Genome Database Exercises

 

1)    Are genes in a single metabolic or regulatory pathways located near each other on human chromosomes?

 

Use CGAP (with KEGG pathways) and the UCSC Genome Browser

 

Try the biotin pathway:

http://cgap.nci.nih.gov/Pathways/Kegg/hsa00780

 

Then look up the individual genes on the UCSC Genome Browser:

http://genome.ucsc.edu/

 

Learn about the Ensembl genome browser:

      http://www.embl-heidelberg.de/ExternalInfo/oipa/pr2002/pr031002hg.pdf

 

2)    Compare gene expression in the human brain vs. lung and blood.  Do many of genes that are expressed at higher levels in the brain have obvious neuron-specific functions?

 

Use the CGAP “SAGE Genie”:

http://cgap.nci.nih.gov/SAGE/SDGED

 

Check out the nice “anatomical” display:

http://cgap.nci.nih.gov/SAGE/Viewer?TAG=AACAGCAAAA&CELL=0

 

You could then find the DNA sequences for these differentially expressed genes on the genome and look for common promoter sequences that are responsible for tissue-specific gene expression.

 

3)    The sequence of the mosquito genome has just been completed (Holt et al, Science, Oct 4, 2002, 298:129-149). The Drosophila (fruit fly) genome has been completed for over 2 years (it was the first eukaryotic organism to be completely sequenced). How many genes have been identified in mosquito? What percentage of these have known functions? What is the average level of sequence identity between Mosquito and Drosophila genes (pick a few).

 

-       Use NCBI and ENSEMBL.

 

http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/map_search?chr=agambiae.inf

                  http://www.ensembl.org/Anopheles_gambiae/