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

By Jüri Reimand, Tambet Arak, Jaak Vilo. Nucleic Acids Res., 2011

1,588 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b35489ba2252a7c55acb7624e2fb9ee62157ea1d

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In Molecular Biology

1. Jaak Vilo
2. Tauno Metsalu
3. Fran Supek
4. Nives Skunca
5. Zhiao Shi
6. Tambet Arak
7. Guangyan Zhou
8. Liis Kolberg

Citations in the corpus

• ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap (2015, positive): “Genetic pathways were downloaded from g:Profiler web tool (12).”
• Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups. (2015, neutral): “…biological processes and pathways that play a role in each of these subgroups, we performed gene-ranked pathway enrichment analysis with g:Profiler (Reimand et al., 2011) and used Cytoscape Enrichment Map to visualize processes and pathways that distinguished the different molecular subgroups or…”
• Identification of potentially oncogenic alterations from tumor-only samples reveals Fanconi anemia pathway mutations in bladder carcinomas (2017, methodology): “) Multiple testing correction for p-values calculated using the ontology-focused correction method g:SCS as previously described.(43) FA pathway in Fig.”
• Gene Set Knowledge Discovery with Enrichr (2021, neutral): “For example, g:Profiler (Reimand et al., 2016), DAVID (Sherman & Lempicki, 2009), ToppGene (Chen, Bardes, Aronow, & Jegga, 2009) , Panther (Mi, Muruganujan, Casagrande, & Thomas, 2013), GSEA-P (Subramanian, Kuehn, Gould, Tamayo, & Mesirov, 2007), WebGestalt (Zhang, Kirov, & Snoddy, 2005), Metascape…”
• NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data (2015, neutral): “The most popular web-based tools for integrative analysis of gene list data are probably DAVID 25 and g:Profiler 26 .”
• g:Profiler—a web server for functional interpretation of gene lists (2016 update) (2016, positive): “Since our previous publication in 2011 (30), we have added several new resources for interpreting gene lists and implemented new technologies.”
• New Brain Tumor Entities Emerge from Molecular Classification of CNS-PNETs (2016, positive): “Gene-ranked pathway enrichment analysis (Reimand et al., 2011) of entity-specific genes relative to non-neoplastic brain tissues indicated several general and specific neuronal developmental processes being activated similarly in each of the four entities, but also identified deregulated processes and…”
• Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape (2016, positive): “, 2014), and GO enrichment was calculated by g:Profiler (Reimand et al., 2011).”