ArticleNucleic acids research2018
FunCoup 4: new species, data, and visualization.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
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- IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis.Nucleic acids research · 2022Article
- A novel group of genes that cause endocrine resistance in breast cancer identified by dynamic gene expression analysis.Oncotarget · 2022Article
- Quercetin inhibits angiotensin II-induced vascular smooth muscle cell proliferation and activation of JAK2/STAT3 pathway: A target based networking pharmacology approach.Frontiers in pharmacology · 2022Article
- Therapeutic potential of the Proprotein Convertase Subtilisin/Kexin family in vascular disease.Frontiers in pharmacology · 2022Article
- Identifying large-scale interaction atlases using probabilistic graphs and external knowledge.Journal of clinical and translational science · 2022Article
- Ten Years of Collaborative Progress in the Quest for Orthologs.Molecular biology and evolution · 2021Article
- The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.Nucleic acids research · 2021Article
- Comprehensive network modeling from single cell RNA sequencing of human and mouse reveals well conserved transcription regulation of hematopoiesis.BMC genomics · 2020Article
- Uncovering cancer gene regulation by accurate regulatory network inference from uninformative data.NPJ systems biology and applications · 2020Article
- Evaluation of blood gene expression levels in facioscapulohumeral muscular dystrophy patients.Scientific reports · 2020Article
- Integrated regulatory models for inference of subtype-specific susceptibilities in glioblastoma.Molecular systems biology · 2020Article
- Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms.Scientific reports · 2020Article
- Pathway-specific model estimation for improved pathway annotation by network crosstalk.Scientific reports · 2020Article
- Genome-wide functional association networks: background, data & state-of-the-art resources.Briefings in bioinformatics · 2020Review
- ppiGReMLIN: a graph mining based detection of conserved structural arrangements in protein-protein interfaces.BMC bioinformatics · 2020Article
- Functional Innovation in the Evolution of the Calcium-Dependent System of the Eukaryotic Endoplasmic Reticulum.Frontiers in genetics · 2020Article
- Advances and Applications in the Quest for Orthologs.Molecular biology and evolution · 2019Article
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This release of the FunCoup database (http://funcoup.sbc.su.se) is the fourth generation of one of the most comprehensive databases for genome-wide functional association networks. These functional associations are inferred via integrating various data types using a naive Bayesian algorithm and orthology based information transfer across different species. This approach provides high coverage of the included genomes as well as high quality of inferred interactions. In this update of FunCoup we introduce four new eukaryotic species: Schizosaccharomyces pombe, Plasmodium falciparum, Bos taurus, Oryza sativa and open the database to the prokaryotic domain by including networks for Escherichia coli and Bacillus subtilis. The latter allows us to also introduce a new class of functional association between genes - co-occurrence in the same operon. We also supplemented the existing classes of functional association: metabolic, signaling, complex and physical protein interaction with up-to-date information. In this release we switched to InParanoid v8 as the source of orthology and base for calculation of phylogenetic profiles. While populating all other evidence types with new data we introduce a new evidence type based on quantitative mass spectrometry data. Finally, the new JavaScript based network viewer provides the user an intuitive and responsive platform to further evaluate the results.
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