title: g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments.
abstract: g:Profiler (http://biit.cs.ut.ee/gprofiler/) is a public web server for characterising and manipulating gene lists resulting from mining high-throughput genomic data. g:Profiler has a simple, user-friendly web interface with powerful visualisation for capturing Gene Ontology (GO), pathway, or transcription factor binding site enrichments down to individual gene levels. Besides standard multiple testing corrections, a new improved method for estimating the true effect of multiple testing over complex structures like GO has been introduced. Interpreting ranked gene lists is supported from the same interface with very efficient algorithms. Such ordered lists may arise when studying the most significantly affected genes from high-throughput data or genes co-expressed with the query gene. Other important aspects of practical data analysis are supported by modules tightly integrated with g:Profiler. These are: g:Convert for converting between different database identifiers; g:Orth for finding orthologous genes from other species; and g:Sorter for searching a large body of public gene expression data for co-expression. g:Profiler supports 31 different species, and underlying data is updated regularly from sources like the Ensembl database. Bioinformatics communities wishing to integrate with g:Profiler can use alternative simple textual outputs.
authors.affiliation: Institute of Computer Science, University of Tartu, Liivi 2, 50409 Tartu, Estonia.
authors.forename: Jüri
authors.initials: J
authors.lastname: Reimand
authors.forename: Meelis
authors.initials: M
authors.lastname: Kull
authors.forename: Hedi
authors.initials: H
authors.lastname: Peterson
authors.forename: Jaanus
authors.initials: J
authors.lastname: Hansen
authors.forename: Jaak
authors.initials: J
authors.lastname: Vilo
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000378:metabolism; D003627:Data Interpretation, Statistical; D020869:Gene Expression Profiling; D023281:Genomics; D006801:Humans; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000378:metabolism; D012984:Software; D014584:User-Computer Interface
chemical_list: D012333:RNA, Messenger; D004247:DNA