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" SoyCSN: "
Wang, JuexinHossain, Md ShakhawatLyu, ZhenSchmutz, JeremyStacey, GaryXu, DongJoshi, Trupti
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AL
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| Record Number
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900824
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LA0b8935pp
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| Title & Author
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SoyCSN: [Article]. Soybean context-specific network analysis and prediction based on tissue-specific transcriptome data.\ Wang, JuexinHossain, Md ShakhawatLyu, ZhenSchmutz, JeremyStacey, GaryXu, DongJoshi, Trupti
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2019
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| Title of Periodical
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Lawrence Berkeley National Laboratory
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| Abstract
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The Soybean Gene Atlas project provides a comprehensive map for understanding gene expression patterns in major soybean tissues from flower, root, leaf, nodule, seed, and shoot and stem. The RNA-Seq data generated in the project serve as a valuable resource for discovering tissue-specific transcriptome behavior of soybean genes in different tissues. We developed a computational pipeline for Soybean context-specific network (SoyCSN) inference with a suite of prediction tools to analyze, annotate, retrieve, and visualize soybean context-specific networks at both transcriptome and interactome levels. BicMix and Cross-Conditions Cluster Detection algorithms were applied to detect modules based on co-expression relationships across all the tissues. Soybean context-specific interactomes were predicted by combining soybean tissue gene expression and protein-protein interaction data. Functional analyses of these predicted networks provide insights into soybean tissue specificities. For example, under symbiotic, nitrogen-fixing conditions, the constructed soybean leaf network highlights the connection between the photosynthesis function and rhizobium-legume symbiosis. SoyCSN data and all its results are publicly available via an interactive web service within the Soybean Knowledge Base (SoyKB) at http://soykb.org/SoyCSN. SoyCSN provides a useful web-based access for exploring context specificities systematically in gene regulatory mechanisms and gene relationships for soybean researchers and molecular breeders.
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