584 / 2019-04-18 12:51:05

FoldGO: a web server to identify functional gene groups responding to a factor within specific ranges of fold changes

auxin, transcriptome, functional annotation

全体主题 > Systems Biology

Enrichment of functionally related genes in the transcriptome in response to a factor found by comparing frequencies of these genes in the genome and differentially expressed genes (DEGs) allows concluding that the function is pertinent to the factor effects. We have developed FoldGO web server (https://webfsgor.sysbio.cytogen.ru), where in addition to this standard analysis we elaborate the approach estimating overrepresentation of functionally related genes in groups of DEGs with similar fold changes compared to the whole DEG set. Using the dataset on auxin influence on Arabidopsis transcriptome, we showed that a vast majority of GO terms were found enriched by both approaches. So for most of the auxin functions, we evaluated the degree of expression changes in response to auxin for DEGs providing for these functions. It allowed selecting the function most precisely regulated by auxin. For example, among biological processes auxin most strongly upregulates its own response and protein targeting to mitochondria, moderately enhances G2/M transition and weakly strengthens translation, gluconeogenesis and response to cadmium. Thus, FoldGO provides for more comprehensive annotation of transcriptome data giving the possibility to identify functionally related DEGs, which expression changes are coordinated by the factor action.
The work was supported by the Russian Foundation for Basic Research (18-04-01130, 18-34-00871).