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arXiv · 1303.3332

CruzDB: software for annotation of genomic intervals with UCSC genome-browser data

Brent S Pedersen·Ivana V Yang·Subhajyoti De
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Abstract

The biological significance of genomic features is often context-dependent. We present CruzDB, a fast and intuitive programmatic interface to the UCSC genome browser that facilitates integrative analyses of diverse local and remotely hosted datasets. We showcase the syntax of CruzDB using miRNA-binding sites as examples, and further demonstrate its utility with 3 novel biological discoveries. First, we find that while exons replicate early, introns tend to replicate late, suggesting a complex replication pattern in gene regions. Second, variants associated with cognitive functions map to lincRNA transcripts of relevant function. Third, lamina-associated domains are highly enriched in olfaction-related genes. CruzDB is available at https://github.com/brentp/cruzdb

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Brent S Pedersen, Ivana V Yang, Subhajyoti De. 2013-07-09. CruzDB: software for annotation of genomic intervals with UCSC genome-browser data. https://arxiv.org/abs/1303.3332

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