Literature DB >> 14764555

CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology.

N H Shah1, N V Fedoroff.   

Abstract

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

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Mesh：

Year:  2004        PMID： 14764555     DOI： 10.1093/bioinformatics/bth056

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  25 in total

1.  Ontological analysis of gene expression data: current tools, limitations, and open problems.

Authors:  Purvesh Khatri; Sorin Drăghici
Journal:  Bioinformatics       Date:  2005-06-30       Impact factor: 6.937

2.  An ontology-neutral framework for enrichment analysis.

Authors:  Rob Tirrell; Uday Evani; Ari E Berman; Sean D Mooney; Mark A Musen; Nigam H Shah
Journal:  AMIA Annu Symp Proc       Date:  2010-11-13

3.  Mu opioid receptors in the medial preoptic area govern social play behavior in adolescent male rats.

Authors:  Changjiu Zhao; Liza Chang; Anthony P Auger; Stephen C Gammie; Lauren V Riters
Journal:  Genes Brain Behav       Date:  2020-05-18       Impact factor: 3.449

4.  Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control, and gene expression regulation.

Authors:  Cristina Pina; Francisco Pinto; José A Feijó; Jörg D Becker
Journal:  Plant Physiol       Date:  2005-05-20       Impact factor: 8.340

5.  Perturbation of spermine synthase gene expression and transcript profiling provide new insights on the role of the tetraamine spermine in Arabidopsis defense against Pseudomonas viridiflava.

Authors:  María Elisa Gonzalez; Francisco Marco; Eugenio Gómez Minguet; Pedro Carrasco-Sorli; Miguel Angel Blázquez; Juan Carbonell; Oscar Adolfo Ruiz; Fernando Luis Pieckenstain
Journal:  Plant Physiol       Date:  2011-05-31       Impact factor: 8.340

6.  microRNAs responsive to ozone-induced oxidative stress in Arabidopsis thaliana.

Authors:  Niranjani J Iyer; Xiaoyun Jia; Ramanjulu Sunkar; Guiliang Tang; Ramamurthy Mahalingam
Journal:  Plant Signal Behav       Date:  2012-04-01

7.  Temporal evolution of the Arabidopsis oxidative stress response.

Authors:  Ramamurthy Mahalingam; Nigam Shah; Alexandra Scrymgeour; Nina Fedoroff
Journal:  Plant Mol Biol       Date:  2005-03       Impact factor: 4.076

8.  GOAL: a software tool for assessing biological significance of genes groups.

Authors:  Alain B Tchagang; Alexander Gawronski; Hugo Bérubé; Sieu Phan; Fazel Famili; Youlian Pan
Journal:  BMC Bioinformatics       Date:  2010-05-06       Impact factor: 3.169

9.  From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations.

Authors:  Pan Du; Gang Feng; Jared Flatow; Jie Song; Michelle Holko; Warren A Kibbe; Simon M Lin
Journal:  Bioinformatics       Date:  2009-06-15       Impact factor: 6.937

10.  Chapter 9: Analyses using disease ontologies.

Authors:  Nigam H Shah; Tyler Cole; Mark A Musen
Journal:  PLoS Comput Biol       Date:  2012-12-27       Impact factor: 4.475
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