title: XSAnno: a framework for building ortholog models in cross-species transcriptome comparisons.
abstract: BACKGROUND
  The accurate characterization of RNA transcripts and expression levels across species is critical for understanding transcriptome evolution. As available RNA-seq data accumulate rapidly, there is a great demand for tools that build gene annotations for cross-species RNA-seq analysis. However, prevailing methods of ortholog annotation for RNA-seq analysis between closely-related species do not take inter-species variation in mappability into consideration.
  
  
  RESULTS
  Here we present XSAnno, a computational framework that integrates previous approaches with multiple filters to improve the accuracy of inter-species transcriptome comparisons. The implementation of this approach in comparing RNA-seq data of human, chimpanzee, and rhesus macaque brain transcriptomes has reduced the false discovery of differentially expressed genes, while maintaining a low false negative rate.
  
  
  CONCLUSIONS
  The present study demonstrates the utility of the XSAnno pipeline in building ortholog annotations and improving the accuracy of cross-species transcriptome comparisons.
authors.forename: Ying
authors.initials: Y
authors.lastname: Zhu
authors.forename: Mingfeng
authors.initials: M
authors.lastname: Li
authors.forename: André M M
authors.initials: AM
authors.lastname: Sousa
authors.affiliation: Department of Neurobiology, Kavli Institute for Neuroscience, Yale School of Medicine, 06510 New Haven, CT, USA. nenad.sestan@yale.edu.
authors.forename: Nenad
authors.initials: N
authors.lastname: Sestan
mesh_terms: D000818:Animals; D001921:Brain / Q000378:metabolism; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D016678:Genome; D015894:Genome, Human; D006801:Humans; D008253:Macaca mulatta / Q000235:genetics; D008957:Models, Genetic; D002679:Pan troglodytes / Q000235:genetics; D017397:Prefrontal Cortex / Q000378:metabolism; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D013045:Species Specificity