MRes Bioinformatics: Systems Biology Lab 2: Networks: Representation & static analysis

Resources

• Analysis and comparison of metabolic pathway databases Ulrike Wittig and Ann De Beuckelaer, Briefings in Bioinformatics 2001 2(2):126-142.

• KEGG: www.genome.ad.jp/kegg

• Pathway Hunter: www.pht.uni-koeln.de

Exercises

1. Give set notation descriptions for the Small Test Graphs 1-6 and Cats, Dog and Rat graph in the lecture notes.

2. Construct adjacency matrices for the undirected Small Test Graphs 1-6 and compute the representation in Base 10 (ordinary numbers).

3. Construct adjacency lists for the directed Small Test Graphs 1-6 and Cats, Dog and Rat graph in the lecture notes.

4. Give a simple algorithm to find paths in a graph and to compute the length of each path. You will have to state how a graph is modelled in your algorithm.

5. Give a simple algorithm to detect circuits in a graph. You will have to state how a graph is modelled in your algorithm.

6. Compute (by hand) paths and circuits for the Small Test Graphs 1-6 and Cats, Dog and Rat graph in the lecture notes.

7. Use Kegg: http://www.genome.ad.jp/kegg-bin/mk_point_html?ec to extract pathways for the following set of EC numbers:

   2.7.2.4
   1.2.1.11
   1.1.1.3
   2.3.1.46
   4.2.99.9
   4.4.1.8
   2.1.1.13
   2.5.1.6
   

8. Use Pathway Hunter: http://www.pht.uni-koeln.de to perform pathway searches.

9. Have a look at the facilities in AraCyc www.arabidopsis.org/biocyc/. There is an active pop-up metabolic map and a search facility at http://www.arabidopsis.org:1555/ARA/server.html. What do you think of the pathway searching facilities?

10. MaizeGDB has some pathway search facilities. Rather unsophisticated...