Authors:
Katherine Duchinski
1
;
Margaret Antonio
2
;
Dennis Watson
3
and
Paul Anderson
1
Affiliations:
1
College of Charleston, United States
;
2
Boston College, United States
;
3
Medical University of South Carolina, United States
Keyword(s):
RNA-sequencing, RNA-Seq, Meta-analysis, Differential Expression, Transcriptomics, Comparative Analysis.
Abstract:
Understanding the genetic basis of disease may lead to the development of life-saving diagnostics and therapeutics.
RNA-sequencing (RNA-seq) gives a snapshot of cellular processes via high-throughput transcriptome
sequencing. Meta-analysis of multiple RNA-Seq experiments has the potential to (a) elucidate gene function
under different conditions and (b) compare results in replicate experiments. To simplify such meta-analyses,
we created the Dataset Exploration And Curation Tool (DEACT), an interactive, user-friendly web application.
DEACT allows users to (1) interactively visualize RNA-Seq data, (2) select genes of interest through
the user interface, and (3) download subsets for downstream analyses. We tested DEACT using two complementary
RNA-seq studies resulting from knockdown and gain-of-function FLI1 in an aggressive breast
cancer cell line. We performed fixed gene-set enrichment analysis on four subsets of genes selected through
DEACT. Each subset implicated different metabolic
pathways, demonstrating the power of DEACT in driving
downstream analysis of complementary RNA-Seq studies.
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