The database allows users to predict pathways that are relevant to a query gene, which would help to infer gene functions. We developed a new database, named Co-expressed Pathways DataBase for Tomato, which is available at. In addition, we evaluated our approaches using receiver operating characteristic curves, which concluded that the p-score could improve the performance of the ORA. Therefore, we introduced a new measure for evaluating the relationship between the gene and pathway, termed the percentile ( p)-score, which enables users to predict functionally relevant pathways without being affected by the internal correlation in pathways. We found that internal correlation in pathways affected the significance levels of the enrichment analyses.
To achieve this, we used the ORA approach with several thresholds to select co-expressed genes, and performed gene set enrichment analysis (GSEA) applied to a ranked list of genes ordered by the co-expression degree. 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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