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Bioinformatics Advance Access originally published online on September 17, 2008
Bioinformatics 2008 24(22):2602-2607; doi:10.1093/bioinformatics/btn489
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Functional modules integrating essential cellular functions are predictive of the response of leukaemia cells to DNA damage

Katrin Sameith 1,{dagger}, Philipp Antczak 1, Elliot Marston 1, Nil Turan 1, Dieter Maier 3, Tanja Stankovic 2 and Francesco Falciani 1,*

1School of Biosciences and Institute of Biomedical Research (IBR), 2CRUK Institute for Cancer Studies, University of Birmingham, Birmingham, B152TT, UK and 3Biomax Informatics AG, Lochhamer Str. 9, 82152 Martinsried, Germany

*To whom correspondence should be addressed.


  Abstract

Motivation: Childhood B-precursor lymphoblastic leukaemia (ALL) is the most common paediatric malignancy. Despite the fact that 80% of ALL patients respond to anti-cancer drugs, the patho-physiology of this disease is still not fully understood. mRNA expression-profiling studies that have been performed have not yet provided novel insights into the mechanisms behind cellular response to DNA damage. More powerful data analysis techniques may be required for identifying novel functional pathways involved in the cellular responses to DNA damage.

Results: In order to explore the possibility that unforeseen biological processes may be involved in the response to DNA damage, we have developed and applied a novel procedure for the identification of functional modules in ALL cells. We have discovered that the overall activity of functional modules integrating protein degradation and mRNA processing is predictive of response to DNA damage.

Availability: Supplementary material including R code, additional results, experimental datasets, as well as a detailed description of the methodology are available at http://www.bip.bham.ac.uk/vivo/fumo.html.

Contact: f.falciani{at}bham.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: John Quackenbush

{dagger}Present address: Holstege Group, UMC Utrecht, Utrecht, 3508 AB, The Netherlands.

Received on March 12, 2008; revised on September 5, 2008; accepted on September 12, 2008

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