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A First Step towards Learning which uORFs Regulate Gene Expression

Selpi ; Bryant, Christopher H. ; Kemp, Graham J. L. ; Cvijovic, Marija

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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Abstract:
We have taken a first step towards learning which upstream Open Reading Frames (uORFs) regulate gene expression (i.e., which uORFs are functional) in the yeast Saccharomyces cerevisiae. We do this by integrating data from several resources and combining a bioinformatics tool, ORF Finder, with a machine learning technique, inductive logic programming (ILP). Here, we report the challenge of using ILP as part of this integrative system, in order to automatically generate a model that identifies functional uORFs. Our method makes searching for novel functional uORFs more efficient than random sampling. An attempt has been made to predict novel functional uORFs using our method. Some preliminary evidence that our model may be biologically meaningful is presented.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Selpi ; Bryant, Christopher H. ; Kemp, Graham J. L. ; Cvijovic, Marija  (2006)  A First Step towards Learning which uORFs Regulate Gene Expression. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 3(2), 2006. Special Issue: 3rd Integrative Bioinformatics Workshop, Harpenden, United Kingdom, 2

Online-Journal: http://journal.imbio.de/index.php?paper_id=31
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2007/212

Also published by Shaker:
Ralf Hofestädt, Thoralf Töpel (eds.). Integrative Bioinformatics -
Yearbook 2006. Shaker, 2007.


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