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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
 

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Prediction of cis-regulatory elements of coregulated genes.

We present a computational pipeline to predict cis-regulatory elements composing results based on different algorithms: Clover, Cluster-Buster, an own implementation of human/rat/mouse sequence identity and our ITB algorithm. The procedure uses information from the human genome sequence, NCBI gene annotations, verified eukaryotic promoters ( EPD), experimentally proven binding sites (Transfac) and homologies to mouse and rat (HomGL/HomoloGene). We test the approach on 18 upstream regions of experimentally verified AP-1 target genes. About a half of the known sites belong to high-scoring candidates. Three top-scoring elements are confirmed by Cluster-Buster and high homologies. The same analysis we applied to genes found to be up- or downregulated due to mutated RAS. We performed a detailed literature and computational search for promoter regions. Indications of overrepresented Elk-1 and AP-1 motifs are found via a comparison with shuffled sequences. In some promoters consistent predictions of clustered binding sites were obtained.[1]

References

  1. Prediction of cis-regulatory elements of coregulated genes. Kiełbase, S.M., Blüthgen, N., Sers, C., Schäfer, R., Herzel, H. Genome informatics series : proceedings of the ... Workshop on Genome Informatics. Workshop on Genome Informatics. (2004) [Pubmed]
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