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Comparisons between Arabidopsis thaliana and Drosophila melanogaster in relation to Coding and Noncoding Sequence Length and Gene Expression.

Caldwell R, Lin YX, Zhang R - Int J Genomics (2015)

Bottom Line: Advances in high-quality sequencing technologies and large-scale resource datasets have increased the understanding of relationships and cross-referencing of expression data to the large genome data.Although a negative correlation between expression level and gene (especially transcript) length has been generally accepted, there have been some conflicting results arising from the literature concerning the impacts of different regions of genes, and the underlying reason is not well understood.In conclusion, the information described in this study provides the basis for further exploration into gene regulation with regard to coding and noncoding sequence length.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, University of Wollongong, Northfields Avenue, Keiraville, Wollongong, NSW 2522, Australia.

ABSTRACT
There is a continuing interest in the analysis of gene architecture and gene expression to determine the relationship that may exist. Advances in high-quality sequencing technologies and large-scale resource datasets have increased the understanding of relationships and cross-referencing of expression data to the large genome data. Although a negative correlation between expression level and gene (especially transcript) length has been generally accepted, there have been some conflicting results arising from the literature concerning the impacts of different regions of genes, and the underlying reason is not well understood. The research aims to apply quantile regression techniques for statistical analysis of coding and noncoding sequence length and gene expression data in the plant, Arabidopsis thaliana, and fruit fly, Drosophila melanogaster, to determine if a relationship exists and if there is any variation or similarities between these species. The quantile regression analysis found that the coding sequence length and gene expression correlations varied, and similarities emerged for the noncoding sequence length (5' and 3' UTRs) between animal and plant species. In conclusion, the information described in this study provides the basis for further exploration into gene regulation with regard to coding and noncoding sequence length.

No MeSH data available.


Related in: MedlinePlus

Quantile regression plot for Drosophila melanogaster with quantiles range from 0.1 to 0.9 in increments of 0.1, respectively.
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fig8: Quantile regression plot for Drosophila melanogaster with quantiles range from 0.1 to 0.9 in increments of 0.1, respectively.

Mentions: For the CDS length, each species shows a different pattern among the quantiles. For Arabidopsis (Table 2/Figure 5), the pattern shows a positive correlation for the first six (6) quantiles, and then from the 7th quantile there appears to be negative correlation. This would indicate that within the first six quantiles as the CDS length increases, the gene expression increases, and this is reversed past the 7th quantile. The Drosophila result (Table 5/Figure 8) in all quantiles shows negative correlation, indicating that as the CDS length increases, gene expression decreases. This shows two very distinctive patterns between the animal and plant species when the CDS is examined.


Comparisons between Arabidopsis thaliana and Drosophila melanogaster in relation to Coding and Noncoding Sequence Length and Gene Expression.

Caldwell R, Lin YX, Zhang R - Int J Genomics (2015)

Quantile regression plot for Drosophila melanogaster with quantiles range from 0.1 to 0.9 in increments of 0.1, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4465843&req=5

fig8: Quantile regression plot for Drosophila melanogaster with quantiles range from 0.1 to 0.9 in increments of 0.1, respectively.
Mentions: For the CDS length, each species shows a different pattern among the quantiles. For Arabidopsis (Table 2/Figure 5), the pattern shows a positive correlation for the first six (6) quantiles, and then from the 7th quantile there appears to be negative correlation. This would indicate that within the first six quantiles as the CDS length increases, the gene expression increases, and this is reversed past the 7th quantile. The Drosophila result (Table 5/Figure 8) in all quantiles shows negative correlation, indicating that as the CDS length increases, gene expression decreases. This shows two very distinctive patterns between the animal and plant species when the CDS is examined.

Bottom Line: Advances in high-quality sequencing technologies and large-scale resource datasets have increased the understanding of relationships and cross-referencing of expression data to the large genome data.Although a negative correlation between expression level and gene (especially transcript) length has been generally accepted, there have been some conflicting results arising from the literature concerning the impacts of different regions of genes, and the underlying reason is not well understood.In conclusion, the information described in this study provides the basis for further exploration into gene regulation with regard to coding and noncoding sequence length.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, University of Wollongong, Northfields Avenue, Keiraville, Wollongong, NSW 2522, Australia.

ABSTRACT
There is a continuing interest in the analysis of gene architecture and gene expression to determine the relationship that may exist. Advances in high-quality sequencing technologies and large-scale resource datasets have increased the understanding of relationships and cross-referencing of expression data to the large genome data. Although a negative correlation between expression level and gene (especially transcript) length has been generally accepted, there have been some conflicting results arising from the literature concerning the impacts of different regions of genes, and the underlying reason is not well understood. The research aims to apply quantile regression techniques for statistical analysis of coding and noncoding sequence length and gene expression data in the plant, Arabidopsis thaliana, and fruit fly, Drosophila melanogaster, to determine if a relationship exists and if there is any variation or similarities between these species. The quantile regression analysis found that the coding sequence length and gene expression correlations varied, and similarities emerged for the noncoding sequence length (5' and 3' UTRs) between animal and plant species. In conclusion, the information described in this study provides the basis for further exploration into gene regulation with regard to coding and noncoding sequence length.

No MeSH data available.


Related in: MedlinePlus