@inproceedings{f4b05c6c28b94fa4a76d28155b34c203,
title = "Bioinformatics strategies for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing",
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 treatment 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.",
keywords = "Alu elements, Bioinformatics, ChIP-seq, Co/post-transcriptional processing, DNAme, Epigenetic modification, Methyl-CpG, Methylation, NMD, RNA-editing, RNA-seq, Splicing, Transcriptome",
author = "Champion, {Mia D.} and Hlady, {Ryan A.} and Huihuang Yan and Jared Evans and Jeff Nie and Lee, {Jeong Heon} and James Bogenberger and Kannabiran Nandakumar and Jaime Davila and Raymond Moore and Asha Nair and Daniel O'Brien and Zhu, {Yuan Xiao} and Kortum, {K. Martin} and Tamas Ordog and Zhiguo Zhang and Joseph, {Richard W.} and Stewart, {A. Keith} and Kocher, {Jean Pierre} and Eric Jonasch and Robertson, {Keith D.} and Raoul Tibes and Ho, {Thai H.}",
year = "2015",
doi = "10.5220/0005248001630170",
language = "English (US)",
series = "BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015",
publisher = "SciTePress",
pages = "163--170",
editor = "Oscar Pastor and Christine Sinoquet and Ana Fred and Hugo Gamboa and Dirk Elias",
booktitle = "BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015",
note = "6th International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2015 ; Conference date: 12-01-2015 Through 15-01-2015",
}