title: CruzDB: software for annotation of genomic intervals with UCSC genome-browser database.
abstract: BACKGROUND
  The biological significance of genomic features is often context dependent. Annotating a particular dataset with existing external data can provide insight into function.
  
  
  RESULTS
  We present CruzDB, a fast and intuitive programmatic interface to the University of California, Santa Cruz (UCSC) genome browser that facilitates integrative analyses of diverse local and remotely hosted datasets. We showcase the syntax of CruzDB using microRNA binding sites as examples, and further demonstrate its utility with three biological discoveries. First, DNA replication timing is stratified in gene regions-exons tend to replicate early and introns late during S phase. Second, several non-coding variants associated with cognitive functions map to lincRNA transcripts of relevant function, suggesting potential function of these regulatory RNAs in neuronal diseases. Third, lamina-associated genomic regions are highly enriched in olfaction-related genes, indicating a role of nuclear organization in their regulation.
authors.affiliation: Department of Medicine, University of Colorado Denver, School of Medicine, Denver, CO, USA and Molecular Oncology Program, University of Colorado Cancer Center, Aurora, CO, USA.
authors.forename: Brent S
authors.initials: BS
authors.lastname: Pedersen
authors.forename: Ivana V
authors.initials: IV
authors.lastname: Yang
authors.forename: Subhajyoti
authors.initials: S
authors.lastname: De
mesh_terms: D004261:DNA Replication; D030541:Databases, Genetic; D005091:Exons / Q000235:genetics*; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D007438:Introns / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics; D012984:Software; D020506:Untranslated Regions / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D062085:RNA, Long Noncoding; D020506:Untranslated Regions
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