UCSC$Genome$Browser$and$ ENCODE$tutorialpromoter.bx.psu.edu/Yue_slides.pdf · The Genome Browser project team relies on public funding to support our work. Donations are welcome we

UCSC  Genome  Browser  and  ENCODE  tutorial    

Feng  Yue  Assistant  Professor  

Dept.  of  Biochem  &  Molecular  Biology  Penn  State  School  of  Medicine,    

Outline  

•  Overview  of  UCSC  genome  browser;  •  Search  for  a  gene/genomic  region;  •  Display  a  track  (gene  expression,  TF  binding  sites,  histone  modificaOon,  et  al);  

•  Blat  a  sequence;  •  Search  for  orthologou  sequences;  •  Search  for  datasets  on  ENCODE  website;  •  Slides  and  links  available:  hSp://www.yuelab.org  

UCSC  genome  browser  hSps://genome.ucsc.edu  

Display  TranscripOon  Factor  Binding  Signals  

BLAT:  Search  a  genome  

CTCCTAGTCCAGTGGAGGGAGACAAACACCAATCA  

Search  orthoglous  sequence    genome.ucsc.edu/cgi-­‐bin/hgLiVOver  

chr21  32871466  32871500  

•  QuesOon:  Can  you  find  the  orthologous  regions  using  a  method/too  I  just  showed  you?  – Hint:  you  know  the  genomic  sequence…  

ENCODE:  encyclopedia  of  dna  elements  hSps://www.encodeproject.org