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Analysis of a human brain transcriptome map.

Qiu P, Benbow L, Liu S, Greene JR, Wang L - BMC Genomics (2002)

Bottom Line: 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.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.This report demonstrates a novel approach for tissue specific transcriptome mapping using EST-based quantitative assessment.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Group and Human Genomic Research Department, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, USA. ping.qiu@spcorp.com

ABSTRACT

Background: 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.

Results: Examination 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.

Conclusions: This report demonstrates a novel approach for tissue specific transcriptome mapping using EST-based quantitative assessment.

No MeSH data available.


Related in: MedlinePlus

Differential expression between tumor tissues vs. non-tumor tissues (chromosome 19). a) An example of transition from a brain low TDF region on chromosome 19 (53 Mbp–58 Mbp) in normal tissue libraries to high TDF region in brain tumor libraries; b) Corresponding non-tumor breast tissue vs. tumor breast tissue transcriptome map on the same chromosome. The brain low TDF region observed that changed to high TDF region in a) was not observed in b).
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Figure 4: Differential expression between tumor tissues vs. non-tumor tissues (chromosome 19). a) An example of transition from a brain low TDF region on chromosome 19 (53 Mbp–58 Mbp) in normal tissue libraries to high TDF region in brain tumor libraries; b) Corresponding non-tumor breast tissue vs. tumor breast tissue transcriptome map on the same chromosome. The brain low TDF region observed that changed to high TDF region in a) was not observed in b).

Mentions: Our analysis strongly suggests that brain-enriched genes are distributed throughout the genome in a non-random fashion. Some regions are dense with brain-enriched genes or brain specific expression. It would be interesting to know if any of these patterns change during tumorgenesis. A similar analysis was performed using ESTs generated from brain tumor libraries and their digital expression profile relative to the pooled tissue was plotted against the genome. The chromosomal distributions of these putative brain tumor enriched transcripts and the normal brain enriched transcripts are quite different. Table 3 lists all the chromosome regions with high TDF in non-tumor brain libraries (TDFNB) which become low TDF or neutral TDF in brain tumor (TDFTB). Chr15, 21–25 Mbp, Chr12, 85–89 Mbp, and Chr18, 45–52 Mbp (Figure 3) are some of the examples. While most of the low TDF regions in normal brain remain low in brain tumor, a few regions did become high TDF regions in brain tumor tissues (Table 3). Chr2, 93–99 Mbp and Chr19, 53–58 Mbp (Figure 4) are two examples. The digital expression profile in those regions was further confirmed by using data from Incyte LifeSeq (data not shown).


Analysis of a human brain transcriptome map.

Qiu P, Benbow L, Liu S, Greene JR, Wang L - BMC Genomics (2002)

Differential expression between tumor tissues vs. non-tumor tissues (chromosome 19). a) An example of transition from a brain low TDF region on chromosome 19 (53 Mbp–58 Mbp) in normal tissue libraries to high TDF region in brain tumor libraries; b) Corresponding non-tumor breast tissue vs. tumor breast tissue transcriptome map on the same chromosome. The brain low TDF region observed that changed to high TDF region in a) was not observed in b).
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC103672&req=5

Figure 4: Differential expression between tumor tissues vs. non-tumor tissues (chromosome 19). a) An example of transition from a brain low TDF region on chromosome 19 (53 Mbp–58 Mbp) in normal tissue libraries to high TDF region in brain tumor libraries; b) Corresponding non-tumor breast tissue vs. tumor breast tissue transcriptome map on the same chromosome. The brain low TDF region observed that changed to high TDF region in a) was not observed in b).
Mentions: Our analysis strongly suggests that brain-enriched genes are distributed throughout the genome in a non-random fashion. Some regions are dense with brain-enriched genes or brain specific expression. It would be interesting to know if any of these patterns change during tumorgenesis. A similar analysis was performed using ESTs generated from brain tumor libraries and their digital expression profile relative to the pooled tissue was plotted against the genome. The chromosomal distributions of these putative brain tumor enriched transcripts and the normal brain enriched transcripts are quite different. Table 3 lists all the chromosome regions with high TDF in non-tumor brain libraries (TDFNB) which become low TDF or neutral TDF in brain tumor (TDFTB). Chr15, 21–25 Mbp, Chr12, 85–89 Mbp, and Chr18, 45–52 Mbp (Figure 3) are some of the examples. While most of the low TDF regions in normal brain remain low in brain tumor, a few regions did become high TDF regions in brain tumor tissues (Table 3). Chr2, 93–99 Mbp and Chr19, 53–58 Mbp (Figure 4) are two examples. The digital expression profile in those regions was further confirmed by using data from Incyte LifeSeq (data not shown).

Bottom Line: 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.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.This report demonstrates a novel approach for tissue specific transcriptome mapping using EST-based quantitative assessment.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Group and Human Genomic Research Department, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, USA. ping.qiu@spcorp.com

ABSTRACT

Background: 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.

Results: Examination 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.

Conclusions: This report demonstrates a novel approach for tissue specific transcriptome mapping using EST-based quantitative assessment.

No MeSH data available.


Related in: MedlinePlus