Abstract
The binding events of DNA-binding proteins can be extensively characterized by high density ChIP-chip tiling array data. The binding sites and binding occupancy patterns are all very useful to understand the DNA-protein interaction. We propose a statistical procedure which focuses on identifying the interaction signal regions and the patterns of interaction using peakedness and skewness tests. Its utility to annotate the binding signals by analyzing the Tbp1 and Rpb1 ChIP-chip datasets in fission yeast is demonstrated.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Mockler, T.C., Chan, S., Sundaresan, A., Chen, H., Jacobsen, S.E., Ecker, J.R.: Applications of DNA tiling arrays for whole-genome analysis. Genomics 85(1), 1–15 (2005)
Yazaki, J., Gregory, B.D., Ecker, J.R.: Mapping the genome landscape using tiling array technology. Current Opinion in Plant Biology 10(5), 534–542 (2007)
Buck, M.J., Lieb, J.D.: ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83(3), 349–360 (2004)
Iyer, V.R., Horak, C.E., Scafe, C.S., Botstein, D., Snyder, M., Brown, P.O.: Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409(6819), 533–538 (2001)
Qi, Y., Rolfe, A., MacIsaac, K.D., Gerber, G.K., Pokholok, D., Zeitlinger, J., Danford, T., Dowell, R.D., Fraenkel, E., Jaakkola, T.S., Young, R.A., Gifford, D.K.: High-resolution computational models of genome binding events. Nature Biotechnology 24(8), 963–970 (2006)
Kim, T.H., Barrera, L.O., Zheng, M., Qu, C., Singer, M.A., Richmond, T.A., Wu, Y., Green, R.D., Ren, B.: A high-resolution map of active promoters in the human genome. Nature 436(7052), 876–880 (2005)
Zheng, M., Barrera, L.O., Ren, B., Wu, Y.N.: ChIP-chip: data, model, and analysis. Biometrics 63(3), 787–796 (2007)
Glynn, E.F., Megee, P.C., Yu, H., Mistrot, C., Unal, E., Koshland, D.E., DeRisi, J.L., Gerton, J.L.: Genome-wide mapping of the cohesin complex in the yeast saccharomyces cerevisiae. PLoS Biology 2(9), E259 (2004)
Wade, J.T., Struhl, K.: The transition from transcriptional initiation to elongation. Current Opinion in Genetics & Development 18(2), 130–136 (2008)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Li, J., Zhu, L., Eshaghi, M., Liu, J., Karuturi, R.K.M. (2010). Deciphering Transcription Factor Binding Patterns from Genome-Wide High Density ChIP-chip Tiling Array Data. In: Borodovsky, M., Gogarten, J.P., Przytycka, T.M., Rajasekaran, S. (eds) Bioinformatics Research and Applications. ISBRA 2010. Lecture Notes in Computer Science(), vol 6053. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-13078-6_25
Download citation
DOI: https://doi.org/10.1007/978-3-642-13078-6_25
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-13077-9
Online ISBN: 978-3-642-13078-6
eBook Packages: Computer ScienceComputer Science (R0)