CLENCH

CLENCH: A program for calculating Cluster ENriCHment using the Gene Ontology. Summary: Analysis of microarray data most often produces lists of genes with similar expression patterns, which are then subdivided into functional categories for biological interpretation. Such functional categorization is most commonly accomplished using Gene Ontology (GO) categories. Although there are several programs that identify and analyze functional categories for human, mouse and yeast genes, none of them accept Arabidopsis thaliana data. In order to address this need for A.thaliana community, we have developed a program that retrieves GO annotations for A.thaliana genes and performs functional category analysis for lists of genes selected by the user. Availability: http://www.personal.psu.edu/nhs109/Clench

References in zbMATH (referenced in 4 articles )

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  1. Faure, Andre J.; Seoighe, Cathal; Mulder, Nicola J.: Investigating the effect of paralogs on microarray gene-set analysis (2011) ioport
  2. Jupiter, Daniel; Şahutoğlu, Jessica; Vanburen, Vincent: TreeHugger: a new test for enrichment of gene ontology terms (2010)
  3. Tchagang, Alain B.; Gawronski, Alexander; Bérubé, Hugo; Phan, Sieu; Famili, Fazel; Pan, Youlian: GOAL: A software tool for assessing biological significance of genes groups (2010) ioport
  4. Speer, Nora; Spiet, Christian; Zell, Andreas: Biological cluster validity indices based on the gene ontology (2005)