GeneTrail—advanced gene set enrichment analysis

By Christina Backes, Andreas Keller, Jan Küntzer, B. Kneissl, N. Comtesse, Yasser A. Elnakady, R. Müller, E. Meese, Hans-Peter Lenhof. Nucleic Acids Res., 2007

369 citations recorded by the source corpus.

We present a comprehensive and efficient gene set analysis tool, called ‘GeneTrail’ that offers a rich functionality and is easy to use. Our web-based application facilitates the statistical evaluation of high-throughput genomic or proteomic data sets with respect to enrichment of functional categories. GeneTrail covers a wide variety of biological categories and pathways, among others KEGG, TRANSPATH, TRANSFAC, and GO. Our web server provides two common statistical approaches, ‘Over-Representation Analysis’ (ORA) comparing a reference set of genes to a test set, and ‘Gene Set Enrichment Analysis’ (GSEA) scoring sorted lists of genes. Besides other newly developed features, GeneTrail's statistics module includes a novel dynamic-programming algorithm that improves the P-value computation of GSEA methods considerably. GeneTrail is freely accessible at http://genetrail.bioinf.uni-sb.de

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5941eef480744e281b3fb48dfe640af215bee586

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Citations in the corpus

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists (2008, positive): “Moreover, a number of tools, such as Onto-Express (62), easyGO (66), GoMiner (10), eGOn (42), GoSurfer (25), GOFFA (50) and GeneTrail (57), are able to display the enrichment analysis results on the DAG or a tree structure so that users may easily explore the enrichment results in neighboring nodes.”
Gene-set approach for expression pattern analysis (2008, methodology): “2007 GeneTrail Fisher’s exact test, hypergeometric test, sample randomization competitive gene or sample [42]”
GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists (2009, neutral): “A few tools have been developed that use a threshold free approach including GSEA [12], FatiScan [13], GO-stat [14], GeneTrail [15] and iGA [16].”
EnrichNet: network-based gene set enrichment analysis (2012, background): “To identify and prioritize these putative associations, a wide range of enrichment analysis tools have been developed in recent years, ∗ To whom correspondence should be addressed.”
Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges (2012, neutral): “de) [87]”
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update (2016, methodology): “…test, the Z-score and the combined score, as well as other similar published methods, for example, the over representation analysis (ORA) method (11), as well as simple methods such as the Jaccard distance or the number of overlapping genes, we processed 489 experiments that genetically…”
DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways (2012, background): “GeneTrail (15) is a web server hosting gene set enrichment and over-representation capabilities against various databases, such as GO and KEGG.”
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 (26”