g:Profiler—a web server for functional interpretation of gene lists (2011 update)

Abstract

Functional interpretation of candidate gene lists is an essential task in modern biomedical research. Here, we present the 2011 update of g:Profiler (http://biit.cs.ut.ee/gprofiler/), a popular collection of web tools for functional analysis. g:GOSt and g:Cocoa combine comprehensive methods for interpreting gene lists, ordered lists and list collections in the context of biomedical ontologies, pathways, transcription factor and microRNA regulatory motifs and protein–protein interactions. Additional tools, namely the biomolecule ID mapping service (g:Convert), gene expression similarity searcher (g:Sorter) and gene homology searcher (g:Orth) provide numerous ways for further analysis and interpretation. In this update, we have implemented several features of interest to the community: (i) functional analysis of single nucleotide polymorphisms and other DNA polymorphisms is supported by chromosomal queries; (ii) network analysis identifies enriched protein–protein interaction modules in gene lists; (iii) functional analysis covers human disease genes; and (iv) improved statistics and filtering provide more concise results. g:Profiler is a regularly updated resource that is available for a wide range of species, including mammals, plants, fungi and insects.

Molecular Pathways and Functional Analysis of miRNA Expression Associated with Paclitaxel-Induced Apoptosis in Hepatocellular Carcinoma Cells

“…miRNA target genes were identified using the miRWalk online database [17]. We used g:Profiler for the gene annotation, and pathway enrichment analysis [18,19] and STRING for the predicted protein interactions [20]. …”

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“…Genetic correlations between traits associated with pleiotropic QTL were estimated in a multi-traits animal model using ASReml. Gene ontology (GO) term enrichment analysis on genes within/near pleiotropic QTL was performed using the GO database and web tool g:Profiler (Reimand et al, 2011). Only GO terms with significant P value of 0.05 (Benjamini-Honchberg FDR corrected), and associated with biological processes and Kyoto encyclopedia of genes and genomes (KEGG) pathway were retained.…”

Bioinformatics resources for pollen

“…In this study, after the conventional normalization procedures, here performed using dChip 1.3 (Li 2008), statistically significant differentially expressed genes were determined using four different criteria: (1) probes p values \ 0.05; (2) the p values FDR correction to minimize false discovery rate; (3) absolute expression value (fold change) of ±[3; (4) expression levels of [100, well above background. Gene ontology term enrichment was here performed using the g:Profiler (Reimand et al 2011) and GoToolBox (Martin et al 2004) tools.…”