Could be relevant for you SB boys/girls as well... Klaas Stefanie De Bodt wrote:
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=PubMed&list_uids=17764576
Research article . Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors Aakash Chawade , Marcus Brautigam , Angelica Lindlof , Olof Olsson and Bjorn Olsson BMC Genomics 2007, 8:304 doi:10.1186/1471-2164-8-304 Background With the advent of microarray technology, it has become feasible to identify virtually all genes in an organism that are induced by a certain developmental or environmental change. However, relying solely on gene expression data may be of limited value if the aim is to infer the underlying genetic networks. Development of computational methods to obtain more complex networks is therefore desirable. Here we propose one such method and, using cold acclimation in Arabidopsis as an example, demonstrate that the resulting network can be used to identify hitherto un-described putative regulatory pathways. Results A putative network of cold-related genes is identified by applying our proposed method to previously published Arabidopsis microarray data from cold acclimated plants at six different time points and promoter motif sequence data extracted from ~24,000 Arabidopsis promoters, followed by a functional annotation analysis of interacting genes. The inferred network includes some of the previously characterised cold acclimation pathways, and hitherto un-described putative regulatory interactions between transcription factor (TF) genes and other genes, which encode TFs or other proteins. Part of the obtained transcription factor regulatory network is presented here. More detailed information can be accessed from the supplementary data. Conclusions Microarray gene expression data is of tremendous value to characterise global gene expression during environmental stress or during specific developmental stages, but is of even more value when combined with other information sources. Here we applied a rule-based method that combines microarray gene expression data with promoter motif structures inferred from genomic DNA and previous knowledge of the specific transcription factors involved. By using this method to study the cold acclimation process in Arabidopsis, more complex putative genetic regulatory networks than previously described were elucidated. -- ================================================================== Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele@psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ ==================================================================