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Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees
Xiaoyu Chen1, Mathieu Blanchette
1McGill Centre for Bioinformatics, 3775 University Street, room 332, Montreal, Quebec, Canada, H3A 2B4. xchen@cs.washington.edu
BMC Bioinformatics
|February 27, 2008
Summary
This study introduces a novel Bayesian network to identify cis-regulatory modules controlling tissue-specific gene expression. The method accurately predicts known modules and uncovers new transcription factor combinations driving specific gene activity.
Area of Science:
- Genomics and Molecular Biology
- Computational Biology
- Bioinformatics
Background:
- Cis-regulatory modules are crucial for controlling gene expression patterns in vertebrates.
- These modules are key determinants of tissue-specific gene activity.
Purpose of the Study:
- To develop a computational approach for identifying cis-regulatory modules.
- To predict modules responsible for tissue-specific gene regulation.
Main Methods:
- A Bayesian network was developed, integrating transcription factor binding sites, expression data, and target gene expression.
- A regression tree models the impact of combined transcription factor binding.
- An unsupervised EM-like algorithm was employed for network parameter learning.
Main Results:
- The approach successfully identified known human liver and erythroid-specific cis-regulatory modules.
- Application to 10 tissues predicted novel transcription factor combinations associated with specific expression patterns.
Conclusions:
- The developed Bayesian network is effective for identifying tissue-specific cis-regulatory modules.
- The method highlights the importance of combinatorial transcription factor binding in regulating tissue-specific gene expression.
Related Concept Videos
02:02Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
02:02Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
01:30General Transcription Factors
Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
02:16Transcription Factors
Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
01:19Survival Tree
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02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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