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

S. K. Loftus, Y. Chen, G. Gooden, J. F. Ryan, G. Birznieks, M. Hilliard, A. D. Baxevanis, M. Bittner, P. Meltzer, J. Trent, W. Pavan

Research output: Contribution to journalArticle

Abstract

With cDNA microarrays, it is now possible to compare the expression of many genes simultaneously. To maximize the likelihood of finding genes whose expression is altered under the experimental conditions, it would be advantageous to be able to select clones for tissue-appropriate cDNA sets. We have taken advantage of the extensive sequence information in the dbEST expressed sequence tag (EST) database to identify a neural crest-derived melanocyte cDNA set for microarray analysis. Analysis of characterized genes with dbEST identified one library that contained ESTs representing 21 neural crest-expressed genes (library 198). The distribution of the ESTs corresponding to these genes was biased toward being derived from library 198. This is in contrast to the EST distribution profile for a set of control genes, characterized to be more ubiquitously expressed in multiple tissues (P <1 x 10-9). From library 198, a subset of 852 clustered ESTs were selected 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 (Mel1 array) were differentially expressed in melanoma cell lines compared with a non-neural crest kidney epithelial cell line (P <1 x 10-8). 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.

Original languageEnglish (US)
Pages (from-to)9277-9280
Number of pages4
JournalProceedings of the National Academy of Sciences of the United States of America
Volume96
Issue number16
DOIs
StatePublished - Aug 3 1999
Externally publishedYes

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Informatics
Neural Crest
Melanocytes
Expressed Sequence Tags
Microarray Analysis
Oligonucleotide Array Sequence Analysis
Libraries
Genes
Complementary DNA
Gene Expression
Cell Line
Gene Library
Melanoma
Clone Cells
Epithelial Cells
Databases
Kidney

ASJC Scopus subject areas

  • Genetics
  • General

Cite this

Informatic selection of a neural crest-melanocyte cDNA set for microarray analysis. / Loftus, S. K.; Chen, Y.; Gooden, G.; Ryan, J. F.; Birznieks, G.; Hilliard, M.; Baxevanis, A. D.; Bittner, M.; Meltzer, P.; Trent, J.; Pavan, W.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, No. 16, 03.08.1999, p. 9277-9280.

Research output: Contribution to journalArticle

Loftus, SK, Chen, Y, Gooden, G, Ryan, JF, Birznieks, G, Hilliard, M, Baxevanis, AD, Bittner, M, Meltzer, P, Trent, J & Pavan, W 1999, 'Informatic selection of a neural crest-melanocyte cDNA set for microarray analysis', Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 16, pp. 9277-9280. https://doi.org/10.1073/pnas.96.16.9277
Loftus, S. K. ; Chen, Y. ; Gooden, G. ; Ryan, J. F. ; Birznieks, G. ; Hilliard, M. ; Baxevanis, A. D. ; Bittner, M. ; Meltzer, P. ; Trent, J. ; Pavan, W. / Informatic selection of a neural crest-melanocyte cDNA set for microarray analysis. In: Proceedings of the National Academy of Sciences of the United States of America. 1999 ; Vol. 96, No. 16. pp. 9277-9280.
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