ArticleJournal of computational biology : a journal of computational molecular cell biology2024
Fast Context-Aware Analysis of Genome Annotation Colocalization.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
An annotation is a set of genomic intervals sharing a particular function or property. Examples include genes or their exons, sequence repeats, regions with a particular epigenetic state, and copy number variants. A common task is to compare two annotations to determine if one is enriched or depleted in the regions covered by the other. We study the problem of assigning statistical significance to such a comparison based on a null model representing random unrelated annotations. To incorporate more background information into such analyses, we propose a new null model based on a Markov chain that differentiates among several genomic contexts. These contexts can capture various confounding factors, such as GC content or assembly gaps. We then develop a new algorithm for estimating
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