R3SP8V last accessed: 2022-11-04

Other names: the interactome browser

mentha archives evidence collected from different sources and presents these data in a complete and comprehensive way. Its data comes from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. The aggregated data forms an interactome which includes many organisms. mentha is a resource that offers a series of tools to analyse selected proteins in the context of a network of interactions.

Webpage:

http://mentha.uniroma2.it/

Licence:

Name: Public Domain
URL: http://mentha.uniroma2.it/about.php

Publications:

Publications
More detailed information about this field from each metasource.

mentha: a resource for browsing integrated protein-interaction networks
PMID: 23900247
metasource: Fairsharing.org
version: FAIRsharing.org: mentha; mentha; DOI: https://doi.org/10.25504/FAIRsharing.j1eyq2; Last edited: Jan. 8, 2019, 1:24 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.386477

mentha: a resource for browsing integrated protein-interaction networks PubMed citations: 137.

137 articles citing: mentha: a resource for browsing integrated protein-interaction networks

Mutations in SORL1 and MTHFDL1 possibly contribute to the development of Alzheimer's disease in a multigenerational Colombian Family. PMID:35905044
PHILM2Web: A high-throughput database of macromolecular host-pathogen interactions on the Web. PMID:35776535
IMEx Databases: Displaying Molecular Interactions into a Single, Standards-Compliant Dataset. PMID:35507258
Predicted mouse interactome and network-based interpretation of differentially expressed genes. PMID:35390003
Integrating protein copy numbers with interaction networks to quantify stoichiometry in clathrin-mediated endocytosis. PMID:35354856
HAUS5 Is A Potential Prognostic Biomarker With Functional Significance in Breast Cancer. PMID:35280773
An Integrative Network Approach to Identify Common Genes for the Therapeutics in Tuberculosis and Its Overlapping Non-Communicable Diseases. PMID:35153741
Comprehensive evaluation of computational methods for predicting cancer driver genes. PMID:35037014
Shared Molecular Mechanisms between Atherosclerosis and Periodontitis by Analyzing the Transcriptomic Alterations of Peripheral Blood Monocytes. PMID:34899963
PangenomeNet: a pan-genome-based network reveals functional modules on antimicrobial resistome for Escherichia coli strains. PMID:34758735
Systematic discovery of signaling pathways linking immune activation to schizophrenia. PMID:34746692
Getting to know each other: PPIMem, a novel approach for predicting transmembrane protein-protein complexes. PMID:34630938
Identifying Protein Complexes With Clear Module Structure Using Pairwise Constraints in Protein Interaction Networks. PMID:34512712
Enzymes in the Cholesterol Synthesis Pathway: Interactomics in the Cancer Context. PMID:34440098
Heterogeneous graph attention networks for drug virus association prediction. PMID:34419588
PI3K-AKT, JAK2-STAT3 pathways and cell-cell contact regulate maspin subcellular localization. PMID:34391444
Global effects of RAB3GAP1 dysexpression on the proteome of mouse cortical neurons. PMID:34363538
Identification of Key Pathways and Genes in Obesity Using Bioinformatics Analysis and Molecular Docking Studies. PMID:34248836
Transcriptional drug repositioning and cheminformatics approach for differentiation therapy of leukaemia cells. PMID:34131166
DGLinker: flexible knowledge-graph prediction of disease-gene associations. PMID:34125897
Model-based analysis uncovers mutations altering autophagy selectivity in human cancer. PMID:34059679
KEA3: improved kinase enrichment analysis via data integration. PMID:34019655
The microRNA analysis portal is a next-generation tool for exploring and analyzing miRNA-focused data in the literature. PMID:33903708
Quantitative Proteomic Approach Reveals Altered Metabolic Pathways in Response to the Inhibition of Lysine Deacetylases in A549 Cells under Normoxia and Hypoxia. PMID:33806075
Genome-wide RNAi screen for regulators of UPRmt in Caenorhabditis elegans mutants with defects in mitochondrial fusion. PMID:33784383
Quantitative Proteomics Reveals that the OGT Interactome Is Remodeled in Response to Oxidative Stress. PMID:33716169
Novel gene signatures for stage classification of the squamous cell carcinoma of the lung. PMID:33649335
Elucidating the network features and evolutionary attributes of intra- and interspecific protein-protein interactions between human and pathogenic bacteria. PMID:33420198
Multi-resolution visualization and analysis of biomolecular networks through hierarchical community detection and web-based graphical tools. PMID:33351828
Towards a unified open access dataset of molecular interactions. PMID:33262342
Predicted rat interactome database and gene set linkage analysis. PMID:33216897
Plasma Proteomics Identify Biomarkers and Pathogenesis of COVID-19. PMID:33128875
Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of differentially expressed genes. PMID:33076954
Determining the interaction status and evolutionary fate of duplicated homomeric proteins. PMID:32853212
Sex differences in circulating proteins in heart failure with preserved ejection fraction. PMID:32831121
Insight into the structures of Interleukin-18 systems. PMID:32769049
Dynamic rewiring of the human interactome by interferon signaling. PMID:32539747
Intrinsically disordered regions are abundant in simplexvirus proteomes and display signatures of positive selection. PMID:32411391
MyoMiner: explore gene co-expression in normal and pathological muscle. PMID:32393257
A reference map of the human binary protein interactome. PMID:32296183
Precision medicine - networks to the rescue. PMID:32199228
DISNET: a framework for extracting phenotypic disease information from public sources. PMID:32110491
Predicted Drosophila Interactome Resource and web tool for functional interpretation of differentially expressed genes. PMID:32103267
Metabolic reprogramming of fibro/adipogenic progenitors facilitates muscle regeneration. PMID:32019766
Developing a virus-microRNA interactome using cytoscape. PMID:31993337
A network analysis to identify mediators of germline-driven differences in breast cancer prognosis. PMID:31949161
Refining modules to determine functionally significant clusters in molecular networks. PMID:31874644
Statistical characteristics of amino acid covariance as possible descriptors of viral genomic complexity. PMID:31804522
Sequence-Derived Markers of Drug Targets and Potentially Druggable Human Proteins. PMID:31803227
'One DB to rule them all'-the RING: a Regulatory INteraction Graph combining TFs, genes/proteins, SNPs, diseases and drugs. PMID:31682269
CancerGeneNet: linking driver genes to cancer hallmarks. PMID:31598703
Conserved Central Intraviral Protein Interactome of the Herpesviridae Family. PMID:31575665
Tissue-specific mouse mRNA isoform networks. PMID:31562339
SCRIBER: accurate and partner type-specific prediction of protein-binding residues from proteins sequences. PMID:31510679
A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. PMID:31494632
Evaluation of α-synuclein and apolipoprotein E as potential biomarkers in cerebrospinal fluid to monitor pharmacotherapeutic efficacy in dopamine dictated disease states of Parkinson's disease and schizophrenia. PMID:31410011
SMAC, a computational system to link literature, biomedical and expression data. PMID:31324861
Mapping the protein-protein and genetic interactions of cancer to guide precision medicine. PMID:31288129
Systematic identification of recognition motifs for the hub protein LC8. PMID:31266884
DeepPhagy: a deep learning framework for quantitatively measuring autophagy activity in Saccharomyces cerevisiae. PMID:31204567
Protein interactions and consensus clustering analysis uncover insights into herpesvirus virion structure and function relationships. PMID:31199794
Plasma protein biomarkers and their association with mutually exclusive cardiovascular phenotypes: the FIBRO-TARGETS case-control analyses. PMID:31062082
Detailed prediction of protein sub-nuclear localization. PMID:31014229
A bioinformatics investigation into the pharmacological mechanisms of the effect of Fufang Danshen on pain based on methodologies of network pharmacology. PMID:30976033
A Multireporter Bacterial 2-Hybrid Assay for the High-Throughput and Dynamic Assay of PDZ Domain-Peptide Interactions. PMID:30969105
MorCVD: A Unified Database for Host-Pathogen Protein-Protein Interactions of Cardiovascular Diseases Related to Microbes. PMID:30858555
Network controllability analysis of intracellular signalling reveals viruses are actively controlling molecular systems. PMID:30765882
Context-specific interactions in literature-curated protein interaction databases. PMID:30340458
Genomic data integration systematically biases interactome mapping. PMID:30332399
Evaluation of Serum Apolipoprotein E as a Potential Biomarker for Pharmacological Therapeutic Efficacy Monitoring in Dopamine Dictated Disease Spectrum of Schizophrenia and Parkinson's disease: A Preliminary Study. PMID:30327579
Tumor-preventing activity of aspirin in multiple cancers based on bioinformatic analyses. PMID:30280037
Prediction of protein group function by iterative classification on functional relevance network. PMID:30192921
Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. PMID:30082644
ProfPPIdb: Pairs of physical protein-protein interactions predicted for entire proteomes. PMID:30020956
The arrhythmogenic cardiomyopathy-specific coding and non-coding transcriptome in human cardiac stromal cells. PMID:29940860
Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. PMID:29917034
Identification of Central Regulators of Calcium Signaling and ECM-Receptor Interaction Genetically Associated With the Progression and Recurrence of Atrial Fibrillation. PMID:29868113
INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species. PMID:29746660
Functional and structural characterization of osteocytic MLO-Y4 cell proteins encoded by genes differentially expressed in response to mechanical signals in vitro. PMID:29712973
Upregulated VEGFA and DLL4 act as potential prognostic genes for clear cell renal cell carcinoma. PMID:29618931
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. PMID:29605183
SPV: a JavaScript Signaling Pathway Visualizer. PMID:29590303
Double agents: genes with both oncogenic and tumor-suppressor functions. PMID:29540752
A network-based meta-analysis for characterizing the genetic landscape of human aging. PMID:29270911
Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions. PMID:29257115
Exploring digenic inheritance in arrhythmogenic cardiomyopathy. PMID:29221435
Molecular Interaction Search Tool (MIST): an integrated resource for mining gene and protein interaction data. PMID:29155944
Investigation of candidate genes and mechanisms underlying postmenopausal osteoporosis using bioinformatics analysis. PMID:29138843
BCNTB bioinformatics: the next evolutionary step in the bioinformatics of breast cancer tissue banking. PMID:29136180
The Pancreatic Expression Database: 2018 update. PMID:29059374
Evaluating phenotype-driven approaches for genetic diagnoses from exomes in a clinical setting. PMID:29044180
DISNOR: a disease network open resource. PMID:29036667
Spatiotemporal profile of postsynaptic interactomes integrates components of complex brain disorders. PMID:28671696
Downregulated USP3 mRNA functions as a competitive endogenous RNA of SMAD4 by sponging miR-224 and promotes metastasis in colorectal cancer. PMID:28655924
Rewiring of the inferred protein interactome during blood development studied with the tool PPICompare. PMID:28376810
A Comprehensive View of the β-Arrestinome. PMID:28321204
Bioinformatics analysis of the proteins interacting with LASP-1 and their association with HBV-related hepatocellular carcinoma. PMID:28266596
Both Intrinsic Substrate Preference and Network Context Contribute to Substrate Selection of Classical Tyrosine Phosphatases. PMID:28159843
A scored human protein-protein interaction network to catalyze genomic interpretation. PMID:27892958
Physicochemical properties that control protein aggregation also determine whether a protein is retained or released from necrotic cells. PMID:27810968
Computational assessment of feature combinations for pathogenic variant prediction. PMID:27468419
HVint: A Strategy for Identifying Novel Protein-Protein Interactions in Herpes Simplex Virus Type 1. PMID:27384951
Controllability of protein-protein interaction phosphorylation-based networks: Participation of the hub 14-3-3 protein family. PMID:27195976
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. PMID:27131791
Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling. PMID:27114452
An inter-species protein-protein interaction network across vast evolutionary distance. PMID:27107014
APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone. PMID:27092780
FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in Drosophila eye development. PMID:26998229
PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data. PMID:26966684
Comparing Alzheimer's and Parkinson's diseases networks using graph communities structure. PMID:26935435
Quantitative Proteomics Analysis Reveals the Min System of Escherichia coli Modulates Reversible Protein Association with the Inner Membrane. PMID:26889046
Lamina Associated Polypeptide 1 (LAP1) Interactome and Its Functional Features. PMID:26784240
Compartmentalization and Functionality of Nuclear Disorder: Intrinsic Disorder and Protein-Protein Interactions in Intra-Nuclear Compartments. PMID:26712748
HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species. PMID:26708988
SIGNOR: a database of causal relationships between biological entities. PMID:26467481
Age-related obesity and type 2 diabetes dysregulate neuronal associated genes and proteins in humans. PMID:26337083
Meta-Analysis of Large-Scale Toxicogenomic Data Finds Neuronal Regeneration Related Protein and Cathepsin D to Be Novel Biomarkers of Drug-Induced Toxicity. PMID:26335687
Integrated inference and evaluation of host-fungi interaction networks. PMID:26300851
OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization. PMID:26272982
High-throughput prediction of RNA, DNA and protein binding regions mediated by intrinsic disorder. PMID:26109352
Integrated web visualizations for protein-protein interaction databases. PMID:26077899
The hierarchical organization of natural protein interaction networks confers self-organization properties on pseudocells. PMID:26050708
Gene Perturbation Atlas (GPA): a single-gene perturbation repository for characterizing functional mechanisms of coding and non-coding genes. PMID:26039571
CleavPredict: A Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events. PMID:25996941
CellWhere: graphical display of interaction networks organized on subcellular localizations. PMID:25883154
Systematic imaging reveals features and changing localization of mRNAs in Drosophila development. PMID:25838129
Shared resources, shared costs--leveraging biocuration resources. PMID:25776020
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. PMID:25652942
A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology. PMID:25648416
Virus-host interactomics: new insights and opportunities for antiviral drug discovery. PMID:25593595
MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities. PMID:25378329
VirusMentha: a new resource for virus-host protein interactions. PMID:25217587
Detecting protein complexes in protein interaction networks using a ranking algorithm with a refined merging procedure. PMID:24944073
Protein-protein interactions and genetic diseases: The interactome. PMID:24892209
Combining affinity proteomics and network context to identify new phosphatase substrates and adapters in growth pathways. PMID:24847354
NetVenn: an integrated network analysis web platform for gene lists. PMID:24771340
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. PMID:24234451

Tags:

Tags
More detailed information about this field from each metasource.

animals
metasource: re3data.org
version: re3data.org: mentha; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SP8V last accessed: 2022-11-04

human
metasource: re3data.org
version: re3data.org: mentha; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SP8V last accessed: 2022-11-04

microbes
metasource: re3data.org
version: re3data.org: mentha; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SP8V last accessed: 2022-11-04

plants
metasource: re3data.org
version: re3data.org: mentha; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SP8V last accessed: 2022-11-04

protein-protein interactoin ppi
metasource: re3data.org
version: re3data.org: mentha; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SP8V last accessed: 2022-11-04

transcripts
metasource: re3data.org
version: re3data.org: mentha; editing status 2019-01-17; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3SP8V last accessed: 2022-11-04

protein interactions
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.386477

rare diseases
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:31.386477

animals human microbes plants protein-protein interactoin ppi transcripts protein interaction rare diseases

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VirusMentha

Molecular INTeraction database

Human Protein-Protein Interaction rEference

Protein Interaction Network Analysis platform

Reproducible interactome

Biological General Repository for Interaction Datasets

Human protein-protein interaction network database search

Bacterial Protein Interaction Database

Database of Interacting Proteins

Agile Protein Interactomes Dataserver

AtPID

Manually Curated Database of Rice Proteins

IntAct molecular interaction database

Protein-Protein Interaction Ontology

Compartmentalized Protein-Protein Interaction

IMEx

Human Reference Protein Interactome Mapping Project

DroID - Drosophila Interactions Database

Interaction Reference Index Web Interface

STRING