ArticleNucleic acids research2013
Reverse engineering and analysis of large genome-scale gene networks.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- MCPNet: a parallel maximum capacity-based genome-scale gene network construction framework.Bioinformatics (Oxford, England) · 2023Article
- Identification of the novel FOXP3-dependent TFrontiers in immunology · 2023Article
- Machine learning-based microarray analyses indicate low-expression genes might collectively influence PAH disease.PLoS computational biology · 2019Article
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- Mitogen-activated protein kinases, Fus3 and Kss1, regulate chronological lifespan in yeast.Aging · 2017Article
- Improving GRN re-construction by mining hidden regulatory signals.IET systems biology · 2017Article
- RD26 mediates crosstalk between drought and brassinosteroid signalling pathways.Nature communications · 2017Article
- Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories.Microarrays (Basel, Switzerland) · 2016Article
- Transcriptional regulatory networks in Arabidopsis thaliana during single and combined stresses.Nucleic acids research · 2016Article
- The Wright stuff: reimagining path analysis reveals novel components of the sex determination hierarchy in Drosophila melanogaster.BMC systems biology · 2015Article
- Co-existence of intact stemness and priming of neural differentiation programs in mES cells lacking Trim71.Scientific reports · 2015Article
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- Proteomics for systems toxicology.Computational and structural biotechnology journal · 2014Review
- Construction and verification of the transcriptional regulatory response network of Streptococcus mutans upon treatment with the biofilm inhibitor carolacton.BMC genomics · 2014Article
- Transcriptome-based network analysis reveals a spectrum model of human macrophage activation.Immunity · 2014Article
- Structural bioinformatics of the interactome.Annual review of biophysics · 2014Review
- DeGNServer: deciphering genome-scale gene networks through high performance reverse engineering analysis.BioMed research international · 2013Article
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Authors and funding
4 authors.
Funding
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Abstract
Reverse engineering the whole-genome networks of complex multicellular organisms continues to remain a challenge. While simpler models easily scale to large number of genes and gene expression datasets, more accurate models are compute intensive limiting their scale of applicability. To enable fast and accurate reconstruction of large networks, we developed Tool for Inferring Network of Genes (TINGe), a parallel mutual information (MI)-based program. The novel features of our approach include: (i) B-spline-based formulation for linear-time computation of MI, (ii) a novel algorithm for direct permutation testing and (iii) development of parallel algorithms to reduce run-time and facilitate construction of large networks. We assess the quality of our method by comparison with ARACNe (Algorithm for the Reconstruction of Accurate Cellular Networks) and GeneNet and demonstrate its unique capability by reverse engineering the whole-genome network of Arabidopsis thaliana from 3137 Affymetrix ATH1 GeneChips in just 9 min on a 1024-core cluster. We further report on the development of a new software Gene Network Analyzer (GeNA) for extracting context-specific subnetworks from a given set of seed genes. Using TINGe and GeNA, we performed analysis of 241 Arabidopsis AraCyc 8.0 pathways, and the results are made available through the web.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.