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POXO: a web-enabled tool series to discover transcription factor binding sites
1 Institute of Biotechnology, University of Helsinki PO Box 56 (Viikinkaari 5), FIN-00014 Helsinki, Finland 2 Department of Biological and Environmental Sciences, Genetics, University of Helsinki PO Box 56 (Viikinkaari 5), FIN-00014 Helsinki, Finland 3 Laboratory of Functional Genomics and Bioinformatics, Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences 4 Deparment of Biochemistry, University of Kuopio PO Box 1627, FIN-70211 Kuopio, Finland 5 Department of Computer Science, University of Kuopio PO Box 1627, FIN-70211 Kuopio, Finland
*To whom correspondence should be addressed. Tel: +358 9 19159115; Fax: +358 9 19159079; Email: liisa.holm{at}helsinki.fi
Received February 14, 2006. Revised March 8, 2006. Accepted April 7, 2006.
We present POXO, a comprehensive tool series to discover transcription factor binding sites from co-expressed genes (www.bioinfo.biocenter.helsinki.fi/poxo). POXO manages tasks such as functional evaluation and grouping of genes, sequence retrieval, pattern discovery and pattern verification. It also allows users to tailor analytical pipelines from these tools, with single mouse clicks. One typical pipeline of POXO begins by examining the biological functions that a set of co-expressed genes are involved in. In this examination, the functional coherence of the gene set is evaluated and representative functions are associated with the gene set. This examination can also be used to group genes into functionally similar subsets, if several biological processes are affected in the experiment. The next step in the pipeline is then to discover over-represented nucleotide patterns from the upstream sequences of the selected gene sets. This enables to investigate the possibility that the genes are co-regulated by common cis-elements. If over-represented patterns are found, similar ones can then be clustered together and be verified. The performance of POXO is demonstrated by analysing expression data from pathogen treated Arabidopsis thaliana. In this example, POXO detected activated gene sets and suggested transcription factors responsible for their regulation.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
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