ArticlePloS one2013
LegumeGRN: a gene regulatory network prediction server for functional and comparative studies.
Article in PloS one, 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.
- Article
- Identification of the novel FOXP3-dependent TFrontiers in immunology · 2023Article
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- Network inference performance complexity: a consequence of topological, experimental and algorithmic determinants.Bioinformatics (Oxford, England) · 2019Article
- Exploration of the effects of aPeerJ · 2019Article
- Parallel Algorithms for Inferring Gene Regulatory Networks: A Review.Current genomics · 2018Review
- Cationic liposomes induce cytotoxicity in HepG2 via regulation of lipid metabolism based on whole-transcriptome sequencing analysis.BMC pharmacology & toxicology · 2018Article
- Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Applications of Bayesian network models in predicting types of hematological malignancies.Scientific reports · 2018Article
- The G-Box Transcriptional Regulatory Code in Arabidopsis.Plant physiology · 2017Article
- Nod factors potentiate auxin signaling for transcriptional regulation and lateral root formation in Medicago truncatula.Journal of experimental botany · 2017Article
- Root adaptations to soils with low fertility and aluminium toxicity.Annals of botany · 2016Article
- Comparative transcriptome profiling of longissimus muscle tissues from Qianhua Mutton Merino and Small Tail Han sheep.Scientific reports · 2016Article
- Quantitative Resistance toFrontiers in plant science · 2016Article
- Identification of Gene Modules Associated with Low Temperatures Response in Bambara Groundnut by Network-Based Analysis.PloS one · 2016Article
- A Snapshot of Functional Genetic Studies in Medicago truncatula.Frontiers in plant science · 2016Review
- Detecting causality from nonlinear dynamics with short-term time series.Scientific reports · 2014Article
- Global transcriptome-wide analysis of CIK cells identify distinct roles of IL-2 and IL-15 in acquisition of cytotoxic capacity against tumor.BMC medical genomics · 2014Article
Corrections and comments
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Authors and funding
11 authors.
Funding
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Abstract
Building accurate gene regulatory networks (GRNs) from high-throughput gene expression data is a long-standing challenge. However, with the emergence of new algorithms combined with the increase of transcriptomic data availability, it is now reachable. To help biologists to investigate gene regulatory relationships, we developed a web-based computational service to build, analyze and visualize GRNs that govern various biological processes. The web server is preloaded with all available Affymetrix GeneChip-based transcriptomic and annotation data from the three model legume species, i.e., Medicago truncatula, Lotus japonicus and Glycine max. Users can also upload their own transcriptomic and transcription factor datasets from any other species/organisms to analyze their in-house experiments. Users are able to select which experiments, genes and algorithms they will consider to perform their GRN analysis. To achieve this flexibility and improve prediction performance, we have implemented multiple mainstream GRN prediction algorithms including co-expression, Graphical Gaussian Models (GGMs), Context Likelihood of Relatedness (CLR), and parallelized versions of TIGRESS and GENIE3. Besides these existing algorithms, we also proposed a parallel Bayesian network learning algorithm, which can infer causal relationships (i.e., directionality of interaction) and scale up to several thousands of genes. Moreover, this web server also provides tools to allow integrative and comparative analysis between predicted GRNs obtained from different algorithms or experiments, as well as comparisons between legume species. The web site is available at http://legumegrn.noble.org.
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