## Modeling Dependencies in Protein-DNA Binding Sites (2003)

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Citations: | 78 - 2 self |

### BibTeX

@INPROCEEDINGS{Barash03modelingdependencies,

author = {Yoseph Barash and Gal Elidan and Nir Friedman and Tommy Kaplan},

title = {Modeling Dependencies in Protein-DNA Binding Sites},

booktitle = {},

year = {2003},

pages = {28--37},

publisher = {ACM Press}

}

### Years of Citing Articles

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### Abstract

The availability of whole genome sequences and high-throughput genomic assays opens the door for in silico analysis of transcription regulation. This includes methods for discovering and characterizing the binding sites of DNA-binding proteins, such as transcription factors. A common representation of transcription factor binding sites is aposition specific score matrix (PSSM). This representation makes the strong assumption that binding site positions are independent of each other. In this work, we explore Bayesian network representations of binding sites that provide different tradeoffs between complexity (number of parameters) and the richness of dependencies between positions. We develop the formal machinery for learning such models from data and for estimating the statistical significance of putative binding sites. We then evaluate the ramifications of these richer representations in characterizing binding site motifs and predicting their genomic locations. We show that these richer representations improve over the PSSM model in both tasks.

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Citation Context ...ill appear in the co-regulated cluster. Similarly, we want the distribution to reflect that few non-regulated genes will appear in the cluster. A more interesting case involves ChIP localization data =-=[29, 35, 38]. -=-In this case the observation is a p-value that the sequence is enriched in the immnuprecipitation assay. A significant localization p-value is an indication that the sequence is bound by the assay’s... |

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