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?