FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes

By Fátima Al-Shahrour, Ramón Díaz-Uriarte, Joaquín Dopazo. Bioinform., 2004

1,184 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/7a27877026d41260203e80cb2ba9a2389cc98bb0

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Citations in the corpus

KOBAS server: a web-based platform for automated annotation and pathway identification (2006, methodology): “A variety of web-based tools have been developed for GO-based analysis, including Gotcha (2), GoFigure (3), FatiGO (4), GFINDer (5), GOstat (6), NetAffx (7), GOToolBox (8) and Onto-Tools (9).”
GO: : TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes (2004, methodology): “These include FunSpec (Robinson et al., 2002), Onto-Express (Draghici et al., 2003a,b; Khatri et al., 2002) and FatiGO (Al-Shahrour et al., 2004) which are web applications; GoMiner (Zeeberg et al., 03), a Java application; GeneMerge (Castillo Davis and Hartl, 2003), which is a standalone Perl…”
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update (2016, methodology): “Early tools such as FatiGO (2), BiNGO (3) and TermFinder (4) first realized this concept.”
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases (2011, background): “Most of them focus on identiﬁcation of enriched functional categories based on Gene Ontology (GO) (7), such as FuncAssociate (8), Ontologizer (9), BiNGO (10), FatiGO (11), GOToolBox (11) and GFinder (12).”
MicroRNA-directed transcriptional gene silencing in mammalian cells (2008, methodology): “The gene ontology (GO) ‘‘biological process’’ categories (21) containing the highest percentage of the 1,200 candidate target genes represented genes involved in regulation of transcription or apoptosis (Fig.”
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists (2007, background): “A number of publicly available bioinformatics tools have addressed the first three points above, including, but not limited to, GoMiner, DAVID, EASE, GOstat, Onto-express, GoToolBox, FatiGO, GOSSIP, GFINDer, GOBar, and so on [1-25].”
ARED 3.0: the large and diverse AU-rich transcriptome (2005, methodology): “This analysis was performed using FatiGO and GOStat programs (10,11).”
GeneTrail—advanced gene set enrichment analysis (2007, methodology): “Some of the developed tools focus on the analysis of only one type of functional categories for example various Gene Ontology (GO) (1) based tools, among them FatiGO (2), BiNGO (3), and GOstat (4).”
Improved human disease candidate gene prioritization using mouse phenotype (2007, background): “Functional enrichment approaches [2-4] focusing on gene sets that share common biological function, chromo-Published somal location, or regulation although successful in identifying enriched biological themes are not suitable for gene prioritization.”
Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary (2005, neutral): “Theyincludetheweb-based applicationsFatiGO(Al-Shahrour et al ., 2004), GFinder (Masseroli et al ., 2004), Gostat (Beissbarth and Speed, 2004), NetAffx GO Mining Tool (Cheng et al ., 2004a), Onto-Express (Draghici et al ., 2003), the JAVA application GoMiner (Zeeberg et al ., 2003), the R package…”
Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus. (2010, methodology): “Gene Ontology analysis was done with the FatiGO tool (Al-Shahrour et al. 2004), which uses a statistical test (Fisher’s exact test) to detect significant over-representation of GO terms in one of the sets (list of selected genes) with respect to the other one (the rest of the genome).”
Pathways to the analysis of microarray data. (2005, methodology): “FatIGO (GEPAS) Fisher Exact test, various multiple testing correction, permutation GO Web http://fatigo.bioinfo.cnio.es/ Part of GEPAS, selected organisms [40, 41 ]”