FIDEA: a server for the functional interpretation of differential expression analysis

Abstract

The results of differential expression analyses provide scientists with hundreds to thousands of differentially expressed genes that need to be interpreted in light of the biology of the specific system under study. This requires mapping the genes to functional classifications that can be, for example, the KEGG pathways or InterPro families they belong to, their GO Molecular Function, Biological Process or Cellular Component. A statistically significant overrepresentation of one or more category terms in the set of differentially expressed genes is an essential step for the interpretation of the biological significance of the results. Ideally, the analysis should be performed by scientists who are well acquainted with the biological problem, as they have a wealth of knowledge about the system and can, more easily than a bioinformatician, discover less obvious and, therefore, more interesting relationships. To allow experimentalists to explore their data in an easy and at the same time exhaustive fashion within a single tool and to test their hypothesis quickly and effortlessly, we developed FIDEA. The FIDEA server is located at http://www.biocomputing.it/fidea; it is free and open to all users, and there is no login requirement.

Novel Long Noncoding RNAs (lncRNAs) in Myogenesis: a miR-31 Overlapping lncRNA Transcript Controls Myoblast Differentiation

“…The gene ontology (GO) analysis was performed on a subset of protein-coding genes (see Fig. S1D in the supplemental material) using FIDEA (29). In line with the expected acquisition of a muscle signature, the GO diagram corresponding to DM conditions reveals an overrepresentation of myogenic transcripts, among them those controlling muscle system process, muscle contraction, and muscle structure development.…”

RBM5 reduces small cell lung cancer growth, increases cisplatin sensitivity and regulates key transformation-associated pathways

“…First, the Functional Interpretation of Differential Expression Analysis (FIDEA) (D'Andrea et al, 2013) program with the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database (Kanehisa and Goto, 2000; Kanehisa et al, 2014) was used, thus differentially expressed genes are placed in known signaling pathways to determine if these pathways are significantly up- or downregulated. Analysis results are presented in Fig.…”

“…Pathway enrichment was investigated using the FIDEA (Functional Interpretation of Differential Expression Analysis) program (D'Andrea et al, 2013) with the KEGG database (Kanehisa and Goto, 2000; Kanehisa et al, 2016). Pathway analysis was also performed using GSAASeqSP (Gene Set Association Analysis for RNA-Seq with Sample Permutation) (Xiong et al, 2014) with the Molecular Signatures Database (MSigDB) Hallmark gene set collection (Liberzon et al, 2015).…”

A naturally occuring insertion of a single amino acid rewires transcriptional regulation by glucocorticoid receptor isoforms

“…However, the fact that these isoforms are conserved in mammalian genomes argues for a functional role. Furthermore, we found that the two GR isoforms have different activities, and enrichment analysis of the functional classifications of the isoform-specific target genes (27) showed that different functional categories were enriched (Dataset S1), indicating that alternative splicing of GR could allow GR to have context-specific activities. Because GRγ is naturally expressed at low levels (5-10%) compared with GRα (16), we also tested how having an excess of GRα influenced the ability of GRγ to regulate transcription of a reporter construct containing the GBR for the GRγ-specific gene, JPH2.…”