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