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SoyTSN: A web-based prediction tool for soybean tissue specific network within SoyKB | IEEE Conference Publication | IEEE Xplore

SoyTSN: A web-based prediction tool for soybean tissue specific network within SoyKB


Abstract:

Soybean tissue-specific network helps identify and visualize the gene-gene relationships in various tissues [1]. We have built SoyTSN, a web-based tool for tissue-specifi...Show More

Abstract:

Soybean tissue-specific network helps identify and visualize the gene-gene relationships in various tissues [1]. We have built SoyTSN, a web-based tool for tissue-specific network prediction in soybean using 14 tissues RNA-Seq datasets including flower, root, nodule, leaf, stem, seed, etc. SoyTSN first combines multiple tissue specific RNA-Seq studies, and later Cross-Conditions Cluster Detection (C3D) algorithm [2] was applied to detect modules based on co-expression relationships across all the tissues. Following this soybean tissue-specific interactomes were inferred by combining tissue-specific expression and protein-protein interaction from the STRING database [3]. All these relationships between various soybean genes were collected and stored in Soybean Knowledge Base (SoyKB)[4] and can be queried using SoyTSN. For every query gene, SoyTSN computes and visualizes any of the 14 tissue specific networks both at the expression and interactome level. Users can compare the gene-gene relationship differences at different confidence levels across all the soybean tissues.
Date of Conference: 13-16 November 2017
Date Added to IEEE Xplore: 18 December 2017
ISBN Information:
Conference Location: Kansas City, MO, USA