eXPRESSION: An in silico tool to predict patterns of gene expression

Deborah A. Ferguson, Jing Tzyh Alan Chiang, James A. Richardson, Jonathan Graff

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

In embryological studies, expression pattern analyses are of special importance since genes that have temporally and spatially restricted expression are not only essential as lineage markers but are often causative in formation of specific fates. Further, where a molecule is expressed can be quite revealing in regard to its endogenous function. We present a gene discovery tool, termed eXPRESSION, that utilizes the public EST databases to identify genes matching desired transcriptional profiles. We first tested and validated the ability of eXPRESSION to discover tissue-specific genes in the adult mouse; empirically as well as with DNA microarrays and RT-PCRs. These studies showed that eXPRESSION predictions could identify genes that are specifically expressed in adult mouse tissues. Next, we developed a novel search strategy to find genes that are expressed in specific regions or tissues of the developing mouse embryo. With these tools, we identified several novel genes that exhibited a neural-specific or neural-enriched expression pattern during murine development. The data show that eXPRESSION is widely applicable and may be used to identify both adult and embryonic tissue- or organ-specific genes with minimal cost and effort.

Original languageEnglish (US)
Pages (from-to)619-628
Number of pages10
JournalGene Expression Patterns
Volume5
Issue number5
DOIs
StatePublished - Jun 2005

Fingerprint

Computer Simulation
Gene Expression
Genes
Expressed Sequence Tags
Genetic Association Studies
Oligonucleotide Array Sequence Analysis
Embryonic Structures
Databases
Costs and Cost Analysis
Polymerase Chain Reaction

Keywords

  • Bioinformatics
  • CNS
  • EST profiling
  • Gene discovery
  • In silico
  • Neural-specific expression
  • Tissue-specific expression

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Cellular and Molecular Neuroscience
  • Developmental Neuroscience

Cite this

eXPRESSION : An in silico tool to predict patterns of gene expression. / Ferguson, Deborah A.; Chiang, Jing Tzyh Alan; Richardson, James A.; Graff, Jonathan.

In: Gene Expression Patterns, Vol. 5, No. 5, 06.2005, p. 619-628.

Research output: Contribution to journalArticle

Ferguson, Deborah A. ; Chiang, Jing Tzyh Alan ; Richardson, James A. ; Graff, Jonathan. / eXPRESSION : An in silico tool to predict patterns of gene expression. In: Gene Expression Patterns. 2005 ; Vol. 5, No. 5. pp. 619-628.
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