GeneMerge—post-genomic analysis, data mining, and hypothesis testing
作者： C. I. Castillo-Davis , D. L. Hartl
DOI: 10.1093/BIOINFORMATICS/BTG114
关键词:
摘要: Summary: GeneMerge is a web-based and standalone program written in PERL that returns range of functional genomic data for given set study genes provides statistical rank scores over-representation particular functions or categories the set. Functional categorical all kinds can be analyzed with GeneMerge, facilitating regulatory metabolic pathway analysis, tests population genetic hypotheses, cross-experiment comparisons, chromosomal clustering, among others. perform analyses on wide variety quickly easily facilitates both mining hypothesis testing. Availability: available free charge academic use over web download from: http://www.oeb.harvard.edu/hartl/lab/publications/ GeneMerge.html.
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oxfordjournals.org参考文章(13)
Robert Reuven Sokal, F. James Rohlf, Biometry: The Principles and Practice of Statistics in Biological Research ,(1969)
Laurie Issel-Tarver, Karen R. Christie, Kara Dolinski, Rey Andrada, Rama Balakrishnan, Catherine A. Ball, Gail Binkley, Stan Dong, Selina S. Dwight, Dianna G. Fisk, Midori Harris, Mark Schroeder, Anand Sethuraman, Kane Tse, Shuai Weng, David Botstein, J. Michael Cherry, Saccharomyces Genome Database. Methods in Enzymology. ,vol. 350, pp. 329- 346 ,(2002) , 10.1016/S0076-6879(02)50972-1
Aaron E. Hirsh, Hunter B. Fraser, Protein dispensability and rate of evolution Nature. ,vol. 411, pp. 1046- 1049 ,(2001) , 10.1038/35082561
Cheng Li, Wing Hung Wong, Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application Genome Biology. ,vol. 2, pp. 1- 11 ,(2001) , 10.1186/GB-2001-2-8-RESEARCH0032
P. Sudarsanam, V. R. Iyer, P. O. Brown, F. Winston, Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 97, pp. 3364- 3369 ,(2000) , 10.1073/PNAS.97.7.3364
Paul Grosu, Jeffrey P Townsend, Daniel L Hartl, Duccio Cavalieri, Pathway Processor: A Tool for Integrating Whole-Genome Expression Results into Metabolic Networks Genome Research. ,vol. 12, pp. 1121- 1126 ,(2002) , 10.1101/GR.226602
S Asburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel‐Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock, Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics. ,vol. 25, pp. 25- 29 ,(2000) , 10.1038/75556
Minoru Kanehisa, Susumu Goto, Shuichi Kawashima, Akihiro Nakaya, The KEGG databases at GenomeNet Nucleic Acids Research. ,vol. 30, pp. 42- 46 ,(2002) , 10.1093/NAR/30.1.42
Elizabeth A Winzeler, Daniel D Shoemaker, Anna Astromoff, Hong Liang, Keith Anderson, Bruno Andre, Rhonda Bangham, Rocio Benito, Jef D Boeke, Howard Bussey, Angela M Chu, Carla Connelly, Karen Davis, Fred Dietrich, Sally Whelen Dow, Mohamed El Bakkoury, Françoise Foury, Stephen H Friend, Erik Gentalen, Guri Giaever, Johannes H Hegemann, Ted Jones, Michael Laub, Hong Liao, Nicole Liebundguth, David J Lockhart, Anca Lucau-Danila, Marc Lussier, Nasiha M'Rabet, Patrice Menard, Michael Mittmann, Chai Pai, Corinne Rebischung, Jose L Revuelta, Linda Riles, Christopher J Roberts, Petra Ross-MacDonald, Bart Scherens, Michael Snyder, Sharon Sookhai-Mahadeo, Reginald K Storms, Steeve Véronneau, Marleen Voet, Guido Volckaert, Teresa R Ward, Robert Wysocki, Grace S Yen, Kexin Yu, Katja Zimmermann, Peter Philippsen, Mark Johnston, Ronald W Davis, None, Functional Characterization of the S. cerevisiae Genome by Gene Deletion and Parallel Analysis Science. ,vol. 285, pp. 901- 906 ,(1999) , 10.1126/SCIENCE.285.5429.901
Guri Giaever, Angela M Chu, Li Ni, Carla Connelly, Linda Riles, Steeve Véronneau, Sally Dow, Ankuta Lucau-Danila, Keith Anderson, Bruno André, Adam P Arkin, Anna Astromoff, Mohamed El Bakkoury, Rhonda Bangham, Rocio Benito, Sophie Brachat, Stefano Campanaro, Matt Curtiss, Karen Davis, Adam Deutschbauer, Karl-Dieter Entian, Patrick Flaherty, Francoise Foury, David J Garfinkel, Mark Gerstein, Deanna Gotte, Ulrich Güldener, Johannes H Hegemann, Svenja Hempel, Zelek Herman, Daniel F Jaramillo, Diane E Kelly, Steven L Kelly, Peter Kötter, Darlene LaBonte, David C Lamb, Ning Lan, Hong Liang, Hong Liao, Lucy Liu, Chuanyun Luo, Marc Lussier, Rong Mao, Patrice Menard, Siew Loon Ooi, Jose L Revuelta, Christopher J Roberts, Matthias Rose, Petra Ross-Macdonald, Bart Scherens, Greg Schimmack, Brenda Shafer, Daniel D Shoemaker, Sharon Sookhai-Mahadeo, Reginald K Storms, Jeffrey N Strathern, Giorgio Valle, Marleen Voet, Guido Volckaert, Ching-yun Wang, Teresa R Ward, Julie Wilhelmy, Elizabeth A Winzeler, Yonghong Yang, Grace Yen, Elaine Youngman, Kexin Yu, Howard Bussey, Jef D Boeke, Michael Snyder, Peter Philippsen, Ronald W Davis, Mark Johnston, None, Functional profiling of the Saccharomyces cerevisiae genome. Nature. ,vol. 418, pp. 387- 391 ,(2002) , 10.1038/NATURE00935