ArticleNucleic acids research2014
FunCoup 3.0: database of genome-wide functional coupling networks.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed.
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- Dual Costimulatory and Coinhibitory Targeting with a Hybrid Fusion Protein as an Immunomodulatory Therapy in Lupus Nephritis Mice Models.International journal of molecular sciences · 2022Article
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- Gene coexpression networks reveal molecular interactions underlying cichlid jaw modularity.BMC ecology and evolution · 2021Article
- Versatile knowledge guided network inference method for prioritizing key regulatory factors in multi-omics data.Scientific reports · 2021Article
- 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
- Genome-wide functional association networks: background, data & state-of-the-art resources.Briefings in bioinformatics · 2020Review
- Deriving disease modules from the compressed transcriptional space embedded in a deep autoencoder.Nature communications · 2020Article
- Prioritizing candidate diseases-related metabolites based on literature and functional similarity.BMC bioinformatics · 2019Article
- A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases.Journal of integrative bioinformatics · 2019Review
- A network-based pathway-extending approach using DNA methylation and gene expression data to identify altered pathways.Scientific reports · 2019Article
- Disease gene prediction for molecularly uncharacterized diseases.PLoS computational biology · 2019Article
- Benchmarker: An Unbiased, Association-Data-Driven Strategy to Evaluate Gene Prioritization Algorithms.American journal of human genetics · 2019Article
- Using deep maxout neural networks to improve the accuracy of function prediction from protein interaction networks.PloS one · 2019Article
- When pitch adds to volume: coregulation of transcript diversity predicts gene function.BMC genomics · 2018Article
- Biased Inference of Selection Due to GC-Biased Gene Conversion and the Rate of Protein Evolution in Flycatchers When Accounting for It.Molecular biology and evolution · 2018Article
- FunGeneNet: a web tool to estimate enrichment of functional interactions in experimental gene sets.BMC genomics · 2018Article
- FunCoup 4: new species, data, and visualization.Nucleic acids research · 2018Article
5 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
We present an update of the FunCoup database (http://FunCoup.sbc.su.se) of functional couplings, or functional associations, between genes and gene products. Identifying these functional couplings is an important step in the understanding of higher level mechanisms performed by complex cellular processes. FunCoup distinguishes between four classes of couplings: participation in the same signaling cascade, participation in the same metabolic process, co-membership in a protein complex and physical interaction. For each of these four classes, several types of experimental and statistical evidence are combined by Bayesian integration to predict genome-wide functional coupling networks. The FunCoup framework has been completely re-implemented to allow for more frequent future updates. It contains many improvements, such as a regularization procedure to automatically downweight redundant evidences and a novel method to incorporate phylogenetic profile similarity. Several datasets have been updated and new data have been added in FunCoup 3.0. Furthermore, we have developed a new Web site, which provides powerful tools to explore the predicted networks and to retrieve detailed information about the data underlying each prediction.
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