Abstract
RNA-sequencing (RNA-seq) analysis enables to study gene-environment interactions and their impact on the transcriptome. The variety of techniques and software packages for statistical analysis available tailors RNA-seq processing for a specific experiment. Three individual studies, each dissecting a different environmental factor including exercise and a specific immunological challenge, resulted in significant findings. In the first study, mice with the indoleamine 2,3-dioxygenase gene knocked out suffered from the same inflammation as wild type mice when injected with Bacillus Calmette-Guerin, but interestingly did not exhibit any of the depressive symptomatology which characteristically accompanies the infection. RNA-seq data was extracted from these mice, and statistical analysis revealed which genes may be responsible for this phenomenon, which could potentially provide researchers with the tools to create genetic treatments of depression occurring as a byproduct of inflammatory disorders. The second study of gene factors in Myostatin knock-out mice that were either allowed to or restricted from exercise revealed novel gene links for muscle development. Knowledge of genes involved in muscle growth post-development can allow for treatment of muscle atrophy in adults. A final study aimed to use a dependence-like preference for exercise as a murine model for substance addiction. Mice were selected for their drive towards exercise and then either allowed or deprived of the reward. These results showcase the power of advanced statistical methods of RNA-seq analysis.
| Original language | English (US) |
|---|---|
| Title of host publication | Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014 |
| Publisher | International Society for Computers and Their Applications |
| Pages | 43-47 |
| Number of pages | 5 |
| ISBN (Print) | 9781632665140 |
| State | Published - Jan 1 2014 |
| Event | 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014 - Las Vegas, NV, United States Duration: Mar 24 2014 → Mar 26 2014 |
Publication series
| Name | Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014 |
|---|
Other
| Other | 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014 |
|---|---|
| Country | United States |
| City | Las Vegas, NV |
| Period | 3/24/14 → 3/26/14 |
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ASJC Scopus subject areas
- Information Systems
- Health Informatics
Cite this
Advanced statistical analysis of RNA-Seq differential gene expression profiles of animal gene-environment interactions. / Caetano-Anollés, Kelsey; Nixon, Scott; Mishra, Sanjibita; Rodriguez-Zas, Sandra L.
Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014. International Society for Computers and Their Applications, 2014. p. 43-47 (Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
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TY - GEN
T1 - Advanced statistical analysis of RNA-Seq differential gene expression profiles of animal gene-environment interactions
AU - Caetano-Anollés, Kelsey
AU - Nixon, Scott
AU - Mishra, Sanjibita
AU - Rodriguez-Zas, Sandra L.
PY - 2014/1/1
Y1 - 2014/1/1
N2 - RNA-sequencing (RNA-seq) analysis enables to study gene-environment interactions and their impact on the transcriptome. The variety of techniques and software packages for statistical analysis available tailors RNA-seq processing for a specific experiment. Three individual studies, each dissecting a different environmental factor including exercise and a specific immunological challenge, resulted in significant findings. In the first study, mice with the indoleamine 2,3-dioxygenase gene knocked out suffered from the same inflammation as wild type mice when injected with Bacillus Calmette-Guerin, but interestingly did not exhibit any of the depressive symptomatology which characteristically accompanies the infection. RNA-seq data was extracted from these mice, and statistical analysis revealed which genes may be responsible for this phenomenon, which could potentially provide researchers with the tools to create genetic treatments of depression occurring as a byproduct of inflammatory disorders. The second study of gene factors in Myostatin knock-out mice that were either allowed to or restricted from exercise revealed novel gene links for muscle development. Knowledge of genes involved in muscle growth post-development can allow for treatment of muscle atrophy in adults. A final study aimed to use a dependence-like preference for exercise as a murine model for substance addiction. Mice were selected for their drive towards exercise and then either allowed or deprived of the reward. These results showcase the power of advanced statistical methods of RNA-seq analysis.
AB - RNA-sequencing (RNA-seq) analysis enables to study gene-environment interactions and their impact on the transcriptome. The variety of techniques and software packages for statistical analysis available tailors RNA-seq processing for a specific experiment. Three individual studies, each dissecting a different environmental factor including exercise and a specific immunological challenge, resulted in significant findings. In the first study, mice with the indoleamine 2,3-dioxygenase gene knocked out suffered from the same inflammation as wild type mice when injected with Bacillus Calmette-Guerin, but interestingly did not exhibit any of the depressive symptomatology which characteristically accompanies the infection. RNA-seq data was extracted from these mice, and statistical analysis revealed which genes may be responsible for this phenomenon, which could potentially provide researchers with the tools to create genetic treatments of depression occurring as a byproduct of inflammatory disorders. The second study of gene factors in Myostatin knock-out mice that were either allowed to or restricted from exercise revealed novel gene links for muscle development. Knowledge of genes involved in muscle growth post-development can allow for treatment of muscle atrophy in adults. A final study aimed to use a dependence-like preference for exercise as a murine model for substance addiction. Mice were selected for their drive towards exercise and then either allowed or deprived of the reward. These results showcase the power of advanced statistical methods of RNA-seq analysis.
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M3 - Conference contribution
AN - SCOPUS:84905841425
SN - 9781632665140
T3 - Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014
SP - 43
EP - 47
BT - Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014
PB - International Society for Computers and Their Applications
ER -