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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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fig10: Quantile regression plot for Arabidopsis thaliana with quantiles range from 0.1 to 0.9 in increments of 0.1, respectively.

Mentions: The quantile regression statistical analyses were again applied to the second set of gene expression data to substantiate this method under different gene expression experiments. The results show very similar patterns to the previous gene expression experiment, indicating the model is robust in studying the relationship between gene expression and the length of coding and noncoding regions in different species (Tables 7–12/Figures 10–15). Both gene expression datasets showed statistical significance across all quantile groups, indicating a relationship between the coding and noncoding length and gene expression in animal and plant species.


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

fig10: Quantile regression plot for Arabidopsis thaliana with quantiles range from 0.1 to 0.9 in increments of 0.1, respectively.
Mentions: The quantile regression statistical analyses were again applied to the second set of gene expression data to substantiate this method under different gene expression experiments. The results show very similar patterns to the previous gene expression experiment, indicating the model is robust in studying the relationship between gene expression and the length of coding and noncoding regions in different species (Tables 7–12/Figures 10–15). Both gene expression datasets showed statistical significance across all quantile groups, indicating a relationship between the coding and noncoding length and gene expression in animal and plant species.

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