Positive correlation between gene coexpression and positional clustering in the zebrafish genome - PubMed (original) (raw)
Positive correlation between gene coexpression and positional clustering in the zebrafish genome
Yen Kaow Ng et al. BMC Genomics. 2009.
Abstract
Background: Co-expressing genes tend to cluster in eukaryotic genomes. This paper analyzes correlation between the proximity of eukaryotic genes and their transcriptional expression pattern in the zebrafish (Danio rerio) genome using available microarray data and gene annotation.
Results: The analyses show that neighbouring genes are significantly coexpressed in the zebrafish genome, and the coexpression level is influenced by the intergenic distance and transcription orientation. This fact is further supported by examining the coexpression level of genes within positional clusters in the neighbourhood model. There is a positive correlation between gene coexpression and positional clustering in the zebrafish genome.
Conclusion: The study provides another piece of evidence for the hypothesis that coexpressed genes do cluster in the eukaryotic genomes.
Figures
Figure 1
Distribution of 10,000 mean R values calculated from randomized genome. Each plot shows the distribution of 10,000 mean R values. Each mean R value is calculated by first randomly permuting the gene order of the genome, and then averaging the R values for every pair of neighboring genes in the resulting gene order. The mean R value in the real genome is shown as a single line on each plot. Both plots are based on the same gene expression dataset: (A) the results on the original dataset (average of mean R = 0.03086, σ = 0.00384); (B) the results after tandem duplicates are removed (average of mean R = 0.03071, σ = 0.00389).
Figure 2
Mean of pair-wise R values in blocks of size 3 to 20 (▲), shown with standard error. This is compared to the mean of 100 values obtained similarly, each from the same analysis after a random permutation of: (1) the gene order of the entire genome (△); (2) the order of genes in each chromosome (□); (3) the order of non-overlapping blocks of 3 consecutive genes (■). Plots (△), (□) and (■) are shown with standard deviations. The points in (A) are from analyses with the full dataset, while (B) are from analyses after tandem duplicates are removed.
Figure 3
Mean R of gene pairs of up to 50 kbp apart. Gene pairs of up to 50 kbp apart were binned according to their intergenic distance, shown with regression lines. (A) is from the full dataset, whereas (B) from the resulting dataset after tandem duplicates are removed.
Figure 4
Mean R of neighboring gene pairs in different -lg _p_-value intervals. Mean R values of neighboring gene pairs in -lg p intervals. All _p_-values were calculated with D = 25K. Gene pairs grouped into parallel, divergent, and convergent orientations are plotted similarly. There is only one gene pair has -lg _p_-value in the interval 5~6, for both the divergent and convergent cases. They are hence omitted from the plot.
Figure 5
Results from the same analysis as in Figure 4 after tandem duplicates are removed.
Figure 6
Average distance between neighboring gene pairs in different -lg _p_-value intervals.
References
- Roy PJ, Stuart JM, Lund J, Kim SK. Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature. 2002;418:975–979. - PubMed
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