This page includes supplementary information for the Canadian Bioinformatics Workshop [http://bioinformatics.ca/workshops/beyond Interpreting Gene Lists from Omics Studies]
Module 1 - Introduction to Gene Lists
- Lab gene list file: attachment:module1YeastGenes.txt
- Lab URLs:
Synergizer - http://llama.med.harvard.edu/cgi/synergizer/translate
Ensembl BioMart - http://www.ensembl.org/index.html
- Questions:
- Synergizer
- How many genes could be converted to Entrez Gene?
- How many genes could not?
- How many genes were not recognized?
- Could you find conversions elsewhere? (hint: try the Entrez Gene web site)
- Why could YDL023C not be converted to Entrez Gene?
- Why was YER056CA not recognized?
- How many genes had multiple Entrez Gene IDs? Why?
BioMart
- How many Entrez Gene IDs did you input?
- How many Ensembl genes did you get back?
- How many GO annotations did you retrieve?
- What was the most frequent GO term?
- What was the most frequent evidence code?
- Synergizer
Finished early?
Try gathering additional data from BioMart
- Have you tried to collect data for your own gene list?
Additional resources
Challenging ID mapping problems, like having ID lists for multiple species, may require use of multiple ID mapping services to solve. Additional ID mapping services are linked to from http://baderlab.org/IdentifierMapping