. PMID:35805909
Genome-wide characterization of copy number variations in diffuse large B-cell lymphoma with implications in targeted therapy. PMID:35693879
PRECOGx: exploring GPCR signaling mechanisms with deep protein representations. PMID:35639758
Analysis of Huntington's Disease Modifiers Using the Hyperbolic Mapping of the Protein Interaction Network. PMID:35628660
Regulation of protein complex partners as a compensatory mechanism in aneuploid tumors. PMID:35575458
Computational methods, databases and tools for synthetic lethality prediction. PMID:35352098
Identifying and Validating Networks of Oncology Biomarkers Mined From the Scientific Literature. PMID:35342286
Finding New Ways How to Control BACE1. PMID:35305135
Distinct Epileptogenic Mechanisms Associated with Seizures in Wolf-Hirschhorn Syndrome. PMID:35278209
In silico prediction of HIV-1-host molecular interactions and their directionality. PMID:35134057
Mapping oncogenic protein interactions for precision medicine. PMID:35113472
How Far Are We from the Completion of the Human Protein Interactome Reconstruction? PMID:35053288
Proteome-scale mapping of binding sites in the unstructured regions of the human proteome. PMID:35044719
BioProfiling.jl: Profiling biological perturbations with high-content imaging in single cells and heterogeneous populations. PMID:34935929
Improving Analysis and Annotation of Microarray Data with Protein Interactions. PMID:34902122
Testing biological network motif significance with exponential random graph models. PMID:34841042
Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities. PMID:34799561
Role of FRG1 in predicting the overall survivability in cancers using multivariate based optimal model. PMID:34795329
IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis. PMID:34755877
Network analysis reveals rare disease signatures across multiple levels of biological organization. PMID:34753928
Synthesis of scaffold-free, three dimensional, osteogenic constructs following culture of skeletal osteoprogenitor cells on glass surfaces. PMID:34746337
Network-based protein-protein interaction prediction method maps perturbations of cancer interactome. PMID:34727106
Performance Assessment of the Network Reconstruction Approaches on Various Interactomes. PMID:34676243
Getting to know each other: PPIMem, a novel approach for predicting transmembrane protein-protein complexes. PMID:34630938
Using informative features in machine learning based method for COVID-19 drug repurposing. PMID:34544500
OGT Protein Interaction Network (OGT-PIN): A Curated Database of Experimentally Identified Interaction Proteins of OGT. PMID:34502531
Enzymes in the Cholesterol Synthesis Pathway: Interactomics in the Cancer Context. PMID:34440098
Topological network based drug repurposing for coronavirus 2019. PMID:34324563
Functional Roles of Bromodomain Proteins in Cancer. PMID:34298819
Transfer learning via multi-scale convolutional neural layers for human-virus protein-protein interaction prediction. PMID:34273146
Prioritizing and characterizing functionally relevant genes across human tissues. PMID:34270548
Identification of candidate biomarkers and therapeutic agents for heart failure by bioinformatics analysis. PMID:34218797
Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms. PMID:34197603
StrongestPath: a Cytoscape application for protein-protein interaction analysis. PMID:34187355
Pretraining model for biological sequence data. PMID:34050350
KEA3: improved kinase enrichment analysis via data integration. PMID:34019655
Characterization and comparison of gene-centered human interactomes. PMID:34010955
A self-attention model for inferring cooperativity between regulatory features. PMID:33950192
A SARS-CoV-2 (COVID-19) biological network to find targets for drug repurposing. PMID:33931664
Shared Neurodevelopmental Perturbations Can Lead to Intellectual Disability in Individuals with Distinct Rare Chromosome Duplications. PMID:33922640
In silico comparative analysis of LRRK2 interactomes from brain, kidney and lung. PMID:33915162
The VRNetzer platform enables interactive network analysis in Virtual Reality. PMID:33893283
Performance improvement for a 2D convolutional neural network by using SSC encoding on protein-protein interaction tasks. PMID:33845759
Identification of multipotent drugs for COVID-19 therapeutics with the evaluation of their SARS-CoV2 inhibitory activity. PMID:33841751
Identification of hub genes related to the progression of type 1 diabetes by computational analysis. PMID:33827531
Construction of Gene Modules and Analysis of Prognostic Biomarkers for Cervical Cancer by Weighted Gene Co-Expression Network Analysis. PMID:33816217
Exploring Common Therapeutic Targets for Neurodegenerative Disorders Using Transcriptome Study. PMID:33815473
Increasing brain palmitoylation rescues behavior and neuropathology in Huntington disease mice. PMID:33789888
Identification of potential and novel target genes in pituitary prolactinoma by bioinformatics analysis. PMID:33709028
Computational Analysis Indicates That PARP1 Acts as a Histone Deacetylases Interactor Sharing Common Lysine Residues for Acetylation, Ubiquitination, and SUMOylation in Alzheimer's and Parkinson's Disease. PMID:33681613
HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis. PMID:33677507
A systems-based method to repurpose marketed therapeutics for antiviral use: a SARS-CoV-2 case study. PMID:33593923
UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network. PMID:33575553
The Role of Low Complexity Regions in Protein Interaction Modes: An Illustration in Huntingtin. PMID:33572172
Integrated network analysis reveals new genes suggesting COVID-19 chronic effects and treatment. PMID:33569598
Contextualized Protein-Protein Interactions. PMID:33511361
Improving gene network inference with graph wavelets and making insights about ageing-associated regulatory changes in lungs. PMID:33381809
Towards a unified open access dataset of molecular interactions. PMID:33262342
PINA 3.0: mining cancer interactome. PMID:33231689
LL-37-Induced Autophagy Contributed to the Elimination of Live Porphyromonas gingivalis Internalized in Keratinocytes. PMID:33178622
Network medicine in Cardiovascular Research. PMID:33165538
IHP-PING-generating integrated human protein-protein interaction networks on-the-fly. PMID:33129201
Evolution of Sequence-based Bioinformatics Tools for Protein-protein Interaction Prediction. PMID:33093807
Reconstructed signaling and regulatory networks identify potential drugs for SARS-CoV-2 infection. PMID:33083801
Predicting candidate genes from phenotypes, functions and anatomical site of expression. PMID:33051643
Evolutionary Study of Disorder in Protein Sequences. PMID:33036302
Identification of putative master regulators in rheumatoid arthritis synovial fibroblasts using gene expression data and network inference. PMID:33004899
Transcriptomic analysis delineates potential signature genes and miRNAs associated with the pathogenesis of asthma. PMID:32770056
The Disordered Cellular Multi-Tasker WIP and Its Protein-Protein Interactions: A Structural View. PMID:32708183
Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19. PMID:32550253
Dynamic rewiring of the human interactome by interferon signaling. PMID:32539747
PINOT: an intuitive resource for integrating protein-protein interactions. PMID:32527260
ccNetViz: a WebGL-based JavaScript library for visualization of large networks. PMID:32516383
The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification. PMID:32507889
MIPPIE: the mouse integrated protein-protein interaction reference. PMID:32496562
Integrative analysis of large-scale loss-of-function screens identifies robust cancer-associated genetic interactions. PMID:32463358
Unbiased Profiling of the Human Proinsulin Biosynthetic Interaction Network Reveals a Role for Peroxiredoxin 4 in Proinsulin Folding. PMID:32457219
Post-translational Modification Crosstalk and Hotspots in Sirtuin Interactors Implicated in Cardiovascular Diseases. PMID:32425973
Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis. PMID:32326049
Nuclear inclusions of pathogenic ataxin-1 induce oxidative stress and perturb the protein synthesis machinery. PMID:32145456
A Novel Approach for Drug-Target Interactions Prediction Based on Multimodal Deep Autoencoder. PMID:32047432
IGF1-mediated human embryonic stem cell self-renewal recapitulates the embryonic niche. PMID:32034154
Mechanisms of tissue and cell-type specificity in heritable traits and diseases. PMID:31913361
Integrating protein localization with automated signaling pathway reconstruction. PMID:31787091
Assessing the reliability of gene expression measurements in very-low-numbers of human monocyte-derived macrophages. PMID:31784632
A network-based approach to identify deregulated pathways and drug effects in metabolic syndrome. PMID:31740673
PCOSBase: a manually curated database of polycystic ovarian syndrome. PMID:31725861
Mapping the perturbome network of cellular perturbations. PMID:31723137
First Insights on the Presence of the Unfolded Protein Response in Human Spermatozoa. PMID:31694346
7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs. PMID:31653198
Biological Network Approaches and Applications in Rare Disease Studies. PMID:31614842
Measuring rank robustness in scored protein interaction networks. PMID:31462221
Identification of gene co-expression modules and hub genes associated with lymph node metastasis of papillary thyroid cancer. PMID:31332712
HACE1 deficiency leads to structural and functional neurodevelopmental defects. PMID:31321300
Membrane protein-regulated networks across human cancers. PMID:31311925
Exploring the Molecular Mechanism of the Drug-Treated Breast Cancer Based on Gene Expression Microarray. PMID:31311202
Disease gene prediction for molecularly uncharacterized diseases. PMID:31276496
mTOR Signaling Pathway Regulates Sperm Quality in Older Men. PMID:31234465
Protein-Protein Interaction Network Analysis Reveals Several Diseases Highly Associated with Polycystic Ovarian Syndrome. PMID:31216618
GScluster: network-weighted gene-set clustering analysis. PMID:31072324
Pathway centrality in protein interaction networks identifies putative functional mediating pathways in pulmonary disease. PMID:30971743
Evaluating measures of association for single-cell transcriptomics. PMID:30962620
A Network Module for the Perseus Software for Computational Proteomics Facilitates Proteome Interaction Graph Analysis. PMID:30931570
Geometric characterisation of disease modules. PMID:30839777
Isoform-specific GSK3A activity is negatively correlated with human sperm motility. PMID:30824926
Network-guided prediction of aromatase inhibitor response in breast cancer. PMID:30742607
A network biology approach to unraveling inherited axonopathies. PMID:30737464
Comparative Analysis of Normalization Methods for Network Propagation. PMID:30723490
Exploiting locational and topological overlap model to identify modules in protein interaction networks. PMID:30642247
Homolog-Selective Degradation as a Strategy to Probe the Function of CDK6 in AML. PMID:30595531
Manifold learning and maximum likelihood estimation for hyperbolic network embedding. PMID:30533502
Embracing the Dark Side: Computational Approaches to Unveil the Functionality of Genes Lacking Biological Annotation in Drug-Induced Liver Injury. PMID:30515189
N-cadherin signaling via Trio assembles adherens junctions to restrict endothelial permeability. PMID:30463880
A Network Pharmacology Approach to Uncover the Molecular Mechanisms of Herbal Formula Ban-Xia-Xie-Xin-Tang. PMID:30410554
IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species. PMID:30407591
Context-specific interactions in literature-curated protein interaction databases. PMID:30340458
Genomic data integration systematically biases interactome mapping. PMID:30332399
Network, Transcriptomic and Genomic Features Differentiate Genes Relevant for Drug Response. PMID:30319692
Factors of the bone marrow microniche that support human plasma cell survival and immunoglobulin secretion. PMID:30209264
An Overview of Current Methods to Confirm Protein-Protein Interactions. PMID:30129399
Proteome-wide analysis of phospho-regulated PDZ domain interactions. PMID:30126976
The Synergistic Combination of Everolimus and Paroxetine Exerts Post-ischemic Neuroprotection In Vitro. PMID:30062636
Correcting the F508del-CFTR variant by modulating eukaryotic translation initiation factor 3-mediated translation initiation. PMID:30006345
PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants. PMID:29873773
PPI network analyses of human WD40 protein family systematically reveal their tendency to assemble complexes and facilitate the complex predictions. PMID:29745845
The latent geometry of the human protein interaction network. PMID:29635317
Efficient pathway enrichment and network analysis of GWAS summary data using GSA-SNP2. PMID:29562348
From gene networks to drugs: systems pharmacology approaches for AUD. PMID:29497781
Biological Implications of Differential Expression of Mitochondrial-Shaping Proteins in Parkinson's Disease. PMID:29267236
The OncoPPi Portal: an integrative resource to explore and prioritize protein-protein interactions for cancer target discovery. PMID:29186335
Interaction profiling of RNA-binding ubiquitin ligases reveals a link between posttranscriptional regulation and the ubiquitin system. PMID:29185492
HEDD: Human Enhancer Disease Database. PMID:29077884 -
Adding protein context to the human protein-protein interaction network to reveal meaningful interactions
PubMed citations: 38.
38 articles citing: Adding protein context to the human protein-protein interaction network to reveal meaningful interactions
Virus-host interaction networks as new antiviral drug targets for IAV and SARS-CoV-2. PMID:35476817
Modulating Angiogenesis by Proteomimetics of Vascular Endothelial Growth Factor. PMID:34968032
Targeting uPA-uPAR interaction to improve intestinal epithelial barrier integrity in inflammatory bowel disease. PMID:34933179
Testing biological network motif significance with exponential random graph models. PMID:34841042
Association of miR-499 Polymorphism and Its Regulatory Networks with Hashimoto Thyroiditis Susceptibility: A Population-Based Case-Control Study. PMID:34576267
Systematic analysis of molecular characterization and clinical relevance of m6A regulators in digestive system pan-cancers. PMID:34102905
Toll-Interacting Protein in Pulmonary Diseases. Abiding by the Goldilocks Principle. PMID:33233920
Network medicine in Cardiovascular Research. PMID:33165538
MIPPIE: the mouse integrated protein-protein interaction reference. PMID:32496562
A dual controllability analysis of influenza virus-host protein-protein interaction networks for antiviral drug target discovery. PMID:31159726
Network-Guided Discovery of Influenza Virus Replication Host Factors. PMID:30563907
Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. PMID:30082644
The evolutionary signal in metagenome phyletic profiles predicts many gene functions. PMID:29991352
Identification of drug-target interaction by a random walk with restart method on an interactome network. PMID:29897326
Biological Implications of Differential Expression of Mitochondrial-Shaping Proteins in Parkinson's Disease. PMID:29267236
PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology. PMID:29023571
AKT1, LKB1, and YAP1 Revealed as MYC Interactors with NanoLuc-Based Protein-Fragment Complementation Assay. PMID:28087810
HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks. PMID:27794551
Comparative analysis of housekeeping and tissue-specific driver nodes in human protein interaction networks. PMID:27612563
NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease. PMID:27392431
Novel insights into human respiratory syncytial virus-host factor interactions through integrated proteomics and transcriptomics analysis. PMID:26760927
Forward Individualized Medicine from Personal Genomes to Interactomes. PMID:26696898
Drug target prioritization by perturbed gene expression and network information. PMID:26615774
Integrated interactions database: tissue-specific view of the human and model organism interactomes. PMID:26516188
Mining protein interactomes to improve their reliability and support the advancement of network medicine. PMID:26442112
Integrative analysis of human protein, function and disease networks. PMID:26399914
Integrated analysis of differential gene expression profiles in hippocampi to identify candidate genes involved in Alzheimer's disease. PMID:26324066
Correcting for the study bias associated with protein-protein interaction measurements reveals differences between protein degree distributions from different cancer types. PMID:26300911
HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases. PMID:26157625
Comprehensive comparison of large-scale tissue expression datasets. PMID:26157623
Construction and analyses of human large-scale tissue specific networks. PMID:25513809
Walking the interactome for candidate prioritization in exome sequencing studies of Mendelian diseases. PMID:25078397
Protein conservation and variation suggest mechanisms of cell type-specific modulation of signaling pathways. PMID:24922536
Molecular network analysis enhances understanding of the biology of mental disorders. PMID:24733456
Functional and genomic analyses of alpha-solenoid proteins. PMID:24278209
PainNetworks: a web-based resource for the visualisation of pain-related genes in the context of their network associations. PMID:24036287
Identifying proteins controlling key disease signaling pathways. PMID:23812988
A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks. PMID:23812986 - http://dx.doi.org/10.1093/nar/1942
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protein
metasource: Fairsharing.org
version: FAIRsharing.org: HIPPIE; Human Protein-Protein Interaction rEference; DOI: https://doi.org/10.25504/FAIRsharing.3pt56w; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein interaction
metasource: Fairsharing.org
version: FAIRsharing.org: HIPPIE; Human Protein-Protein Interaction rEference; DOI: https://doi.org/10.25504/FAIRsharing.3pt56w; Last edited: Jan. 8, 2019, 1:25 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
Tags
More detailed information about this field from each metasource.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: HIPPIE; Human Protein-Protein Interaction rEference; DOI: https://doi.org/10.25504/FAIRsharing.3pt56w; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: HIPPIE; Human Protein-Protein Interaction rEference; DOI: https://doi.org/10.25504/FAIRsharing.3pt56w; Last edited: Jan. 8, 2019, 1:25 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 protein interaction metabolic and signaling pathways protein-protein interactions
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