Abstract
Chromatin precipitation technologies such as ChIP and FAIRE combined with microarray or sequencing technologies have facilitated identification of DNA-protein interaction sites in the genome of interest. At some loci, the interaction of a nucleus protein with DNA may be distributed instead of being localized. As the high density mapping of the interaction sites is feasible recently, we developed Regional Piecewise Linear Modeling (RPLM) to model the locus-dependent distribution of DNA-protein interaction signal that reveals the heterogeneity of the roles of a protein. It requires fewer parameters to tune than otherwise required by similar methods such as MPeak and JBD. We also incorporate a procedure, using SOM, into RPLM to visualize the interaction locus certainty. The application of our approach on ChIP-chip datasets of two transcription factors has revealed the differences in their roles and shown the major difference between localised and distributed interactions.
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Li, J., Yunus, F., Lei, Z., Eshaghi, M., Liu, J., Karuturi, R.K.M. (2009). Modeling and Visualizing Heterogeneity of Spatial Patterns of Protein-DNA Interaction from High-Density Chromatin Precipitation Mapping Data. In: Măndoiu, I., Narasimhan, G., Zhang, Y. (eds) Bioinformatics Research and Applications. ISBRA 2009. Lecture Notes in Computer Science(), vol 5542. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-01551-9_24
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DOI: https://doi.org/10.1007/978-3-642-01551-9_24
Publisher Name: Springer, Berlin, Heidelberg
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