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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan

4 Issues per year


CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

Open Access
Online
ISSN
1613-4516
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Volume 7, Issue 3

Issues

Uncovering the expression patterns of chimeric transcripts using surveys of Affymetrix GeneChips

Joanna Rowsell
  • Departments of Biological and Mathematical Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ United Kingdom of Great Britain and Northern Ireland
  • Institute of Genetics, University of Nottingham, United Kingdom of Great Britain and Northern Ireland
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Renata da Silva Camargo
  • Departments of Biological and Mathematical Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ United Kingdom of Great Britain and Northern Ireland
  • Lonza Biologics plc, Cambridge, United Kingdom of Great Britain and Northern Ireland
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ William B. Langdon
  • Departments of Biological and Mathematical Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ United Kingdom of Great Britain and Northern Ireland
  • Department of Computer Science, King’s College London, United Kingdom of Great Britain and Northern Ireland
  • Other articles by this author:
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/ Maria A. Stalteri
  • Departments of Biological and Mathematical Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, United Kingdom of Great Britain and Northern Ireland
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Andrew P. Harrison
  • Corresponding author
  • Departments of Biological and Mathematical Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, United Kingdom of Great Britain and Northern Ireland
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2010-137

Summary

Background: A chimeric transcript is a single RNA sequence which results from the transcription of two adjacent genes. Recent studies estimate that at least 4% of tandem human gene pairs may form chimeric transcripts. Affymetrix GeneChip data are used to study the expression patterns of tens of thousands of genes and the probe sequences used in these microarrays can potentially map to exotic RNA sequences such as chimeras.

Results: We have studied human chimeras and investigated their expression patterns using large surveys of Affymetrix microarray data obtained from the Gene Expression Omnibus. We show that for six probe sets, a unique probe mapping to a transcript produced by one of the adjacent genes can be used to identify the expression patterns of readthrough transcripts. Furthermore, unique probes mapping to an intergenic exon present only in the MASK-BP3 chimera can be used directly to study the expression levels of this transcript.

Conclusions: We have attempted to implement a new method for identifying tandem chimerism. In this analysis unambiguous probes are needed to measure run-off transcription and probes that map to intergenic exons are particularly valuable for identifying the expression of chimeras.

About the article

Published Online: 2016-10-18

Published in Print: 2010-12-01


Citation Information: Journal of Integrative Bioinformatics, Volume 7, Issue 3, Pages 300–330, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2010-137.

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© 2010 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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