Literature DB >> 12724301

GeneMerge--post-genomic analysis, data mining, and hypothesis testing.

Cristian I Castillo-Davis1, Daniel L Hartl.   

Abstract

SUMMARY: GeneMerge is a web-based and standalone program written in PERL that returns a range of functional and genomic data for a given set of study genes and provides statistical rank scores for over-representation of particular functions or categories in the data set. Functional or categorical data of all kinds can be analyzed with GeneMerge, facilitating regulatory and metabolic pathway analysis, tests of population genetic hypotheses, cross-experiment comparisons, and tests of chromosomal clustering, among others. GeneMerge can perform analyses on a wide variety of genomic data quickly and easily and facilitates both data mining and hypothesis testing. AVAILABILITY: GeneMerge is available free of charge for academic use over the web and for download from: http://www.oeb.harvard.edu/hartl/lab/publications/GeneMerge.html.

Mesh:

Year:  2003        PMID: 12724301     DOI: 10.1093/bioinformatics/btg114

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


  146 in total

1.  The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint.

Authors:  Cristian I Castillo-Davis; Fyodor A Kondrashov; Daniel L Hartl; Rob J Kulathinal
Journal:  Genome Res       Date:  2004-05       Impact factor: 9.043

2.  New strategy for the representation and the integration of biomolecular knowledge at a cellular scale.

Authors:  Roland Barriot; Jérôme Poix; Alexis Groppi; Aurélien Barré; Nicolas Goffard; David Sherman; Isabelle Dutour; Antoine de Daruvar
Journal:  Nucleic Acids Res       Date:  2004-07-07       Impact factor: 16.971

3.  GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes.

Authors:  Elizabeth I Boyle; Shuai Weng; Jeremy Gollub; Heng Jin; David Botstein; J Michael Cherry; Gavin Sherlock
Journal:  Bioinformatics       Date:  2004-08-05       Impact factor: 6.937

4.  A novel benzodioxole-containing inhibitor of Toxoplasma gondii growth alters the parasite cell cycle.

Authors:  Edwin Kamau; Tracy Meehan; Mark D Lavine; Gustavo Arrizabalaga; Gabriela Mustata Wilson; Jon Boyle
Journal:  Antimicrob Agents Chemother       Date:  2011-09-26       Impact factor: 5.191

5.  Y not a dead end: epistatic interactions between Y-linked regulatory polymorphisms and genetic background affect global gene expression in Drosophila melanogaster.

Authors:  Pan-Pan Jiang; Daniel L Hartl; Bernardo Lemos
Journal:  Genetics       Date:  2010-06-15       Impact factor: 4.562

6.  Epigenetic effects of polymorphic Y chromosomes modulate chromatin components, immune response, and sexual conflict.

Authors:  Bernardo Lemos; Alan T Branco; Daniel L Hartl
Journal:  Proc Natl Acad Sci U S A       Date:  2010-08-23       Impact factor: 11.205

7.  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

8.  Search for basonuclin target genes.

Authors:  Junwen Wang; Shengliang Zhang; Richard M Schultz; Hung Tseng
Journal:  Biochem Biophys Res Commun       Date:  2006-08-10       Impact factor: 3.575

9.  Babel's tower revisited: a universal resource for cross-referencing across annotation databases.

Authors:  Sorin Drăghici; Sivakumar Sellamuthu; Purvesh Khatri
Journal:  Bioinformatics       Date:  2006-10-26       Impact factor: 6.937

10.  Transcriptional signature with differential expression of BCL6 target genes accurately identifies BCL6-dependent diffuse large B cell lymphomas.

Authors:  Jose M Polo; Przemyslaw Juszczynski; Stefano Monti; Leandro Cerchietti; Kenny Ye; John M Greally; Margaret Shipp; Ari Melnick
Journal:  Proc Natl Acad Sci U S A       Date:  2007-02-20       Impact factor: 11.205

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