Defining the human foveo–macular transcriptome: compiling distinct data sets

Abstract

Abstract: : Purpose: Transcriptional characterisation of the human foveo–macular region poses several unique complcations, owing to the limited size of this tissue and the absence of a homologous organ in most established model organisms. Until recently, the accumulation of transcriptional information has been limited. We take a bioinformatic approach to examine two distinct gene data sets (one generated by a microarray analysis and a second defined by a library partial sequencing approach) and generate a unified perspective on the foveo–macular gene expression profile. Methods: A human clone array, bearing over 270,000 known human ESTs from various libraries, was screened with human fovea cDNA. This provides a source of data for an array selection approach at defining fovea gene expression. A second macular expression data set was harvested from GenBank that represents a concentrated expressed sequence tag study on this tissue. Both data sets were subjected to in silico analysis using existing, established databases. Results: 3162 UniGene clusters were identified as foveally–expressed by the array analysis method; 2933 UniGene clusters were found to be foveally–expressed by foveo–macular cDNA library partial sequencing. The two datasets display a limited overlap in commonly–identified genes (approximately 13%), implying that neither data set is complete and suggest that additional foveo–macular expressed genes remain to be identified. Certain differences emerge in the two data sets; notably, richness of available data for existing ESTs as opposed to newly sequenced clones differs remarkably. Both methods confirm the presence of certain genes identified as foveally–expressed by foveal dysfunction studies; however, neither method, nor the methods combined, have re–identified every gene known to cause foveo–macular disease. Conclusions: From the analysis of existing expression data bases we have tapped into a wealth of data regarding the foveo–macular transcriptome and functional genomics; additionally, these data illustrate the relative strengths of array analysis and partial library sequencing for transcriptional analysis. The different approaches to characterising fovea gene expression (array screening versus sequencing) has produced datasets with several notable differences that suggest that they represent complimentary approaches at defining the foveo–macular transcriptome.

Keywords: macula/fovea • gene/expression