In this study, we developed a new co-expression database that enables users to predict the function of tomato genes from the results of functional enrichment analyses of co-expressed genes while considering the genes that are not strongly co-expressed. A limitation of this approach may be that users can predict gene functions only based on the strongly co-expressed genes.

Several of these databases also provide functional information on a set of strongly co-expressed genes (i.e., provide biological processes and pathways that are enriched in these strongly co-expressed genes), which is generally analyzed via over-representation analysis (ORA). These databases usually provide users with a co-expression network and a list of strongly co-expressed genes for a query gene. Gene co-expression, the similarity of gene expression profiles under various experimental conditions, has been used as an indicator of functional relationships between genes, and many co-expression databases have been developed for predicting gene functions.

GUID: C9A0A3EE-2162-4DF0-A292-943465F7E285 Data Availability StatementĬo-expressed Pathways DataBase for Tomato is available at.

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