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Evidence for large domains of similarly expressed genes in the Drosophila genome.

Spellman PT, Rubin GM - J. Biol. (2002)

Bottom Line: We found about 200 groups of adjacent and similarly expressed genes, each having between 10 and 30 members; together these groups account for over 20% of assayed genes.Groups do not appear to show any correlation with polytene banding patterns or other known chromosomal structures, nor were genes within groups functionally related to one another.The mechanism underlying this phenomenon is not yet known.

View Article: PubMed Central - HTML - PubMed

Affiliation: Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3400, USA. spellman@bdgp.lbl.gov

ABSTRACT

Background: Transcriptional regulation in eukaryotes generally operates at the level of individual genes. Regulation of sets of adjacent genes by mechanisms operating at the level of chromosomal domains has been demonstrated in a number of cases, but the fraction of genes in the genome subject to regulation at this level is unknown.

Results: Drosophila gene-expression profiles that were determined from over 80 experimental conditions using high-density oligonucleotide microarrays were searched for groups of adjacent genes that show similar expression profiles. We found about 200 groups of adjacent and similarly expressed genes, each having between 10 and 30 members; together these groups account for over 20% of assayed genes. Each group covers between 20 and 200 kilobase pairs of genomic sequence, with a mean group size of about 100 kilobase pairs. Groups do not appear to show any correlation with polytene banding patterns or other known chromosomal structures, nor were genes within groups functionally related to one another.

Conclusions: Groups of adjacent and co-regulated genes that are not otherwise functionally related in any obvious way can be identified by expression profiling in Drosophila. The mechanism underlying this phenomenon is not yet known.

Show MeSH
The number of genes identified as being in groups when different window sizes are used. In order to identify groups of adjacent, similarly expressed genes, the average pair-wise correlation of gene expression was calculated for genes in a sliding window across the genome, and this process was repeated for windows of different sizes. The net number of genes (that is, the number of genes in groups in the ordered dataset minus the number of genes in groups from the random dataset) is plotted against window size.
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Figure 1: The number of genes identified as being in groups when different window sizes are used. In order to identify groups of adjacent, similarly expressed genes, the average pair-wise correlation of gene expression was calculated for genes in a sliding window across the genome, and this process was repeated for windows of different sizes. The net number of genes (that is, the number of genes in groups in the ordered dataset minus the number of genes in groups from the random dataset) is plotted against window size.

Mentions: To ensure that ten-gene windows were appropriate, we repeated the analysis using windows of various sizes. As the window size increases from two to eight genes, the net number of genes in groups (that is, the genes in groups in the ordered dataset minus genes in groups from the random dataset) increases linearly. At a window size of about ten genes, the net number of genes begins to plateau (Figure 1). This suggests that most groups include about ten genes, so we used a window size of ten for the remainder of our analysis. There are no qualitative differences in the nature of groups identified by larger window sizes.


Evidence for large domains of similarly expressed genes in the Drosophila genome.

Spellman PT, Rubin GM - J. Biol. (2002)

The number of genes identified as being in groups when different window sizes are used. In order to identify groups of adjacent, similarly expressed genes, the average pair-wise correlation of gene expression was calculated for genes in a sliding window across the genome, and this process was repeated for windows of different sizes. The net number of genes (that is, the number of genes in groups in the ordered dataset minus the number of genes in groups from the random dataset) is plotted against window size.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC117248&req=5

Figure 1: The number of genes identified as being in groups when different window sizes are used. In order to identify groups of adjacent, similarly expressed genes, the average pair-wise correlation of gene expression was calculated for genes in a sliding window across the genome, and this process was repeated for windows of different sizes. The net number of genes (that is, the number of genes in groups in the ordered dataset minus the number of genes in groups from the random dataset) is plotted against window size.
Mentions: To ensure that ten-gene windows were appropriate, we repeated the analysis using windows of various sizes. As the window size increases from two to eight genes, the net number of genes in groups (that is, the genes in groups in the ordered dataset minus genes in groups from the random dataset) increases linearly. At a window size of about ten genes, the net number of genes begins to plateau (Figure 1). This suggests that most groups include about ten genes, so we used a window size of ten for the remainder of our analysis. There are no qualitative differences in the nature of groups identified by larger window sizes.

Bottom Line: We found about 200 groups of adjacent and similarly expressed genes, each having between 10 and 30 members; together these groups account for over 20% of assayed genes.Groups do not appear to show any correlation with polytene banding patterns or other known chromosomal structures, nor were genes within groups functionally related to one another.The mechanism underlying this phenomenon is not yet known.

View Article: PubMed Central - HTML - PubMed

Affiliation: Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3400, USA. spellman@bdgp.lbl.gov

ABSTRACT

Background: Transcriptional regulation in eukaryotes generally operates at the level of individual genes. Regulation of sets of adjacent genes by mechanisms operating at the level of chromosomal domains has been demonstrated in a number of cases, but the fraction of genes in the genome subject to regulation at this level is unknown.

Results: Drosophila gene-expression profiles that were determined from over 80 experimental conditions using high-density oligonucleotide microarrays were searched for groups of adjacent genes that show similar expression profiles. We found about 200 groups of adjacent and similarly expressed genes, each having between 10 and 30 members; together these groups account for over 20% of assayed genes. Each group covers between 20 and 200 kilobase pairs of genomic sequence, with a mean group size of about 100 kilobase pairs. Groups do not appear to show any correlation with polytene banding patterns or other known chromosomal structures, nor were genes within groups functionally related to one another.

Conclusions: Groups of adjacent and co-regulated genes that are not otherwise functionally related in any obvious way can be identified by expression profiling in Drosophila. The mechanism underlying this phenomenon is not yet known.

Show MeSH