Transcriptomic analysis by RNA-Seq and gene enrichment analysis

Scott E. Nixon, Dianelys González-Peña, Marcus A. Lawson, Robert H. McCusker, Jason O'connor, Robert Dantzer, Keith W. Kelley, Sandra L. Rodriguez-Zas

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

Abstract

The comprehensive and simultaneous analysis of all genes in a biological sample is a powerful capability attributed to RNA-Seq technology. The ability to analyze the entire transcriptome with RNA-Seq demands analysis that effectively addresses the summary action of genes at the categorical level. Maintaining biological relevance is also important, both for network-level effects and the individual genes that may causally influence these larger changes. In this work, transcriptome analysis of two conditions utilizes a pair-wise comparison between control and immunologically challenged mice. Individual genes were evaluated for successful fit of the model (using a Negative Binomial distribution), then tested for differential expression (FDR-adjusted p-value < 0.05) and grouped into functional categories. A total of 2,079 differentially expressed transcripts representing 1,884 genes were detected. Clustering of enriched Gene Ontology terms Biological Processes, Molecular Functions, and KEGG pathways categories uncovered functional clusters relevant to the immunological response expected from the samples studied (defense and inflammatory response, Enrichment Score = 11.2; leukocyte migration, Enrichment Score = 3.1). These results provide a context to the gene expression differences. Consistent with previous microarray-level transcriptomic studies, our work illustrates the broad analysis and fine detail available with current high throughput RNA sequencing.

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
Pages27-31
Number of pages5
ISBN (Print)9781632665140
StatePublished - 2014
Event6th International Conference on Bioinformatics and Computational Biology, BICOB 2014 - Las Vegas, NV, United States
Duration: Mar 24 2014Mar 26 2014

Other

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

Fingerprint

RNA
Genes
Gene Expression Profiling
Binomial Distribution
Biological Phenomena
High-Throughput Nucleotide Sequencing
Gene Ontology
Cluster Analysis
Microarrays
Gene expression
Leukocytes
Ontology
Technology
Gene Expression
Throughput

Keywords

  • Functional analysis
  • Macrophage
  • RNA-Seq
  • Transcriptome

ASJC Scopus subject areas

  • Information Systems
  • Health Informatics

Cite this

Nixon, S. E., González-Peña, D., Lawson, M. A., McCusker, R. H., O'connor, J., Dantzer, R., ... Rodriguez-Zas, S. L. (2014). Transcriptomic analysis by RNA-Seq and gene enrichment analysis. In Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014 (pp. 27-31). International Society for Computers and Their Applications.

Transcriptomic analysis by RNA-Seq and gene enrichment analysis. / Nixon, Scott E.; González-Peña, Dianelys; Lawson, Marcus A.; McCusker, Robert H.; O'connor, Jason; Dantzer, Robert; Kelley, Keith W.; 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. 27-31.

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

Nixon, SE, González-Peña, D, Lawson, MA, McCusker, RH, O'connor, J, Dantzer, R, Kelley, KW & Rodriguez-Zas, SL 2014, Transcriptomic analysis by RNA-Seq and gene enrichment analysis. in Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014. International Society for Computers and Their Applications, pp. 27-31, 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014, Las Vegas, NV, United States, 3/24/14.
Nixon SE, González-Peña D, Lawson MA, McCusker RH, O'connor J, Dantzer R et al. Transcriptomic analysis by RNA-Seq and gene enrichment analysis. In Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014. International Society for Computers and Their Applications. 2014. p. 27-31
Nixon, Scott E. ; González-Peña, Dianelys ; Lawson, Marcus A. ; McCusker, Robert H. ; O'connor, Jason ; Dantzer, Robert ; Kelley, Keith W. ; Rodriguez-Zas, Sandra L. / Transcriptomic analysis by RNA-Seq and gene enrichment analysis. Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014. International Society for Computers and Their Applications, 2014. pp. 27-31
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