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Authors: Mia D. Champion 1 ; Ryan A. Hlady 1 ; Huihuang Yan 1 ; Jared Evans 1 ; Jeff Nie 1 ; Jeong-Heon Lee 1 ; James M. Bogenberger 1 ; Kannabiran Nandakumar 1 ; Jaime Davila 1 ; Raymond Moore 1 ; Asha Nair 1 ; Daniel O'Brien 1 ; Yuan-Xiao Zhu 1 ; K. Martin Kortüm 1 ; Tamas Ordog 1 ; Zhiguo Zhang 1 ; Richard W. Joseph 1 ; A. Keith Stewart 1 ; Jean-Pierre Kocher 1 ; Eric Jonasch 2 ; Keith D. Robertson 1 ; Raoul Tibes 1 and Thai H. Ho 1

Affiliations: 1 Mayo Clinic, United States ; 2 The University of Texas MD Anderson Cancer Center, United States

ISBN: 978-989-758-070-3

Keyword(s): Epigenetic Modification, Splicing, RNA-Editing, Co/Post-Transcriptional Processing, Bioinformatics, NMD, Alu Elements, Transcriptome, RNA-seq, Methylation, ChIP-seq, Methyl-CpG, DNAme

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Genomics and Proteomics ; Next Generation Sequencing ; Systems Biology ; Transcriptomics

Abstract: Epigenetic modifications are associated with the regulation of co/post-transcriptional processing and differential transcript isoforms are known to be important during cancer progression. It remains unclear how disruptions of chromatin-based modifications contribute to tumorigenesis and how this knowledge can be leveraged to develop more potent treatment strategies that target specific isoforms or other products of the co/post-transcriptional regulation pathway. Rapid developments in all areas of next-generation sequencing (DNA, RNA-seq, ChIP-seq, Methyl-CpG, etc.) have provided new opportunities to develop novel integration and data-mining approaches, and also allows for exciting hypothesis driven bioinformatics and computational studies. Here, we present a program that we developed and summarize the results of applying our methods to analyze datasets from patient matched tumor or normal (T/N) paired samples, as well as cell lines that were either sensitive or resistant (S/R) to tr eatment with an anti-cancer drug, 5-Azacytidine (http://sourceforge.net/projects/chiprnaseqpro/). We discuss additional options for user-defined approaches and general guidelines for simultaneously analyzing and annotating epigenetic and RNA-seq datasets in order to identify and rank significant regions of epigenetic deregulation associated with aberrant splicing and RNA-editing. (More)

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Paper citation in several formats:
Champion, M.; Hlady, R.; Yan, H.; Evans, J.; Nie, J.; Lee, J.; Bogenberger, J.; Nandakumar, K.; Davila, J.; Moore, R.; Nair, A.; O'Brien, D.; Zhu, Y.; Kortüm , K.; Ordog, T.; Zhang, Z.; Joseph, R.; Stewart, A.; Kocher, J.; Jonasch, E.; Robertson, K.; Tibes, R. and H. Ho, T. (2015). Bioinformatics Strategies for Identifying Regions of Epigenetic Deregulation Associated with Aberrant Transcript Splicing and RNA-editing.In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015) ISBN 978-989-758-070-3, pages 163-170. DOI: 10.5220/0005248001630170

@conference{bioinformatics15,
author={Mia D. Champion. and Ryan A. Hlady. and Huihuang Yan. and Jared Evans. and Jeff Nie. and Jeong{-}Heon Lee. and James M. Bogenberger. and Kannabiran Nandakumar. and Jaime Davila. and Raymond Moore. and Asha Nair. and Daniel O'Brien. and Yuan{-}Xiao Zhu. and K. Martin Kortüm . and Tamas Ordog. and Zhiguo Zhang. and Richard W. Joseph. and A. Keith Stewart. and Jean{-}Pierre Kocher. and Eric Jonasch. and Keith D. Robertson. and Raoul Tibes. and Thai H. Ho.},
title={Bioinformatics Strategies for Identifying Regions of Epigenetic Deregulation Associated with Aberrant Transcript Splicing and RNA-editing},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015)},
year={2015},
pages={163-170},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0005248001630170},
isbn={978-989-758-070-3},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015)
TI - Bioinformatics Strategies for Identifying Regions of Epigenetic Deregulation Associated with Aberrant Transcript Splicing and RNA-editing
SN - 978-989-758-070-3
AU - Champion, M.
AU - Hlady, R.
AU - Yan, H.
AU - Evans, J.
AU - Nie, J.
AU - Lee, J.
AU - Bogenberger, J.
AU - Nandakumar, K.
AU - Davila, J.
AU - Moore, R.
AU - Nair, A.
AU - O'Brien, D.
AU - Zhu, Y.
AU - Kortüm , K.
AU - Ordog, T.
AU - Zhang, Z.
AU - Joseph, R.
AU - Stewart, A.
AU - Kocher, J.
AU - Jonasch, E.
AU - Robertson, K.
AU - Tibes, R.
AU - H. Ho, T.
PY - 2015
SP - 163
EP - 170
DO - 10.5220/0005248001630170

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