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Welcome to the Digestive Disease Research Center Microarray Core webpage, spotlighting the latest information regarding genomic technologies as they relate to DDRC interests. Members of the DDRC are urged to contact the VMSR to find out how microarray, genotyping, and RNAi technologies may enhance their research. Three VMSR bioinformaticists are available to help members design and plan experiments, obtain high-quality data, and prepare the data for publication. New platforms, products, and analysis techniques allow exploration of genomics in ways never before possible.

Featured research

Kaiser S, Park YK, Franklin JL, Halberg RB, Yu M, Jessen WJ, Freudenberg J, Chen X, Haigis K, Jegga AG, Kong S, Sakthivel B, Xu H, Reichling T, Azhar M, Boivin GP, Roberts RB, Bissahoyo AC, Gonzales F, Bloom GC, Eschrich S, Carter SL, Aronow JE, Kleimeyer J, Kleimeyer M, Ramaswamy V, Settle SH, Boone B, Levy S, Graff JM, Doetschman T, Groden J, Dove WF, Threadgill DW, Yeatman TJ, Coffey RJ Jr, Aronow BJ
Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer.
Genome Biol. 2007; 8(7):R131

This manuscript is the result of collaboration between the Robert Coffey lab at Vanderbilt and the Bruce Aronow lab at the University of Cincinnati. Kaiser et al compared gene expression patterns of human colorectal cancers and mouse colon tumor models to those of mouse colon development embryonic days 13.5-18.5. All microarray experiments were performed by the VMSR. Mouse tumors were analyzed on VMSR-printed 20K mouse cDNA arrays composed of PCR products derived from three sources: the 15K National Institute of Aging mouse cDNA library; the Research Genetics mouse 5K set; and an additional set of cDNAs mapped to RefSeq transcripts. The mouse tumor sample array data were composed of Lowess-normalized Cy3:Cy5 labeling ratios of each individual tumor sample versus a universal E17.5 whole fetal mouse reference RNA. Also available was previously collected mouse expression data for normal E13.5-E18.5 colon samples from inbred C57BL/6J and outbred CD-1 mice run on the same 20K arrays. Human RNA colorectal cancer samples were analyzed on Affymetrix HG-U133 Plus 2.0 microarrays. Expression profiles of mouse tumor, mouse embryonic, and human tumor samples were obtained and analyzed for the occurrence of multiple genes involved in related gene function categories by comparing each list of coordinately regulated genes to categories within Gene Ontology, pathways, or literature-based gene associations. Mouse and human tumor data were compared using gene ortholog mapping and showed a striking recapitulation of embryonic colon gene expression.

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News and Notes

Selected papers of interest

Gardina PJ, Clark TA, Shimada B, Staples MK, Yang Q, Veitch J, Schweitzer A, Awad T, Sugnet C, Dee S, Davies C, Williams A, Turpaz Y
Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array.
BMC Genomics. 2006 Dec 27; 7:325

This manuscript from Affymetrix largely serves to introduce the Exon arrays, and a great deal of space is committed to describing the design and analysis of the array itself. However, they were able to use this array to detect nine splice variants that are present in colon tumors but not in normal colon.

Buchanan FG, Holla V, Katkuri S, Matta P, DuBois RN
Targeting cyclooxygenase-2 and the epidermal growth factor receptor for the prevention and treatment of intestinal cancer.
Cancer Res. 2007 Oct 1; 67(19):9380-8

Buchanan et al used Affymetrix microarrays as a measure of verification, noting that "genes involved in cell cycle progression were negatively regulated" as tumors were reduced during treatment.