Informatic selection of a neural crest-melanocyte cDNA set for microarray analysis

Abstract

While several genes, including three transcription factors (PAX3, MITF & SOX10), that are essential for proper neural crest-melanocyte development in mouse and man have been identified, little is known about target gene regulation. Using cDNA microarrays it is now possible to the compare the expression of many genes simultaneously. We have taken advantage of the extensive sequence information in the dbEST to identify a neural crest-derived melanocyte (NC-M) cDNA set for microarray analysis. Analysis of characterised genes using dbEST identified one library (library 198) that contained ESTs representing 21 neural crest expressed genes and further analysis indicated the distribution of these genes was biased towards being derived from library 198. From library 198, we selected a subset of 852 clustered ESTs that have a library distribution profile similar to that of the 21 neural crest expressed genes. Microarray analysis demonstrated the majority of the neural crest-selected 852 ESTs were differentially expressed in melanoma cell lines compared to a non-neural crest kidney epithelial cell line (P<110-8). This was not observed with an array of 1,238 ESTs that was selected without library origin bias (P=0.204). This study presents an approach for selecting tissue appropriate cDNAs that can be used to examine the expression profiles of developmental processes and diseases and for dissection of pathways involved in neural crest differentiation.