ExQuest, a novel method for displaying quantitative gene expression from ESTs

There is a pressing need for interactive bioinformatics tools that empower investigators with the means to extract information and organize it in a simplified but meaningful format. A wealth of mammalian gene expression data is readily accessible, much of which is based on expressed sequence tags (E...

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Bibliographic Details
Published in:Genomics (San Diego, Calif.) Calif.), 2004-03, Vol.83 (3), p.528-539
Main Authors: Brown, Aaron C, Kai, Kristin, May, Marjorie E, Brown, Donald C, Roopenian, Derry C
Format: Article
Language:English
Subjects:
Animals
Biological and medical sciences
Chromosomes, Mammalian
Computational Biology
Databases, Factual
dbEST
EST
Expressed Sequence Tags
Fundamental and applied biological sciences. Psychology
Gene Expression
Gene Expression Profiling - methods
Genes. Genome
Genetics of eukaryotes. Biological and molecular evolution
Humans
Mice
Models, Biological
Molecular and cellular biology
Molecular genetics
Quantitative trait loci
Transcription, Genetic
Transcriptome
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Summary:There is a pressing need for interactive bioinformatics tools that empower investigators with the means to extract information and organize it in a simplified but meaningful format. A wealth of mammalian gene expression data is readily accessible, much of which is based on expressed sequence tags (ESTs). Many mammalian ESTs are derived from tissue-specific cDNA libraries in which the number of ESTs representing a specific gene approximates the transcriptional expression level in the source tissue. Our program ExQuest (Expressional Quantification of ESTs) organizes the public EST database (dbEST) into hierarchical tissue classes and reports tissue or developmental gene expression patterns for both mRNA and genomic sequences. ExQuest also displays tissue expression patterns of genes in the context of assembled chromosomes. These interactive “transcriptome” maps provide a novel tool for investigating the genomic basis of gene expression as well as prioritizing candidate genes within genetically mapped mutant and quantitative trait loci.
ISSN:0888-7543
1089-8646
DOI:10.1016/j.ygeno.2003.09.012