Dear list members, We have identified 300 genes response to a treatment in our model by cDNA microarray. We have annotated most of these sequences and signed them with different GO terms. Based on literature searching, we believe that these genes can be categorized to several groups such as: Proteinbiosynthesis (Translation), Metabolism, Protection against reactive oxygen species (ROS), Apoptosis, Growth regulation, Inflammation, Heart-related function, Muscle-related function, Development, Transport (cellular and vascular), Angiogenesis. Any comments about how to categorize our genes to these groups quickly and precisely are welcome. Ziping Zhang Molecular Bioscience Research GroupDepartment of Chemistry and Biochemistry 601 University Drive/Centinnal 419 Texas State University San Marcos, Texas 78666-4616 Tel: 512-245-0358 (O); 512-245-2032 (L) Fax: 512-245-1922 _________________________________________________________________ See how Windows Mobile brings your life together—at home, work, or on the go. http://clk.atdmt.com/MRT/go/msnnkwxp1020093182mrt/direct/01/ [[alternative HTML version deleted]]

Hi Ziping, It sounds like you might want to look at the GOStats package. You can find more information here by reading the vignettes: http://www.bioconductor.org/packages/2.3/bioc/html/GOstats.html Marc ziping zhang wrote: > > Dear list members, > > We have identified 300 genes response to a treatment in our model by cDNA microarray. We have annotated most of these sequences and signed them with different GO terms. Based on literature searching, we believe that these genes can be categorized to several groups such as: Proteinbiosynthesis (Translation), Metabolism, Protection against reactive oxygen species (ROS), Apoptosis, Growth regulation, Inflammation, Heart-related function, Muscle-related function, Development, Transport (cellular and vascular), Angiogenesis. Any comments about how to categorize our genes to these groups quickly and precisely are welcome. > > Ziping Zhang > Molecular Bioscience Research GroupDepartment of Chemistry and Biochemistry 601 University Drive/Centinnal 419 > Texas State University San Marcos, Texas 78666-4616 Tel: 512-245-0358 (O); 512-245-2032 (L) > Fax: 512-245-1922 > _________________________________________________________________ > See how Windows Mobile brings your life together?at home, work, or on the go. > http://clk.atdmt.com/MRT/go/msnnkwxp1020093182mrt/direct/01/ > [[alternative HTML version deleted]] > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

You might want to try DAVID david.abcc.ncifcrf.gov or Ingenuity or Pathway Studio, or GeneGo from Metacore. There are also various gene set enrichment approaches in R or Java, such as the one hosted by the Broad Institute. Tom On Oct 2, 2008, at 12:16 PM, ziping zhang wrote: > > Dear list members, > > We have identified 300 genes response to a treatment in our model > by cDNA microarray. We have annotated most of these sequences and > signed them with different GO terms. Based on literature searching, > we believe that these genes can be categorized to several groups > such as: Proteinbiosynthesis (Translation), Metabolism, Protection > against reactive oxygen species (ROS), Apoptosis, Growth > regulation, Inflammation, Heart-related function, Muscle-related > function, Development, Transport (cellular and vascular), > Angiogenesis. Any comments about how to categorize our genes to > these groups quickly and precisely are welcome. > > Ziping Zhang > Molecular Bioscience Research GroupDepartment of Chemistry and > Biochemistry 601 University Drive/Centinnal 419 > Texas State University San Marcos, Texas 78666-4616 Tel: > 512-245-0358 (O); 512-245-2032 (L) > Fax: 512-245-1922 > _________________________________________________________________ > See how Windows Mobile brings your life together?at home, work, or > on the go. > http://clk.atdmt.com/MRT/go/msnnkwxp1020093182mrt/direct/01/ > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor