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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

ISBN: 978-989-758-214-1

ISSN: 2184-4305

Keyword(s): RNA-sequencing, RNA-Seq, Meta-analysis, Differential Expression, Transcriptomics, Comparative Analysis.

Related Ontology Subjects/Areas/Topics: Artificial Intelligence ; Bioinformatics ; Biomedical Engineering ; Next Generation Sequencing ; Soft Computing ; Transcriptomics ; Visualization

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. (More)

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Paper citation in several formats:
Duchinski, K.; Antonio, M.; Watson, D. and Anderson, P. (2017). DEACT: An Online Tool for Analysing Complementary RNA-Seq Studies - A Case Study of Knockdown and Upregulated FLI1 in Breast Cancer Cells. In Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, (BIOSTEC 2017) ISBN 978-989-758-214-1 ISSN 2184-4305, pages 154-159. DOI: 10.5220/0006152901540159

@conference{bioinformatics17,
author={Katherine Duchinski. and Margaret Antonio. and Dennis Watson. and Paul Anderson.},
title={DEACT: An Online Tool for Analysing Complementary RNA-Seq Studies - A Case Study of Knockdown and Upregulated FLI1 in Breast Cancer Cells},
booktitle={Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, (BIOSTEC 2017)},
year={2017},
pages={154-159},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0006152901540159},
isbn={978-989-758-214-1},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, (BIOSTEC 2017)
TI - DEACT: An Online Tool for Analysing Complementary RNA-Seq Studies - A Case Study of Knockdown and Upregulated FLI1 in Breast Cancer Cells
SN - 978-989-758-214-1
IS - 2184-4305
AU - Duchinski, K.
AU - Antonio, M.
AU - Watson, D.
AU - Anderson, P.
PY - 2017
SP - 154
EP - 159
DO - 10.5220/0006152901540159

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