Gprofiler2 -- an R Package for Gene List Functional Enrichment Analysis and Namespace Conversion Toolset G:Profiler

Overview

Journal F1000Res

Specialties Biomedical Engineering
Science

Date 2021 Feb 11

PMID 33564394

Citations 351

Authors

Liis Kolberg

Uku Raudvere

Ivan Kuzmin

Jaak Vilo

Hedi Peterson

Affiliations

Soon will be listed here.

Abstract

g:Profiler ( https://biit.cs.ut.ee/gprofiler) is a widely used gene list functional profiling and namespace conversion toolset that has been contributing to reproducible biological data analysis already since 2007. Here we introduce the accompanying R package, , developed to facilitate programmatic access to g:Profiler computations and databases via REST API. The package provides an easy-to-use functionality that enables researchers to incorporate functional enrichment analysis into automated analysis pipelines written in R. The package also implements interactive visualisation methods to help to interpret the enrichment results and to illustrate them for publications. In addition, gives access to the versatile gene/protein identifier conversion functionality in g:Profiler enabling to map between hundreds of different identifier types or orthologous species. The package is freely available at the CRAN repository.

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References

Love M, Huber W, Anders S . Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15(12):550. PMC: 4302049. DOI: 10.1186/s13059-014-0550-8. View

Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J . Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1):25-9. PMC: 3037419. DOI: 10.1038/75556. View

Chou C, Shrestha S, Yang C, Chang N, Lin Y, Liao K . miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions. Nucleic Acids Res. 2017; 46(D1):D296-D302. PMC: 5753222. DOI: 10.1093/nar/gkx1067. View

Himes B, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B . RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells. PLoS One. 2014; 9(6):e99625. PMC: 4057123. DOI: 10.1371/journal.pone.0099625. View

Yates A, Achuthan P, Akanni W, Allen J, Allen J, Alvarez-Jarreta J . Ensembl 2020. Nucleic Acids Res. 2019; 48(D1):D682-D688. PMC: 7145704. DOI: 10.1093/nar/gkz966. View

Kohler S, Carmody L, Vasilevsky N, Jacobsen J, Danis D, Gourdine J . Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res. 2018; 47(D1):D1018-D1027. PMC: 6324074. DOI: 10.1093/nar/gky1105. View

Subramanian A, Tamayo P, Mootha V, Mukherjee S, Ebert B, Gillette M . Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005; 102(43):15545-50. PMC: 1239896. DOI: 10.1073/pnas.0506580102. View

Pinero J, Ramirez-Anguita J, Sauch-Pitarch J, Ronzano F, Centeno E, Sanz F . The DisGeNET knowledge platform for disease genomics: 2019 update. Nucleic Acids Res. 2019; 48(D1):D845-D855. PMC: 7145631. DOI: 10.1093/nar/gkz1021. View

Howe K, Bolt B, Shafie M, Kersey P, Berriman M . WormBase ParaSite - a comprehensive resource for helminth genomics. Mol Biochem Parasitol. 2016; 215:2-10. PMC: 5486357. DOI: 10.1016/j.molbiopara.2016.11.005. View

10.

Kolberg L, Raudvere U, Kuzmin I, Vilo J, Peterson H . gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler. F1000Res. 2021; 9. PMC: 7859841. DOI: 10.12688/f1000research.24956.2. View

11.

Love M, Anders S, Kim V, Huber W . RNA-Seq workflow: gene-level exploratory analysis and differential expression. F1000Res. 2015; 4:1070. PMC: 4670015. DOI: 10.12688/f1000research.7035.1. View

12.

Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, Fobo G . CORUM: the comprehensive resource of mammalian protein complexes--2009. Nucleic Acids Res. 2009; 38(Database issue):D497-501. PMC: 2808912. DOI: 10.1093/nar/gkp914. View

13.

Uhlen M, Fagerberg L, Hallstrom B, Lindskog C, Oksvold P, Mardinoglu A . Proteomics. Tissue-based map of the human proteome. Science. 2015; 347(6220):1260419. DOI: 10.1126/science.1260419. View

14.

Kanehisa M, Sato Y, Furumichi M, Morishima K, Tanabe M . New approach for understanding genome variations in KEGG. Nucleic Acids Res. 2018; 47(D1):D590-D595. PMC: 6324070. DOI: 10.1093/nar/gky962. View

15.

Matys V, Kel-Margoulis O, Fricke E, Liebich I, Land S, Barre-Dirrie A . TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 2005; 34(Database issue):D108-10. PMC: 1347505. DOI: 10.1093/nar/gkj143. View

16.

Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, cech M . The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 2018; 46(W1):W537-W544. PMC: 6030816. DOI: 10.1093/nar/gky379. View

17.

Reimand J, Kull M, Peterson H, Hansen J, Vilo J . g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res. 2007; 35(Web Server issue):W193-200. PMC: 1933153. DOI: 10.1093/nar/gkm226. View

18.

Yu G, Wang L, Han Y, He Q . clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012; 16(5):284-7. PMC: 3339379. DOI: 10.1089/omi.2011.0118. View

19.

Raudvere U, Kolberg L, Kuzmin I, Arak T, Adler P, Peterson H . g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). Nucleic Acids Res. 2019; 47(W1):W191-W198. PMC: 6602461. DOI: 10.1093/nar/gkz369. View

20.

Kulkarni N, Alessandri L, Panero R, Arigoni M, Olivero M, Ferrero G . Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines. BMC Bioinformatics. 2018; 19(Suppl 10):349. PMC: 6191970. DOI: 10.1186/s12859-018-2296-x. View