Home An Empirical Bayesian Method for Estimating Biological Networks from Temporal Microarray Data
Article
Licensed
Unlicensed Requires Authentication

An Empirical Bayesian Method for Estimating Biological Networks from Temporal Microarray Data

  • Andrea Rau , Florence Jaffrézic , Jean-Louis Foulley and Rebecca W Doerge
Published/Copyright: January 15, 2010
Become an author with De Gruyter Brill
Submit Manuscript Author Information
Statistical Applications in Genetics and Molecular Biology
From the journal Statistical Applications in Genetics and Molecular Biology Volume 9 Issue 1

Gene regulatory networks refer to the interactions that occur among genes and other cellular products. The topology of these networks can be inferred from measurements of changes in gene expression over time. However, because the measurement device (i.e., microarrays) typically yields information on thousands of genes over few biological replicates, these systems are quite difficult to elucidate. An approach with proven effectiveness for inferring networks is the Dynamic Bayesian Network. We have developed an iterative empirical Bayesian procedure with a Kalman filter that estimates the posterior distributions of network parameters. We compare our method to similar existing methods on simulated data and real microarray time series data. We find that the proposed method performs comparably on both model-based and data-based simulations in considerably less computational time. The R and C code used to implement the proposed method are publicly available in the R package ebdbNet.

Published Online: 2010-1-15

©2011 Walter de Gruyter GmbH & Co. KG, Berlin/Boston

Articles in the same Issue

  1. Article
  2. Epistatic Interactions
  3. Testing for Gene-Gene Interaction with AMMI Models
  4. A Bayesian Hierarchical Model for Quantitative Real-Time PCR Data
  5. Informative or Noninformative Calls for Gene Expression: A Latent Variable Approach
  6. Detecting Genotyping Error Using Measures of Degree of Hardy-Weinberg Disequilibrium
  7. Optimisation of HMM Topologies Enhances DNA and Protein Sequence Modelling
  8. The Apportionment of Total Genetic Variation by Categorical Analysis of Variance
  9. Dealing with Heterogeneity between Cohorts in Genomewide SNP Association Studies
  10. An Empirical Bayesian Method for Estimating Biological Networks from Temporal Microarray Data
  11. Parameter Estimation in Multiple-Hidden I.I.D. Models from Biological Multiple Alignment
  12. Asymptotic Distribution of the "Orthogonal" Quantitative Transmission Disequilibrium Test in a Structured Population: Exact Formula
  13. Comparing Spatial Maps of Human Population-Genetic Variation Using Procrustes Analysis
  14. An Internal Calibration Method for Protein-Array Studies
  15. Weighted-LASSO for Structured Network Inference from Time Course Data
  16. Trilocus Disequilibrium Analysis of Multiallelic Markers in Outcrossing Populations
  17. Sparse Partial Least Squares Classification for High Dimensional Data
  18. Reconstructability Analysis as a Tool for Identifying Gene-Gene Interactions in Studies of Human Diseases
  19. Sub-Modular Resolution Analysis by Network Mixture Models
  20. Space Oriented Rank-Based Data Integration
  21. The Generalized Odds Ratio as a Measure of Genetic Risk Effect in the Analysis and Meta-Analysis of Association Studies
  22. Network Enrichment Analysis in Complex Experiments
  23. Shrinkage Estimation of Effect Sizes as an Alternative to Hypothesis Testing Followed by Estimation in High-Dimensional Biology: Applications to Differential Gene Expression
  24. Buckley-James Boosting for Survival Analysis with High-Dimensional Biomarker Data
  25. A Random Coefficients Model for Regional Co-Expression Associated with DNA Copy Number
  26. Locating Multiple Interacting Quantitative Trait Loci with the Zero-Inflated Generalized Poisson Regression
  27. Classification of Genomic Sequences via Wavelet Variance and a Self-Organizing Map with an Application to Mitochondrial DNA
  28. Confidently Estimating the Number of DNA Replication Origins
  29. Generalizing Moving Averages for Tiling Arrays Using Combined P-Value Statistics
  30. Lasso Logistic Regression, GSoft and the Cyclic Coordinate Descent Algorithm: Application to Gene Expression Data
  31. Granger Causality Analysis of Human Cell-Cycle Gene Expression Profiles
  32. Mapping Quantitative Trait Loci in a Non-Equilibrium Population
  33. On the Optimal Design of Genetic Variant Discovery Studies
  34. On Optimal Selection of Summary Statistics for Approximate Bayesian Computation
  35. Assessment of LD Matrix Measures for the Analysis of Biological Pathway Association
  36. Optimal Tests Shrinking Both Means and Variances Applicable to Microarray Data Analysis
  37. The Detection of Blur in Affymetrix GeneChips
  38. Regression-Based Multi-Trait QTL Mapping Using a Structural Equation Model
  39. Spatial Clustering of Array CGH Features in Combination with Hierarchical Multiple Testing
  40. Predicting Patient Survival from Longitudinal Gene Expression
  41. Including Probe-Level Measurement Error in Robust Mixture Clustering of Replicated Microarray Gene Expression
  42. Reader's Reaction
  43. An Alternative Model of Type A Dependence in a Gene Set of Correlated Genes
  44. Letter to the Editor
  45. Permutation P-values Should Never Be Zero: Calculating Exact P-values When Permutations Are Randomly Drawn
https://doi.org/10.2202/1544-6115.1513

Articles in the same Issue

  1. Article
  2. Epistatic Interactions
  3. Testing for Gene-Gene Interaction with AMMI Models
  4. A Bayesian Hierarchical Model for Quantitative Real-Time PCR Data
  5. Informative or Noninformative Calls for Gene Expression: A Latent Variable Approach
  6. Detecting Genotyping Error Using Measures of Degree of Hardy-Weinberg Disequilibrium
  7. Optimisation of HMM Topologies Enhances DNA and Protein Sequence Modelling
  8. The Apportionment of Total Genetic Variation by Categorical Analysis of Variance
  9. Dealing with Heterogeneity between Cohorts in Genomewide SNP Association Studies
  10. An Empirical Bayesian Method for Estimating Biological Networks from Temporal Microarray Data
  11. Parameter Estimation in Multiple-Hidden I.I.D. Models from Biological Multiple Alignment
  12. Asymptotic Distribution of the "Orthogonal" Quantitative Transmission Disequilibrium Test in a Structured Population: Exact Formula
  13. Comparing Spatial Maps of Human Population-Genetic Variation Using Procrustes Analysis
  14. An Internal Calibration Method for Protein-Array Studies
  15. Weighted-LASSO for Structured Network Inference from Time Course Data
  16. Trilocus Disequilibrium Analysis of Multiallelic Markers in Outcrossing Populations
  17. Sparse Partial Least Squares Classification for High Dimensional Data
  18. Reconstructability Analysis as a Tool for Identifying Gene-Gene Interactions in Studies of Human Diseases
  19. Sub-Modular Resolution Analysis by Network Mixture Models
  20. Space Oriented Rank-Based Data Integration
  21. The Generalized Odds Ratio as a Measure of Genetic Risk Effect in the Analysis and Meta-Analysis of Association Studies
  22. Network Enrichment Analysis in Complex Experiments
  23. Shrinkage Estimation of Effect Sizes as an Alternative to Hypothesis Testing Followed by Estimation in High-Dimensional Biology: Applications to Differential Gene Expression
  24. Buckley-James Boosting for Survival Analysis with High-Dimensional Biomarker Data
  25. A Random Coefficients Model for Regional Co-Expression Associated with DNA Copy Number
  26. Locating Multiple Interacting Quantitative Trait Loci with the Zero-Inflated Generalized Poisson Regression
  27. Classification of Genomic Sequences via Wavelet Variance and a Self-Organizing Map with an Application to Mitochondrial DNA
  28. Confidently Estimating the Number of DNA Replication Origins
  29. Generalizing Moving Averages for Tiling Arrays Using Combined P-Value Statistics
  30. Lasso Logistic Regression, GSoft and the Cyclic Coordinate Descent Algorithm: Application to Gene Expression Data
  31. Granger Causality Analysis of Human Cell-Cycle Gene Expression Profiles
  32. Mapping Quantitative Trait Loci in a Non-Equilibrium Population
  33. On the Optimal Design of Genetic Variant Discovery Studies
  34. On Optimal Selection of Summary Statistics for Approximate Bayesian Computation
  35. Assessment of LD Matrix Measures for the Analysis of Biological Pathway Association
  36. Optimal Tests Shrinking Both Means and Variances Applicable to Microarray Data Analysis
  37. The Detection of Blur in Affymetrix GeneChips
  38. Regression-Based Multi-Trait QTL Mapping Using a Structural Equation Model
  39. Spatial Clustering of Array CGH Features in Combination with Hierarchical Multiple Testing
  40. Predicting Patient Survival from Longitudinal Gene Expression
  41. Including Probe-Level Measurement Error in Robust Mixture Clustering of Replicated Microarray Gene Expression
  42. Reader's Reaction
  43. An Alternative Model of Type A Dependence in a Gene Set of Correlated Genes
  44. Letter to the Editor
  45. Permutation P-values Should Never Be Zero: Calculating Exact P-values When Permutations Are Randomly Drawn
Sign up now to receive a 20% welcome discount
Institutional Access
How does access work?
Have an idea on how to improve our website?
Please write us.
© 2025 De Gruyter Brill
Downloaded on 10.9.2025 from https://www.degruyterbrill.com/document/doi/10.2202/1544-6115.1513/html
Scroll to top button