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Abstract
BackgroundGenome wide transcriptome maps can provide tools to identify candidate genes that are over-expressed or silenced in certain disease tissue and increase our understanding of the structure and organization of the genome. Expressed Sequence Tags (ESTs) from the public dbEST and proprietary Incyte LifeSeq databases were used to derive a transcript map in conjunction with the working draft assembly of the human genome sequence.ResultsExamination of ESTs derived from brain tissues (excluding brain tumor tissues) suggests that these genes are distributed on chromosomes in a non-random fashion. Some regions on the genome are dense with brain-enriched genes while some regions lack brain-enriched genes, suggesting a significant correlation between distribution of genes along the chromosome and tissue type. ESTs from brain tumor tissues have also been mapped to the human genome working draft. We reveal that some regions enriched in brain genes show a significant decrease in gene expression in brain tumors, and, conversely that some regions lacking in brain genes show an increased level of gene expression in brain tumors.ConclusionsThis report demonstrates a novel approach for tissue specific transcriptome mapping using EST-based quantitative assessment.
Highlights
Genome wide transcriptome maps can provide tools to identify candidate genes that are over-expressed or silenced in certain disease tissue and increase our understanding of the structure and organization of the genome
Full-length cDNA data are currently available for only 10,000 human genes [5], less than one-third of the total using the most conservative recent estimates of human gene numbers [6,7]
Since the number of sequence tags is reported to be proportional to the abundance of cognate transcripts in the tissue or cell type used to make a given cDNA library, the number of Expressed Sequence Tags (ESTs) within a chromosome region should reflect the abundance of the cognate transcripts in that region
Summary
Genome wide transcriptome maps can provide tools to identify candidate genes that are over-expressed or silenced in certain disease tissue and increase our understanding of the structure and organization of the genome. Expressed Sequence Tags (ESTs) from the public dbEST and proprietary Incyte LifeSeq databases were used to derive a transcript map in conjunction with the working draft assembly of the human genome sequence. ESTs have been used extensively for gene discovery and for transcript mapping of genes from a wide number of organisms [2–4]. Even with the finished working draft of the human genome, the generation of a complete and non-redundant catalog of human genes is still a big challenge facing the genome research community. Evidence of differential expression is one of the most important criteria in prioritizing the exploitation of genes in both academic and pharmaceutical research [8–10]
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