Home Validation in Genomics: CpG Island Methylation Revisited
Article
Licensed
Unlicensed Requires Authentication

Validation in Genomics: CpG Island Methylation Revisited

  • Mark R Segal
Published/Copyright: December 26, 2006
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 5 Issue 1

In a recent article in PLoS Genetics, Bock et al., (2006) undertake an extensive computational epigenetics analysis of the ability of DNA sequence-derived features, capturing attributes such as tetramer frequencies, repeats and predicted structure, to predict the methylation status of CpG islands. Their suite of analyses appears highly rigorous with regard to accompanying validation procedures, employing stringent Bonferroni corrections, stratified cross-validation, and follow-up experimental verification. Here, however, we showcase concerns with the validation steps, in part ascribable to the genome scale of the investigation, that serve as a cautionary note and indicate the heightened need for careful selection of analytic and companion validation methods. A series of new analyses of the same CpG island methylation data helps illustrate these issues, not just for this particular study, but also analogous investigations involving high-dimensional predictors with complex between-feature dependencies.

Keywords: multiple testing; cross-validation; local false discovery rate; classification; sequence features
Published Online: 2006-12-26

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

Articles in the same Issue

  1. Article
  2. Low-Order Conditional Independence Graphs for Inferring Genetic Networks
  3. A Generalized Clustering Problem, with Application to DNA Microarrays
  4. A Bayes Regression Approach to Array-CGH Data
  5. Statistical Selection of Maintenance Genes for Normalization of Gene Expressions
  6. Predicting the Strongest Domain-Domain Contact in Interacting Protein Pairs
  7. Dimension Reduction for Classification with Gene Expression Microarray Data
  8. A New Type of Stochastic Dependence Revealed in Gene Expression Data
  9. A New Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity
  10. Quality Optimised Analysis of General Paired Microarray Experiments
  11. Issues of Processing and Multiple Testing of SELDI-TOF MS Proteomic Data
  12. Cross-Validated Bagged Prediction of Survival
  13. Treatment of Uninformative Families in Mean Allele Sharing Tests for Linkage
  14. Quantile-Function Based Null Distribution in Resampling Based Multiple Testing
  15. Combining Results of Microarray Experiments: A Rank Aggregation Approach
  16. Model Selection for Mixtures of Mutagenetic Trees
  17. Pseudo-likelihood for Non-reversible Nucleotide Substitution Models with Neighbour Dependent Rates
  18. A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting
  19. Bayesian Hierarchical Model for Correcting Signal Saturation in Microarrays Using Pixel Intensities
  20. Using Complexity for the Estimation of Bayesian Networks
  21. Detecting Local High-Scoring Segments: a First-Stage Approach for Genome-Wide Association Studies
  22. Examining Protein Structure and Similarities by Spectral Analysis Technique
  23. Parameter Estimation for the Exponential-Normal Convolution Model for Background Correction of Affymetrix GeneChip Data
  24. Approximate Sample Size Calculations with Microarray Data: An Illustration
  25. Numerical Solutions for Patterns Statistics on Markov Chains
  26. A Heuristic Bayesian Method for Segmenting DNA Sequence Alignments and Detecting Evidence for Recombination and Gene Conversion
  27. A Two-Step Multiple Comparison Procedure for a Large Number of Tests and Multiple Treatments
  28. Validation in Genomics: CpG Island Methylation Revisited
  29. An Improved Nonparametric Approach for Detecting Differentially Expressed Genes with Replicated Microarray Data
  30. Letter to the Editor
  31. Treating Expression Levels of Different Genes as a Sample in Microarray Data Analysis: Is it Worth a Risk?
  32. Reader's Reaction
  33. Reader's Reaction to "Dimension Reduction for Classification with Gene Expression Microarray Data" by Dai et al (2006)
https://doi.org/10.2202/1544-6115.1256
Keywords for this article
multiple testing; cross-validation; local false discovery rate; classification; sequence features

Articles in the same Issue

  1. Article
  2. Low-Order Conditional Independence Graphs for Inferring Genetic Networks
  3. A Generalized Clustering Problem, with Application to DNA Microarrays
  4. A Bayes Regression Approach to Array-CGH Data
  5. Statistical Selection of Maintenance Genes for Normalization of Gene Expressions
  6. Predicting the Strongest Domain-Domain Contact in Interacting Protein Pairs
  7. Dimension Reduction for Classification with Gene Expression Microarray Data
  8. A New Type of Stochastic Dependence Revealed in Gene Expression Data
  9. A New Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity
  10. Quality Optimised Analysis of General Paired Microarray Experiments
  11. Issues of Processing and Multiple Testing of SELDI-TOF MS Proteomic Data
  12. Cross-Validated Bagged Prediction of Survival
  13. Treatment of Uninformative Families in Mean Allele Sharing Tests for Linkage
  14. Quantile-Function Based Null Distribution in Resampling Based Multiple Testing
  15. Combining Results of Microarray Experiments: A Rank Aggregation Approach
  16. Model Selection for Mixtures of Mutagenetic Trees
  17. Pseudo-likelihood for Non-reversible Nucleotide Substitution Models with Neighbour Dependent Rates
  18. A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting
  19. Bayesian Hierarchical Model for Correcting Signal Saturation in Microarrays Using Pixel Intensities
  20. Using Complexity for the Estimation of Bayesian Networks
  21. Detecting Local High-Scoring Segments: a First-Stage Approach for Genome-Wide Association Studies
  22. Examining Protein Structure and Similarities by Spectral Analysis Technique
  23. Parameter Estimation for the Exponential-Normal Convolution Model for Background Correction of Affymetrix GeneChip Data
  24. Approximate Sample Size Calculations with Microarray Data: An Illustration
  25. Numerical Solutions for Patterns Statistics on Markov Chains
  26. A Heuristic Bayesian Method for Segmenting DNA Sequence Alignments and Detecting Evidence for Recombination and Gene Conversion
  27. A Two-Step Multiple Comparison Procedure for a Large Number of Tests and Multiple Treatments
  28. Validation in Genomics: CpG Island Methylation Revisited
  29. An Improved Nonparametric Approach for Detecting Differentially Expressed Genes with Replicated Microarray Data
  30. Letter to the Editor
  31. Treating Expression Levels of Different Genes as a Sample in Microarray Data Analysis: Is it Worth a Risk?
  32. Reader's Reaction
  33. Reader's Reaction to "Dimension Reduction for Classification with Gene Expression Microarray Data" by Dai et al (2006)
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 6.11.2025 from https://www.degruyterbrill.com/document/doi/10.2202/1544-6115.1256/html
Scroll to top button