HAR

Hyejung Won, edited on 02/20/2019

All codes should be run in r/3.5.0

Data requirement

• HAR_coordinate.bed: Supplementary Table 1
• evolutionary gene sets (e.g. HARgene.txt): Supplementary Table 2

We used publicly available datasets that were not included in the Supplementary Table.

• Roadmap Epigenomics: http://www.roadmapepigenomics.org/data/
• phastCons: http://compgen.cshl.edu/phast/
• Disease genes: For detailed reference for each paper, check Won et al.
  • ASD: Iossifov et al., Nature (2014); de Rubeis et al., Nature (2014)
  • Schizophrenia: Fromer et al., Nature (2014); Marshall et al., Nature Genetics (2017)
  • Developmental delay: Deciphering Developmental Disorders Study, Nature (2017)
  • Constrained genes: Kosmicki et al. Nature Genetics (2017)
  • Pathogenic missense variants: Samocha et al., bioRxiv (2017)
• Human vs. Rhesus Macaque expression difference: https://github.com/AllenBrainAtlas/DevRhesusLMD
• ExAC: http://exac.broadinstitute.org/
• Brain expression profiles: Kang et al., Nature (2011)

Reference:

Won et al., Nature Communications (2019) Human evolved regulatory elements modulate genes involved in cortical expansion and neurodevelopmental disease susceptibility.