title: POXO: a web-enabled tool series to discover transcription factor binding sites.
abstract: 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.
authors.affiliation: Institute of Biotechnology, University of Helsinki, PO Box 56 (Viikinkaari 5), FIN-00014 Helsinki, Finland.
authors.forename: Matti
authors.initials: M
authors.lastname: Kankainen
authors.forename: Petri
authors.initials: P
authors.lastname: Pehkonen
authors.forename: Päivi
authors.initials: P
authors.lastname: Rosenstöm
authors.forename: Petri
authors.initials: P
authors.lastname: Törönen
authors.forename: Garry
authors.initials: G
authors.lastname: Wong
authors.forename: Liisa
authors.initials: L
authors.lastname: Holm
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D005786:Gene Expression Regulation; D020407:Internet; D050436:Regulatory Elements, Transcriptional; D017422:Sequence Analysis, DNA; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors