ArticleBioinformatics (Oxford, England)2014
Functional association networks as priors for gene regulatory network inference.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Network reconstruction for trans acting genetic loci using multi-omics data and prior information.Genome medicine · 2022Article
- Accurate determination of causalities in gene regulatory networks by dissecting downstream target genes.Frontiers in genetics · 2022Article
- Article
- Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells.Genome research · 2019Article
- STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.Nucleic acids research · 2019Article
- Article
- Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks.Cell reports · 2018Article
- Windowed Granger causal inference strategy improves discovery of gene regulatory networks.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- FunCoup 4: new species, data, and visualization.Nucleic acids research · 2018Article
- Structure Optimization for Large Gene Networks Based on Greedy Strategy.Computational and mathematical methods in medicine · 2018Article
- Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample size.BMC systems biology · 2017Article
- A prior-based integrative framework for functional transcriptional regulatory network inference.Nucleic acids research · 2017Article
- The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.Nucleic acids research · 2017Article
- Langerhans Cells-Programmed by the Epidermis.Frontiers in immunology · 2017Review
- Knowledge-guided fuzzy logic modeling to infer cellular signaling networks from proteomic data.Scientific reports · 2016Article
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Authors and funding
5 authors.
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Abstract
motivationGene regulatory network (GRN) inference reveals the influences genes have on one another in cellular regulatory systems. If the experimental data are inadequate for reliable inference of the network, informative priors have been shown to improve the accuracy of inferences.
resultsThis study explores the potential of undirected, confidence-weighted networks, such as those in functional association databases, as a prior source for GRN inference. Such networks often erroneously indicate symmetric interaction between genes and may contain mostly correlation-based interaction information. Despite these drawbacks, our testing on synthetic datasets indicates that even noisy priors reflect some causal information that can improve GRN inference accuracy. Our analysis on yeast data indicates that using the functional association databases FunCoup and STRING as priors can give a small improvement in GRN inference accuracy with biological data.
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