In these examples we use a set of potential Sp1 binding sites that were identified using a human promoter array.

Example 1

Which of the enriched sites overlap with known DNA elements such as CpG islands?

See ScreenCast

This analysis involves the following steps:

  • Get data → upload interval bed file from computer
    • View in main panel
    • Display in UCSC browser
  • Get data → UCSC table browser
  • Get data for CpG islands for entire genome
  • Operate on genomic intervals → intersect
  • Intersect CpG island with interval bed file
    • Edit title
    • View list in main panel
    • Save the list
  • Create a custom track displaying all three datasets:
    • Sp1 versus CpG
    • CpG islands
    • Sp1 sites

Example 2

What RefSeq genes are within 5000bp of my transcription factor binding sites?

see ScreenCast

This analysis involves the following steps:

  • Get data → upload interval bed file from computer
  • Operate on genomic intervals → Get flanks
  • 5,000 bp downstream, no offset for result interval bed file
  • Rename new file intervals 5000bp downstream
  • Get data → UCSC table browser
  • Get RefSeq gene data
  • Operate on genomic intervals –> intersect
  • Intersect RefSeq genes with interval 5000 bp downstream file