ApiDB/EuPathDB Workshop

UI Exercises

Eileen Kraemer, Brian Brunk
Monday, June 9th - 10:15 am

Exercise 1: Secreted Kinases


  1. Begin at the site: ui.cryptodb.org. Making use of the available queries and search strategy functionality, perform the following tasks:
  2. Identify all genes in C. parvum that are putative kinases (hint, use the keyword search). How many genes did you find?
  3. Now, determine the subset of these that have a signal peptide (and thus may be secreted). How many genes are in the result now?
  4. Further reduce the result to contain only those genes that have evidence for expression from EST alignment data. How many genes are in the result now? What are their gene ids?
  5. Alter the search parameters to identify phosphatases rather than kinases. How many genes did you find? What are their gene ids?
  6. Edit the signal peptide query to match any of the advanced parameters rather than all of the advanced parameters. How does this affect the number of genes in the result?

Exercise 2 : Membrane phosphatases


  1. Making use of the available queries and search strategy functionality, find putative secreted or membrane bound enzymes that are between 10,000 and 50,000 molecular weight and have evidence for expression based on proteomics data.
  2. Identify all genes that contain a signal peptide OR (union) a transmembrane domain. How many genes did you find?
  3. Which of these have a GO term "catalytic activity"? How many genes are in the result now?
  4. Of these putative secreted enzymes, which have a molecular weight between 10000 and 50000 daltons? How many genes are in the result now?
  5. Finally, which of these also have evidence for expression in any experiment based on proteomics data? How many genes are in the result now? What are their gene_ids?