GeneMerge - Post-genomic Analysis, Data Mining, and Hypothesis Testing

By Cristian I. Castillo-Davis, Daniel L. Hartl. Bioinform., 2003

306 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/6f06840ed8e83593a091ed56f5f19777609a3ff9

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Citations in the corpus

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges (2012, methodology): “edu/) [9]”
Potent Induction of Arabidopsis thaliana Flowering by Elevated Growth Temperature (2006, unknown): “We used the GeneMerge tool [54] to determine whether gene products involved in specific biological processes or molecular functions, as defined by their Gene Ontology annotations, preferentially responded to one of the treatments.”
GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists (2007, methodology): “A comparison of GENECODIS with related tools [1,22-25] and an example with test data [26] is provided in Additional data file 3.”
microRNA Target Predictions across Seven Drosophila Species and Comparison to Mammalian Targets (2005, methodology): “microRNA Targets To gain insight into the function of Drosophila microRNAs, we used GeneMerge [26] to analyze the over-representation of specific GO terms [20] in the functional annotation of genes predicted to be targeted by a particular microRNA versus a background gene set (see Materials and Meth”
GOToolBox: functional analysis of gene datasets based on Gene Ontology (2004, unknown): “GeneMerge [22] Hypergeometric Bonferroni TAB/RANK ALL”
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].”
Ontological analysis of gene expression data: current tools, limitations, and open problems (2005, background): “The importance of this step cannot be overstated and has been well recognized in the literature (Al-Shahrour et al., 2004; Beissbarth and Speed, 2004; Berriz et al., 2003; Castillo-Davis and Hartl, 2002; Dr˘ aghici, 2003; Shah and Fedoroff, 2004; Zeeberg et al., 2003).”
Enrichment or depletion of a GO category within a class of genes: which test? (2007, background): “…2004 FuncAssociate Fisher http://llama.med.harvard.edu/cgi/func/funcassociate FunSpec Hypergeometric Robinson et al., 2002 GeneMerge Hypergeometric Castillo-Davis and Hartl, 2003 GFINDer Hypergeometric, binomial, Fishera Masseroli et al., 2004 GoMiner Fisher Zeeberg et al., 2003 GOstat x2, Fisher…”
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 scrip”
Mapping pathways and phenotypes by systematic gene overexpression. (2006, methodology): “The software GeneMerge (Castillo-Davis and Hartl, 2003) was used to find Pfam domains significantly overrepresented among genes sensitive to overexpression (statistical significance was assessed by an e-score corrected for multiple tests).”
QUBIC: a qualitative biclustering algorithm for analyses of gene expression data (2009, unknown): “…same functional class in a bicluster of size n from a genome with a total of N genes can be computed using the following hypergeometric function (31), where P is the percentage of that functional class among all functional classes of genes encoded in the whole genome, Pr ð r j N , p , n Þ For…”
Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary (2005, methodology): “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 Ont”