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• W2796702960 abstract "Abstract Motivation To gain insights into complex biological processes, genome-scale data (e.g., RNA-Seq) are often overlaid on biochemical networks. However, many networks do not have a one-to-one relationship between genes and network edges, due to the existence of isozymes and protein complexes. Therefore, decisions must be made on how to overlay data onto networks. For example, for metabolic networks, these decisions include (1) how to integrate gene expression levels using gene-protein-reaction rules, (2) the approach used for selection of thresholds on expression data to consider the associated gene as “active”, and (3) the order in which these steps are imposed. However, the influence of these decisions has not been systematically tested. Results We compared 20 decision combinations using a transcriptomic dataset across 32 tissues and showed that definition of which reaction may be considered as active is mainly influenced by thresholding approach used. To determine the most appropriate decisions, we evaluated how these decisions impact the acquisition of tissue-specific active reaction lists that recapitulate organ-system tissue groups. These results will provide guidelines to improve data analyses with biochemical networks and facilitate the construction of context-specific metabolic models. Contact nlewisres@ucsd.edu" @default.
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• W2796702960 date "2018-04-16" @default.
• W2796702960 modified "2023-10-15" @default.
• W2796702960 title "Assessing key decisions for transcriptomic data integration in biochemical networks" @default.
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• W2796702960 doi "https://doi.org/10.1101/301945" @default.
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