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NCBI Resources: Gene Expression Exercises

Contains information about the NCBI databases to be used as a teaching tool.

Gene Expression Exercises

Use these scenarios to test your knowledge of the GEO databases.

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Scenario: finding data

You want to find all gene expression studies in GEO that do next generation sequencing on human cancer cells. How would you find these datasets?

Scenario: data visualization

You want to see a visualization of the top differentially expressed genes in the GDS5085 dataset. What Data analysis tool would you use?

Scenario: which database?

You want to know information about expression of the brca2 gene in various tissues and cell lines. Which database is the more efficient way to find this information: GEO DataSets, or GEO Profiles? How many results do you get for studies that have information about this gene in human breast cancer?

Scenario: uncharted data

You find a dataset in GEO that meets your criteria perfectly, but it isn't curated. What tool can you use to analyze uncurated data? Using GSE33253 as an example:

  • Generate a list of the top 250 genes
  • Create a profile graph for the synbindin gene