g:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments

By Jüri Reimand, Meelis Kull, Hedi Peterson, Jaanus Hansen, Jaak Vilo. Nucleic Acids Res., 2007

1,334 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/af74ad7623c1fecc6a6198a3b9546170a2f82e29

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Citations in the corpus

ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems (2010, background): “A wide variety of tools exist for overrepresentation analysis of functional annotations in single gene lists such as DAVID (1), FatiGO (2), g:Profiler (3) etc.”
g:Profiler—a web server for functional interpretation of gene lists (2016 update) (2016, neutral): “While data are frequently updated in some tools such as g:Profiler (9), GOstats (10) and Babelomics (11), many popular tools like DAVID (12) and Bingo (13) have not been updated in years.”
A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies (2010, methodology): “We used the ordered GO profiling method [27] to find significantly enriched GO categories for 30 genes most affected by each factor.”
Pathway and Network Analysis of Cancer Genomes (2015, positive): “One recommended web service g:Profiler 25 applies a modified hypergeometric test to analyze increasingly complete ranked lists of input genes and determines a sub-list with the strongest level of enrichment.”
Characterization of the CLEAR network reveals an integrated control of cellular clearance pathways. (2011, methodology): “It should be noted that a great variety of conditions underlay the acquisition of the experimental data: the TFEB ChIP-seq was performed in HeLa TFEB-3xFLAG stable clones in a steady-state condition; the TFEB overexpression was performed in HeLa cells in condition of transient transfection and the c”
g:Profiler—a web server for functional interpretation of gene lists (2011 update) (2011, positive): “Here, we are proud to present an update note of g:Profiler (15), a web server for functional interpretation and integration of gene lists in the context of versatile biological evidence.”
WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013 (2013, background): “DAVID (2), FatiGO (3) and g:Profiler (4)) are constantly updated to support more organisms and platforms.”
g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update) (2019, methodology): “Only very few of the tools dedicated to enrichment analysis have offered continuous and up-to-date service after their initial release. g:Profiler has remained vital since its first publication in the 2007 NAR web server issue, and has published update articles in 2011 and 2016 (8,15,16).”
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists (2008, neutral): “More than a dozen of the enrichment tools, including recent ones such as EasyGO (66) and g:Profiler (64), as well as the earlier ones such as GoMiner (10), have not implemented multiple test corrections (Supplementary Data 1), but are still widely used by the community in reallife data-mining projec”
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases (2011, background): “A growing number of tools have been developed for pathway and disease identification, including, but not limited to, MAPPFinder (13), EASE (14), DAVID (15,16), ArrayXPath (17), WebGestalt (18), FuncCluster (19), PageMan (20), GENECODIS (21,22), GeneTrail (23), g:Profiler (24), FunNet (25) and PaLS (”
Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network (2011, methodology): “For each gene in the test set, GO enrichment analysis was performed using the g:profiler web server (31).”
NOA: a novel Network Ontology Analysis method (2011, methodology): “For comparison, we use g:profiler (6) to annotate the genes involved in this pathway.”