Transcription factor binding site prediction with multivariate gene expression data
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Publication:2482984
Abstract: Multi-sample microarray experiments have become a standard experimental method for studying biological systems. A frequent goal in such studies is to unravel the regulatory relationships between genes. During the last few years, regression models have been proposed for the de novo discovery of cis-acting regulatory sequences using gene expression data. However, when applied to multi-sample experiments, existing regression based methods model each individual sample separately. To better capture the dynamic relationships in multi-sample microarray experiments, we propose a flexible method for the joint modeling of promoter sequence and multivariate expression data. In higher order eukaryotic genomes expression regulation usually involves combinatorial interaction between several transcription factors. Experiments have shown that spacing between transcription factor binding sites can significantly affect their strength in activating gene expression. We propose an adaptive model building procedure to capture such spacing dependent cis-acting regulatory modules. We apply our methods to the analysis of microarray time-course experiments in yeast and in Arabidopsis. These experiments exhibit very different dynamic temporal relationships. For both data sets, we have found all of the well-known cis-acting regulatory elements in the related context, as well as being able to predict novel elements.
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Cites work
- A Modified Bayes Information Criterion with Applications to the Analysis of Comparative Genomic Hybridization Data
- Coupling hidden Markov models for the discovery of Cis-regulatory modules in multiple species
- Multivariate adaptive regression splines
- Transcription factor binding site prediction with multivariate gene expression data
Cited in
(13)- Informative transcription factor selection using support vector machine-based generalized approximate cross validation criteria
- Research in Computational Molecular Biology
- Transcription factor binding site prediction with multivariate gene expression data
- An OLS-based predictor test for a single-index model for predicting transcription rate from histone acetylation level
- Advances in Neural Networks – ISNN 2005
- Research in Computational Molecular Biology
- Research in Computational Molecular Biology
- A Mixed Model Approach to Identify Yeast Transcriptional Regulatory Motifs via Microarray Experiments
- Statistical significance of combinatorial regulations
- Identifying transcription factor targets using enhanced Bayesian classifier
- Prediction of motifs based on a repeated-measures model for integrating cross-species sequence and expression data
- Statistical methods in integrative analysis for gene regulatory modules
- Flexible statistical modelling of the occurrences of transcription factor binding sites along a DNA sequence
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