In Silico Gene Selection Strategy for Custom Microarray Design

Abstract

Microarray technology has become an important tool for studying large-scale gene expression for a diversity of biological applications. However, there are a number of experimental settings for which commercial arrays are either unsuitable or unavailable despite the existence of sequence information. With the increasing availability of custom array manufacturing services, it is now feasible to design high-density arrays for any organism having sequence data. However, there have been relatively few reports discussing gene selection, an important first step in array design. Here we propose an in silico strategy for custom microarray gene selection that is applicable to a wide range of organisms, based on utilizing public domain microarray information to interrogate existing sequence data and to identify a set of homologous genes in any organism of interest. We demonstrate the utility of this approach by applying it to the selection of candidate genes for a custom Xenopus laevis microarray. A significant finding of this study is that 3%-4% of Xenopus expressed sequence tags (ESTs) are in an orientation contrary to that indicated in the public database entry (http://mssaha.people.wm.edu/suppMSS.html).

Discovery of nutritional biomarkers: future directions based on omics technologies

“…Global expression analysis is often followed by a more detailed interrogation of those specific groups of genes identified as being affected in the first global study. At present, this can be achieved by using customized microarrays (Dondeti et al, 2004) or multi-PCR (multi-polymerase chain reaction) in microfluidic devices, TLDAs (TaqMan Low Density Arrays) (Sorby et al, 2010). In the particular case of nutritranscriptomics, sample availability is more restricted than in the rest of the omics since biological fluids lack cells for RNA extraction, and as such is useful only tissue biopsies or cell lines.…”