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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 Arabidopsis thaliana with quantiles range from 0.1 to 0.9 in increments of 0.1, respectively.
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fig4: Quantile regression plot for Arabidopsis thaliana with quantiles range from 0.1 to 0.9 in increments of 0.1, respectively.

Mentions: The log function was used to transform the data for an improved view of the quantile regions, a method not applied in the analysis above. Distinct patterns in the quantile regression for both the animal and plant species are evident in the analysis. Firstly, the length of the 5′ UTR and the gene expression in both Arabidopsis (Table 1/Figure 4) and Drosophila (Table 4/Figure 7) show a positive correlation in the majority of quantiles, indicating that as the length of the 5′ UTR increases gene expression increases. However, in the Drosophila at the 9th quantile, the pattern changes and shows a negative correlation, indicating that, in this quantile for the Drosophila, the 5′ UTR length increases as the gene expression decreases.


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 Arabidopsis thaliana 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

fig4: Quantile regression plot for Arabidopsis thaliana with quantiles range from 0.1 to 0.9 in increments of 0.1, respectively.
Mentions: The log function was used to transform the data for an improved view of the quantile regions, a method not applied in the analysis above. Distinct patterns in the quantile regression for both the animal and plant species are evident in the analysis. Firstly, the length of the 5′ UTR and the gene expression in both Arabidopsis (Table 1/Figure 4) and Drosophila (Table 4/Figure 7) show a positive correlation in the majority of quantiles, indicating that as the length of the 5′ UTR increases gene expression increases. However, in the Drosophila at the 9th quantile, the pattern changes and shows a negative correlation, indicating that, in this quantile for the Drosophila, the 5′ UTR length increases as the gene expression decreases.

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