MRes Bioinformatics: Systems Biology Lab 1: Data sources

Resources

• Enzyme Classification
• Some resources for pathways are at the Protein Resource List
• aMAZE (WorkBench for the representation, management, annotation and analysis of information on networks of cellular processes: genetic regulation, biochemical pathways, signal transductions.)
• KEGG
• BRENDA
• BioCyc
• MetaCyc
• BioBase (TRANSFAC, TRANSPATH,)
• RegulonDB
• DPinteract (DNA-protein interactions)
• BioModels
• Reactome - a curated knowledgebase of biological pathways
• STKE Database of Cell Signaling
• Gene Ontologies, e.g. GO
• PubMed
• IntAct
• Also, in general: EBI services

Exercises

1. Look up a specific pathway, for example the Citrate cycle (TCA cycle), for a specific organism, in the pathway section in KEGG. For example, the pathways for Saccharomyces cerevisiae.
   Now compare that pathway in your organism, with the same pathway in other organisms. http://www.genome.jp/dbget-bin/get_pathway?org_name=sce&mapno=00010

2. Find out what the compound is for the protein structure unknown1, and search out its EC number, and the pathways in which it is involved. Hints:-
   • Look at the file with a text editor etc -- you may be able to find out enough information to start your hunt in...
   • PubMed -- you can have a look at any papers published about this protein.
   • Look up the name in the EC classification databases (Queen Mary College, or EBI), and find out what the EC number is.
   • Search in Brenda to find out what reactions it is involved in, and in what organisms.
   • Follow the links to KEGG, etc
   • Find out what information is held in KEGG -- find the pathways for different organisms
   • ... and in BioCyc
   • Look up the protein in the GO ontology
   • What interaction partners does it have? [see IntAct]

3. Now to the same for unknown2 or unknown2a. You may find that there is less textual information in the structure file that you expected, so may have to use techniques from lectures on proteins to find out what the protein is [or is related to...]. How do we find out what proteins are related to a given structure? You will need to use a structure comparison server. (Perhaps ours: TOPS?)

4. Hmm - now try tracking down information on unknown3. I haven't given you the structure. What have I given you, and how can you use this information? You will need to perform sequence comparison, using e.g. a blast2 server.