Advanced statistical analysis of RNA-Seq differential gene expression profiles of animal gene-environment interactions

Kelsey Caetano-Anollés, Scott Nixon, Sanjibita Mishra, Sandra L. Rodriguez-Zas

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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 languageEnglish (US)
Title of host publicationProceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014
PublisherInternational Society for Computers and Their Applications
Pages43-47
Number of pages5
ISBN (Print)9781632665140
StatePublished - Jan 1 2014
Event6th International Conference on Bioinformatics and Computational Biology, BICOB 2014 - Las Vegas, NV, United States
Duration: Mar 24 2014Mar 26 2014

Publication series

NameProceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014

Other

Other6th International Conference on Bioinformatics and Computational Biology, BICOB 2014
CountryUnited States
CityLas Vegas, NV
Period3/24/143/26/14

Fingerprint

Gene-Environment Interaction
RNA
Transcriptome
Gene expression
Statistical methods
Animals
Genes
Muscle
Myostatin
Indoleamine-Pyrrole 2,3,-Dioxygenase
RNA Sequence Analysis
Muscular Atrophy
Muscle Development
Mycobacterium bovis
Reward
Growth and Development
Knockout Mice
Substance-Related Disorders
Bacilli
Software packages

ASJC Scopus subject areas

  • Information Systems
  • Health Informatics

Cite this

Caetano-Anollés, K., Nixon, S., Mishra, S., & Rodriguez-Zas, S. L. (2014). Advanced statistical analysis of RNA-Seq differential gene expression profiles of animal gene-environment interactions. In Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014 (pp. 43-47). (Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014). International Society for Computers and Their Applications.

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 proceedingConference contribution

Caetano-Anollés, K, Nixon, S, Mishra, S & Rodriguez-Zas, SL 2014, Advanced statistical analysis of RNA-Seq differential gene expression profiles of animal gene-environment interactions. in Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014. Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014, International Society for Computers and Their Applications, pp. 43-47, 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014, Las Vegas, NV, United States, 3/24/14.
Caetano-Anollés K, Nixon S, Mishra S, Rodriguez-Zas SL. Advanced statistical analysis of RNA-Seq differential gene expression profiles of animal gene-environment interactions. In 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).
Caetano-Anollés, Kelsey ; Nixon, Scott ; Mishra, Sanjibita ; Rodriguez-Zas, Sandra L. / Advanced statistical analysis of RNA-Seq differential gene expression profiles of animal gene-environment interactions. Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014. International Society for Computers and Their Applications, 2014. pp. 43-47 (Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014).
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