Characterizing gene sets with FuncAssociate

By G. Berriz, Oliver D. King, Barbara Bryant, Christopher Sander, Frederick P. Roth. Bioinform., 2003

503 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/50bd6be85ce453aaf7fc419c42009beeb43426a8

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In Molecular Biology

Citations in the corpus

BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks (2005, unknown): “Several tools exist that analyze GO term enrichment in a given gene set (Berriz et al., 2003; Hosack et al., 2003; Zeeberg et al., 2003; Al-Shahrour et al., 2004; Beißbarth and Speed, 2004; Boyle et al., 2004; Masseroli et al., * To whom correspondence should be addressed.”
GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists (2007, methodology): “The p values can then be adjusted for multiple tests using a simulation-based correction approach [10,11] or the false discovery method proposed by Benjamini and Hochberg [12].”
Significance analysis of functional categories in gene expression studies: a structured permutation approach (2005, methodology): “…the null distributions for genelist global statistics are assumed to be hypergeometric (Draghici et al., 2003; Beißbarth and Speed, 2004; Al-Shahrour et al., 2004; Hosack et al., 2003; Zeeberg et al., 2003; Zhong et al., 2004; Berriz et al., 2003) or approximations thereof (Kim and Falkow, 2003).”
Multitask Matrix Completion for Learning Protein Interactions Across Diseases (2016, unknown): “0(4) (Berriz et al., 2003) tool and GO annotations for the three viruses from UniProtKB.”
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): “…Perl script whose source is available; and D ow nloaded from https://academ ic.oup.com /bioinform atics/article-abstract/20/18/3710/202612 by guest on 09 D ecem ber 2019 FuncAssociate (Berriz et al., 2003), which is a web application, comprising Perl and C code that are available for download.”
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).”
Predicting Network Activity from High Throughput Metabolomics (2013, methodology): “The overall significance of a pathway enrichment is estimated based on a method by Berriz et al [44], which ranks the p-value from real data among the p-values from permutation data to adjust for type I error.”
LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data (2009, background): “LRpath displayed robust behavior and improved statistical power compared with tested alternatives.”
Finding Correlated Biclusters from Gene Expression Data (2011, methodology): “FuncAssociate first uses (8) to compute the hypergeometric functional score of a gene set, then uses the Westfall and Young procedure [58] to compute the adjusted significant score of the gene set of the bicluster.”
Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges (2012, methodology): “ca/funcassociate/) [6]”
GENOMIC DATA ANALYSIS (2004, methodology): “Some authors (Berriz et al., 2003; Breitling et al., 2004a) suggest using an optimization procedure to determine the cutoff for each category.”