ArticleStatistical applications in genetics and molecular biology2010
Generalizing moving averages for tiling arrays using combined p-value statistics.
Article in Statistical applications in genetics and molecular biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Epigenome-wide association study reveals a molecular signature of response to phylloquinone (vitamin K1) supplementation.Epigenetics · 2020Trial
- A Pilot Study on the Impact of Vaping on Adolescent Lung Function and Nasal Epithelial Gene Expression.American journal of respiratory cell and molecular biology · 2025Article
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- Methylation analysis by targeted bisulfite sequencing in large for gestational age (LGA) newborns: the LARGAN cohort.Clinical epigenetics · 2023Article
- Epigenome-Wide Associations of Placental DNA Methylation and Behavioral and Emotional Difficulties in Children at 3 Years of Age.International journal of molecular sciences · 2023Article
- Permutation-based significance analysis reduces the type 1 error rate in bisulphite sequencing data analysis of human umbilical cord blood samples.Epigenetics · 2022Article
- An evaluation of the genome-wide false positive rates of common methods for identifying differentially methylated regions using illumina methylation arrays.Epigenetics · 2022Article
- Pregnancy exposure to phthalates and DNA methylation in male placenta - An epigenome-wide association study.Environment international · 2022Article
- Genome-wide methylation and expression analyses reveal the epigenetic landscape of immune-related diseases for tobacco smoking.Clinical epigenetics · 2021Article
- Pregnancy exposure to synthetic phenols and placental DNA methylation - An epigenome-wide association study in male infants from the EDEN cohort.Environmental pollution (Barking, Essex : 1987) · 2021Article
- Statistical and bioinformatic analysis of hemimethylation patterns in non-small cell lung cancer.BMC cancer · 2021Article
- Article
- An evaluation of supervised methods for identifying differentially methylated regions in Illumina methylation arrays.Briefings in bioinformatics · 2019Review
- DNA methylation modules associate with incident cardiovascular disease and cumulative risk factor exposure.Clinical epigenetics · 2019Article
- Transcriptional profiling analysis predicts potential biomarkers for glaucoma: HGF, AKR1B10 and AKR1C3.Experimental and therapeutic medicine · 2018Article
- Genome-wide analysis of the nucleus accumbens identifies DNA methylation signals differentiating low/binge from heavy alcohol drinking.Alcohol (Fayetteville, N.Y.) · 2017Article
- Alcohol-dose-dependent DNA methylation and expression in the nucleus accumbens identifies coordinated regulation of synaptic genes.Translational psychiatry · 2017Article
- seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data.Bioinformatics (Oxford, England) · 2016Article
- DNA methylation and childhood asthma in the inner city.The Journal of allergy and clinical immunology · 2015Article
- Genetics of gene expression characterizes response to selective breeding for alcohol preference.Genes, brain, and behavior · 2014Article
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3 authors.
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Abstract
High density tiling arrays are an effective strategy for genome-wide identification of transcription factor binding regions. Sliding window methods that calculate moving averages of log ratios or t-statistics have been useful for the analysis of tiling array data. Here, we present a method that generalizes the moving average approach to evaluate sliding windows of p-values by using combined p-value statistics. In particular, the combined p-value framework can be useful in situations when taking averages of the corresponding test-statistic for the hypothesis may not be appropriate or when it is difficult to assess the significance of these averages. We exhibit the strengths of the combined p-values methods on Drosophila tiling array data and assess their ability to predict genomic regions enriched for transcription factor binding. The predictions are evaluated based on their proximity to target genes and their enrichment of known transcription factor binding sites. We also present an application for the generalization of the moving average based on integrating two different tiling array experiments.
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