Agile Protein Interactomes Dataserver
Names
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Agile Protein Interactomes Dataserver
metasource: Fairsharing.org
version: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
APID Interactomes
metasource: Fairsharing.org
version: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
APID
metasource: re3data.org
version: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
Agile Protein Interactomes DataServer
metasource: re3data.org
version: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
Names
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Agile Protein Interactomes Dataserver
metasource: Fairsharing.orgversion: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
APID Interactomes
metasource: Fairsharing.orgversion: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
APID
metasource: re3data.orgversion: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
Agile Protein Interactomes DataServer
metasource: re3data.orgversion: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
Other names: APID Interactomes, APID, Agile Protein Interactomes DataServer
Names
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Agile Protein Interactomes Dataserver
metasource: Fairsharing.orgversion: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
APID Interactomes
metasource: Fairsharing.orgversion: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
APID
metasource: re3data.orgversion: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
Agile Protein Interactomes DataServer
metasource: re3data.orgversion: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.
Description
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APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.
metasource: Fairsharing.orgversion: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
APID Interactomes is a database that provides a comprehensive collection of protein interactomes for more than 400 organisms based in the integration of known experimentally validated protein-protein physical interactions (PPIs). Construction of the interactomes is done with a methodological approach to report quality levels and coverage over the proteomes for each organism included. In this way, APID provides interactomes from specific organisms that in 25 cases have more than 500 proteins. As a whole APID includes a comprehensive compendium of 90,379 distinct proteins and 678,441 singular interactions. The analytical and integrative effort done in APID unifies PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. In this way, 8,388 structures have been analyzed to find specific protein-protein interactions reported with details of their molecular interfaces. APID also includes a new data visualization web-tool that allows the construction of sub-interactomes using query lists of proteins of interest and the visual exploration of the corresponding networks, including an interactive selection of the properties of the interactions (i.e. the reliability of the "edges" in the network) and an interactive mapping of the functional environment of the proteins (i.e. the functional annotations of the "nodes" in the network).
metasource: re3data.orgversion: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
Webpage:
http://apid.dep.usal.es/Webpage
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http://apid.dep.usal.es/
metasource: Fairsharing.orgversion: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://cicblade.dep.usal.es:8080/APID/init.action
metasource: re3data.orgversion: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
Licence:
Name: CCLicence name
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CC
metasource: re3data.orgversion: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
Licence URL
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https://creativecommons.org/licenses/by-nc/4.0/
metasource: re3data.orgversion: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
Publications:
Publications
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APID: Agile Protein Interaction DataAnalyzer
PMID: 16845013
metasource: Fairsharing.org
version: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks
PMID: 27131791
metasource: Fairsharing.org
version: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
APID database: redefining protein-protein interaction experimental evidences and binary interactomes
PMID: 30715274
metasource: Fairsharing.org
version: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
APID2NET: unified interactome graphic analyzer
PMID: 17644818
metasource: Fairsharing.org
version: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications
More detailed information about this field from each metasource.
APID: Agile Protein Interaction DataAnalyzer
PMID: 16845013
metasource: Fairsharing.org
version: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks
PMID: 27131791
metasource: Fairsharing.org
version: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
APID database: redefining protein-protein interaction experimental evidences and binary interactomes
PMID: 30715274
metasource: Fairsharing.org
version: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
APID2NET: unified interactome graphic analyzer
PMID: 17644818
metasource: Fairsharing.org
version: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
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APID: Agile Protein Interaction DataAnalyzer
PubMed citations: 99.
99 articles citing: APID: Agile Protein Interaction DataAnalyzer
The Landscape of Virus-Host Protein-Protein Interaction Databases. PMID:35910656
Follistatin-like 1 and its paralogs in heart development and cardiovascular disease. PMID:35867287
An Integrated In Silico, In Vitro and Tumor Tissues Study Identified Selenoprotein S (SELENOS) and Valosin-Containing Protein (VCP/p97) as Novel Potential Associated Prognostic Biomarkers in Triple Negative Breast Cancer. PMID:35158912
ACE2 Netlas: In silico Functional Characterization and Drug-Gene Interactions of ACE2 Gene Network to Understand Its Potential Involvement in COVID-19 Susceptibility. PMID:34512723
Interactome Analysis of KIN (Kin17) Shows New Functions of This Protein. PMID:34449532
Therapeutic and prophylactic effects of macrophage-derived small extracellular vesicles in the attenuation of inflammatory pain. PMID:33607232
Elucidating the network features and evolutionary attributes of intra- and interspecific protein-protein interactions between human and pathogenic bacteria. PMID:33420198
Deciphering cell-cell interactions and communication from gene expression. PMID:33168968
ACE2 Netlas: In-silico functional characterization and drug-gene interactions of ACE2 gene network to understand its potential involvement in COVID-19 susceptibility. PMID:33140059
Exploring dynamic protein-protein interactions in cassava through the integrative interactome network. PMID:32300157
A Comprehensive Survey of Tools and Software for Active Subnetwork Identification. PMID:30891064
APID database: redefining protein-protein interaction experimental evidences and binary interactomes. PMID:30715274
Network spectra for drug-target identification in complex diseases: new guns against old foes. PMID:30596144
Prediction of cassava protein interactome based on interolog method. PMID:29222529
Endothelium-Independent Primitive Myxoid Vascularization Creates Invertebrate-Like Channels to Maintain Blood Supply in Optic Gliomas. PMID:28606795
Bioinformatics analysis of the proteins interacting with LASP-1 and their association with HBV-related hepatocellular carcinoma. PMID:28266596
Path2enet: generation of human pathway-derived networks in an expression specific context. PMID:27801297
RWCFusion: identifying phenotype-specific cancer driver gene fusions based on fusion pair random walk scoring method. PMID:27506935
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. PMID:27131791
Biomolecular Relationships Discovered from Biological Labyrinth and Lost in Ocean of Literature: Community Efforts Can Rescue Until Automated Artificial Intelligence Takes Over. PMID:27066067
Lamina Associated Polypeptide 1 (LAP1) Interactome and Its Functional Features. PMID:26784240
Multiple spatially related pharmacophores define small molecule inhibitors of OLIG2 in glioblastoma. PMID:26517684
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. PMID:26309733
Integrated inference and evaluation of host-fungi interaction networks. PMID:26300851
PrOnto database : GO term functional dissimilarity inferred from biological data. PMID:26089836
Integrated web visualizations for protein-protein interaction databases. PMID:26077899
Extreme multifunctional proteins identified from a human protein interaction network. PMID:26054620
MyProteinNet: build up-to-date protein interaction networks for organisms, tissues and user-defined contexts. PMID:25990735
Improving the Understanding of Pathogenesis of Human Papillomavirus 16 via Mapping Protein-Protein Interaction Network. PMID:25961044
A review on computational systems biology of pathogen-host interactions. PMID:25914674
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. PMID:25652942
Amyloid precursor protein interaction network in human testis: sentinel proteins for male reproduction. PMID:25591988
Overview of computational vaccinology: vaccine development through information technology. PMID:25534541
Multi-omic landscape of rheumatoid arthritis: re-evaluation of drug adverse effects. PMID:25414848
Computational characterization of moonlighting proteins. PMID:25399606
Transcriptomic portrait of human Mesenchymal Stromal/Stem Cells isolated from bone marrow and placenta. PMID:25326687
Protein-protein interaction detection: methods and analysis. PMID:24693427
Plant systems biology: insights, advances and challenges. PMID:24671625
In silico prediction of protein-protein interactions in human macrophages. PMID:24636261
Inferring drug-disease associations from integration of chemical, genomic and phenotype data using network propagation. PMID:24565337
Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources. PMID:24396273
UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks. PMID:24214987
Reconstruction of the experimentally supported human protein interactome: what can we learn? PMID:24088582
Centenarians as super-controls to assess the biological relevance of genetic risk factors for common age-related diseases: a proof of principle on type 2 diabetes. PMID:23804578
An efficient weighted graph strategy to identify differentiation associated genes in embryonic stem cells. PMID:23638139
A dynamic model of the proteins that form the initial iron-sulfur cluster biogenesis machinery in yeast mitochondria. PMID:23463383
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. PMID:23384594
Discovery and analysis of consistent active sub-networks in cancers. PMID:23368093
Identification of MFS proteins in sorghum using semantic similarity. PMID:23299296
Evaluating caveolin interactions: do proteins interact with the caveolin scaffolding domain through a widespread aromatic residue-rich motif? PMID:23028656
Multiple biomarker tissue arrays: A computational approach to identifying protein-protein interactions in the EGFR/ERK signalling pathway. PMID:22937740
A network synthesis model for generating protein interaction network families. PMID:22912671
Crowd sourcing a new paradigm for interactome driven drug target identification in Mycobacterium tuberculosis. PMID:22808064
Integrating literature-constrained and data-driven inference of signalling networks. PMID:22734019
Biomarker identification for prostate cancer and lymph node metastasis from microarray data and protein interaction network using gene prioritization method. PMID:22654636
DroPNet: a web portal for integrated analysis of Drosophila protein-protein interaction networks. PMID:22641854
Pathway detection from protein interaction networks and gene expression data using color-coding methods and A∗ search algorithms. PMID:22577352
Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets. PMID:22482945
Integrated inference and analysis of regulatory networks from multi-level measurements. PMID:22482944
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. PMID:22453911
Charting the NF-κB pathway interactome map. PMID:22403694
Exploring and challenging the network of angiogenesis. PMID:22355580
ANAP: an integrated knowledge base for Arabidopsis protein interaction network analysis. PMID:22345505
A network flow approach to predict drug targets from microarray data, disease genes and interactome network - case study on prostate cancer. PMID:22239822
IMID: integrated molecular interaction database. PMID:22238258
Benchmarking a luciferase complementation assay for detecting protein complexes. PMID:22127214
Comparative interactomics with Funcoup 2.0. PMID:22110034
Multifunctional proteins revealed by overlapping clustering in protein interaction network. PMID:22080466
An in silico approach combined with in vivo experiments enables the identification of a new protein whose overexpression can compensate for specific respiratory defects in Saccharomyces cerevisiae. PMID:22027258
Functional analysis beyond enrichment: non-redundant reciprocal linkage of genes and biological terms. PMID:21949701
Functional integrative levels in the human interactome recapitulate organ organization. PMID:21799769
Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping. PMID:21767381
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
Interaction databases on the same page. PMID:21552234
The Biomolecular Interaction Network Database in PSI-MI 2.5. PMID:21233089
Literature curation of protein interactions: measuring agreement across major public databases. PMID:21183497
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. PMID:21045058
HitPredict: a database of quality assessed protein-protein interactions in nine species. PMID:20947562
iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. PMID:20940177
A computational tool for identifying minimotifs in protein-protein interactions and improving the accuracy of minimotif predictions. PMID:20938975
Protein-protein interactions essentials: key concepts to building and analyzing interactome networks. PMID:20589078
Struct2Net: a web service to predict protein-protein interactions using a structure-based approach. PMID:20513650
Improved microarray-based decision support with graph encoded interactome data. PMID:20419106
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. PMID:20369061
Interactome mapping of the phosphatidylinositol 3-kinase-mammalian target of rapamycin pathway identifies deformed epidermal autoregulatory factor-1 as a new glycogen synthase kinase-3 interactor. PMID:20368287
Biana: a software framework for compiling biological interactions and analyzing networks. PMID:20105306
Graphle: Interactive exploration of large, dense graphs. PMID:20003429
Expression-based network biology identifies alteration in key regulatory pathways of type 2 diabetes and associated risk/complications. PMID:19997558
Protopia: a protein-protein interaction tool. PMID:19828077
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
DASMI: exchanging, annotating and assessing molecular interaction data. PMID:19420069
Protein-protein interaction databases: keeping up with growing interactomes. PMID:19403463
A top-down approach to infer and compare domain-domain interactions across eight model organisms. PMID:19333396
Integrated network analysis platform for protein-protein interactions. PMID:19079255
ConsensusPathDB--a database for integrating human functional interaction networks. PMID:18940869
T2D-Db: an integrated platform to study the molecular basis of Type 2 diabetes. PMID:18605991
Molecular basis for evolving modularity in the yeast protein interaction network. PMID:17997598
The 90S preribosome is a multimodular structure that is assembled through a hierarchical mechanism. PMID:17515605 -
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks
PubMed citations: 41.
41 articles citing: APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks
Analysis of host-pathogen gene association networks reveals patient-specific response to streptococcal and polymicrobial necrotising soft tissue infections. PMID:35505341
A multitask transfer learning framework for the prediction of virus-human protein-protein interactions. PMID:34837942
Global effects of RAB3GAP1 dysexpression on the proteome of mouse cortical neurons. PMID:34363538
Revealing protein-protein interactions at the transcriptome scale by sequencing. PMID:34348091
Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization. PMID:33831302
Novel gene signatures for stage classification of the squamous cell carcinoma of the lung. PMID:33649335
Multivariate Entropy Characterizes the Gene Expression and Protein-Protein Networks in Four Types of Cancer. PMID:33265245
Multimerization of Zika Virus-NS5 Causes Ciliopathy and Forces Premature Neurogenesis. PMID:33147489
Influenza A virus co-opts ERI1 exonuclease bound to histone mRNA to promote viral transcription. PMID:32960265
Post-translational Modification Crosstalk and Hotspots in Sirtuin Interactors Implicated in Cardiovascular Diseases. PMID:32425973
Exomes of Ductal Luminal Breast Cancer Patients from Southwest Colombia: Gene Mutational Profile and Related Expression Alterations. PMID:32365829
In silico Prediction of Protein-Protein Interaction Network Induced by Manganese II in Meyerozyma guilliermondii. PMID:32140149
History of Inflammatory Bowel Diseases. PMID:31739460
Co-expression of synaptic genes in the sponge Amphimedon queenslandica uncovers ancient neural submodules. PMID:31673079
Tissue-specific mouse mRNA isoform networks. PMID:31562339
Machine-learning techniques for the prediction of protein-protein interactions. PMID:31502581
Dependency Between Protein-Protein Interactions and Protein Variability and Evolutionary Rates in Vertebrates: Observed Relationships and Stochastic Modeling. PMID:31302723
Inferring Interaction Networks From Multi-Omics Data. PMID:31249591
In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR. PMID:31244651
Network Biology Identifies Novel Regulators of CFTR Trafficking and Membrane Stability. PMID:31231217
An in-silico approach for discovery of microRNA-TF regulation of DISC1 interactome mediating neuronal migration. PMID:31098296
Folding Status Is Determinant over Traffic-Competence in Defining CFTR Interactors in the Endoplasmic Reticulum. PMID:31014000
Roles of computational modelling in understanding p53 structure, biology, and its therapeutic targeting. PMID:30726928
APID database: redefining protein-protein interaction experimental evidences and binary interactomes. PMID:30715274
Structural disorder in the proteome and interactome of Alkhurma virus (ALKV). PMID:30443749
IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species. PMID:30407591
Disease networks identify specific conditions and pleiotropy influencing multimorbidity in the general population. PMID:30374096
Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. PMID:30082644
Searching the overlap between network modules with specific betweeness (S2B) and its application to cross-disease analysis. PMID:30068933
Proteomic interaction profiling reveals KIFC1 as a factor involved in early targeting of F508del-CFTR to degradation. PMID:30066085
Identification of Central Regulators of Calcium Signaling and ECM-Receptor Interaction Genetically Associated With the Progression and Recurrence of Atrial Fibrillation. PMID:29868113
JAMI: a Java library for molecular interactions and data interoperability. PMID:29642846
The basic tilted helix bundle domain of the prolyl isomerase FKBP25 is a novel double-stranded RNA binding module. PMID:29036638
A Comprehensive Survey of the Roles of Highly Disordered Proteins in Type 2 Diabetes. PMID:28934129
Integrative Analysis of Brain Region-specific Shank3 Interactomes for Understanding the Heterogeneity of Neuronal Pathophysiology Related to SHANK3 Mutations. PMID:28469556
Understanding the roles of intrinsic disorder in subunits of hemoglobin and the disease process of sickle cell anemia. PMID:28232898
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. PMID:27924014
Prediction of Protein-Protein Interactions by Evidence Combining Methods. PMID:27879651
Intrinsic disorder in proteins involved in amyotrophic lateral sclerosis. PMID:27838743
Path2enet: generation of human pathway-derived networks in an expression specific context. PMID:27801297
Unfoldomics of prostate cancer: on the abundance and roles of intrinsically disordered proteins in prostate cancer. PMID:27453073 -
APID database: redefining protein-protein interaction experimental evidences and binary interactomes
PubMed citations: 36.
36 articles citing: APID database: redefining protein-protein interaction experimental evidences and binary interactomes
Biological interacting units identified in human protein networks reveal tissue-functional diversification and its impact on disease. PMID:35891788
Construction and contextualization approaches for protein-protein interaction networks. PMID:35832626
Network approaches for modeling the effect of drugs and diseases. PMID:35704883
The Intricacy of the Viral-Human Protein Interaction Networks: Resources, Data, and Analyses. PMID:35531299
Membranome 3.0: Database of single-pass membrane proteins with AlphaFold models. PMID:35481632
Predicting Protein-Protein Interactions via Random Ferns with Evolutionary Matrix Representation. PMID:35242211
How Far Are We from the Completion of the Human Protein Interactome Reconstruction? PMID:35053288
IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis. PMID:34755877
Regulation of ER Composition and Extent, and Putative Action in Protein Networks by ER/NE Protein TMEM147. PMID:34638576
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
The landscape of alternative polyadenylation in single cells of the developing mouse embryo. PMID:34429411
Revealing protein-protein interactions at the transcriptome scale by sequencing. PMID:34348091
Topological network based drug repurposing for coronavirus 2019. PMID:34324563
CFTR Lifecycle Map-A Systems Medicine Model of CFTR Maturation to Predict Possible Active Compound Combinations. PMID:34299207
Pathogen Moonlighting Proteins: From Ancestral Key Metabolic Enzymes to Virulence Factors. PMID:34203698
mPPI: a database extension to visualize structural interactome in a one-to-many manner. PMID:34156447
Retention time prediction using neural networks increases identifications in crosslinking mass spectrometry. PMID:34050149
A SARS-CoV-2 (COVID-19) biological network to find targets for drug repurposing. PMID:33931664
Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization. PMID:33831302
Integrating 3D structural information into systems biology. PMID:33744294
A systems-based method to repurpose marketed therapeutics for antiviral use: a SARS-CoV-2 case study. PMID:33593923
TWIST1 and chromatin regulatory proteins interact to guide neural crest cell differentiation. PMID:33554859
Data sets on human histone interaction networks. PMID:33299912
Predicted rat interactome database and gene set linkage analysis. PMID:33216897
IHP-PING-generating integrated human protein-protein interaction networks on-the-fly. PMID:33129201
Determinants of correlated expression of transcription factors and their target genes. PMID:33104784
Human Histone Interaction Networks: An Old Concept, New Trends. PMID:33098859
Evolution of Sequence-based Bioinformatics Tools for Protein-protein Interaction Prediction. PMID:33093807
Pyntacle: a parallel computing-enabled framework for large-scale network biology analysis. PMID:33084878
Systematic Analysis of Aberrant Biochemical Networks and Potential Drug Vulnerabilities Induced by Tumor Suppressor Loss in Malignant Pleural Mesothelioma. PMID:32824422
Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19. PMID:32550253
ppiGReMLIN: a graph mining based detection of conserved structural arrangements in protein-protein interfaces. PMID:32293241
Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets. PMID:31798629 -
APID2NET: unified interactome graphic analyzer
PubMed citations: 33.
33 articles citing: APID2NET: unified interactome graphic analyzer
Exploring novel key regulators in breast cancer network. PMID:29927945
Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium. PMID:28567447
ProteINSIDE to Easily Investigate Proteomics Data from Ruminants: Application to Mine Proteome of Adipose and Muscle Tissues in Bovine Foetuses. PMID:26000831
Transcriptome profiling identifies p53 as a key player during calreticulin deficiency: Implications in lipid accumulation. PMID:25946468
A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology. PMID:25648416
Multi-omic landscape of rheumatoid arthritis: re-evaluation of drug adverse effects. PMID:25414848
Prediction of interactions between viral and host proteins using supervised machine learning methods. PMID:25375323
Transcriptomic portrait of human Mesenchymal Stromal/Stem Cells isolated from bone marrow and placenta. PMID:25326687
Neurolysin knockout mice generation and initial phenotype characterization. PMID:24719317
GeneSense: a new approach for human gene annotation integrated with protein-protein interaction networks. PMID:24667292
Genomic convergence and network analysis approach to identify candidate genes in Alzheimer's disease. PMID:24628925
PARK2 and proinflammatory/anti-inflammatory cytokine gene interactions contribute to the susceptibility to leprosy: a case-control study of North Indian population. PMID:24578538
Navigating traditional chinese medicine network pharmacology and computational tools. PMID:23983798
iBIG: an integrative network tool for supporting human disease mechanism studies. PMID:23809576
Centenarians as super-controls to assess the biological relevance of genetic risk factors for common age-related diseases: a proof of principle on type 2 diabetes. PMID:23804578
A travel guide to Cytoscape plugins. PMID:23132118
Systems biology for molecular life sciences and its impact in biomedicine. PMID:22903296
Charting the NF-κB pathway interactome map. PMID:22403694
TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks. PMID:22292669
An in silico approach combined with in vivo experiments enables the identification of a new protein whose overexpression can compensate for specific respiratory defects in Saccharomyces cerevisiae. PMID:22027258
Functional analysis beyond enrichment: non-redundant reciprocal linkage of genes and biological terms. PMID:21949701
Proteomic analysis of virus-host interactions in an infectious context using recombinant viruses. PMID:21911578
GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data. PMID:21777475
A comprehensive map of the mTOR signaling network. PMID:21179025
In silico analyses of proteomic data suggest a role for heat shock proteins in umbilical cord blood hematopoietic stem cells. PMID:20697978
Expression profile and specific network features of the apoptotic machinery explain relapse of acute myeloid leukemia after chemotherapy. PMID:20642818
Protein-protein interactions essentials: key concepts to building and analyzing interactome networks. PMID:20589078
BisoGenet: a new tool for gene network building, visualization and analysis. PMID:20163717
Biana: a software framework for compiling biological interactions and analyzing networks. PMID:20105306
Expression-based network biology identifies alteration in key regulatory pathways of type 2 diabetes and associated risk/complications. PMID:19997558
PIAS proteins: pleiotropic interactors associated with SUMO. PMID:19526197
DASMI: exchanging, annotating and assessing molecular interaction data. PMID:19420069
Dissecting the human plasma proteome and inflammatory response biomarkers. PMID:19105179
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interactome
metasource: Fairsharing.org
version: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
molecular interaction
metasource: Fairsharing.org
version: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein interaction
metasource: Fairsharing.org
version: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
cell biology
metasource: re3data.org
version: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
molecular biology
metasource: re3data.org
version: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
proteins interactions
metasource: re3data.org
version: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
proteome
metasource: re3data.org
version: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
Tags
More detailed information about this field from each metasource.
interactome
metasource: Fairsharing.orgversion: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
molecular interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: APID Interactomes; Agile Protein Interactomes Dataserver; DOI: https://doi.org/10.25504/FAIRsharing.8ye60e; Last edited: April 26, 2021, 8:26 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
cell biology
metasource: re3data.orgversion: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
molecular biology
metasource: re3data.orgversion: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
proteins interactions
metasource: re3data.orgversion: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
proteome
metasource: re3data.orgversion: re3data.org: APID; editing status 2022-06-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3407P last accessed: 2022-11-04
interactome molecular interaction protein protein interaction cell biology molecular biology proteins interactions proteome
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