Data mining:WormMart:Example 5

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How do I retrieve a list of transcription factors which when mutated or targeted by RNAi cause embryonic lethal phenotype?

  • Open WormMart
  • Select Database, e.g. "WormBase Release 188"
  • Select Dataset - "Phenotype"
  • Click on "Filter" link on the left and then on the "+" next to "Phenotype Annotation"
  • Select "Phenotype Inc. Descendents" checkbox and select "embryonic_lethal" from the pull down menu

If you click "Count" button at this point, you should see the number of entries that are annotated with this phenotype (this is not necessary).

Now add a second dataset:

  • Click on second "Dataset" link on the left
  • Choose Additional Dataset - "Gene"
  • Click on "Filter" link on the left (for the second dataset) and then on the "+" next to "Annotation"
  • Select "[Annotation] IDs of Type" checkbox, select "[Function] GO Term ID" and enter GO:0003700 in the box below (corresponds to transcription factor activity)
  • Click on "Attributes" link on the left (for the second dataset) and then on the "+" next to "Function" and select "GO Term Info (merged)" checkbox (if you want to see GO annotations in addition to attributes selected by default, which you can change for each dataset through the Attributes dialog)
  • Press Results button and Export all results to File (also check Unique results only)

Here is what you should see.