Exercise 2

Go to KEGG Organisms page by clicking KEGG Organism from KEGG home page.
3 or 4 letter code is an entry point of various information on each species. For example, click eco for E. coli.
Species name is a link to DBGET keyword search.
Put "triosephosphate isomerase" as keywords.
Follow a gene ID (b3919) link, then you will see various information on the gene including pathways and modules.

Access to KAAS, or follow KAAS link from the GenomeNet page.
Use human glycolysis gene set and p53 pathway gene set as input queries.
You can submit any combination of the options with the query sequences and your e-mail address.
The result will be stored seven days on the server.
You can see sample results here.

Select tomato from EGENES page.
You will see various information for tomato EST contigs, for example, TCA cycle / Carotenoid biosynthesis from the "Pathway maps" link.
Click CrtL-b in Carotenoid biosynthesis map, then three contigs are found to be assigned to this enzyme.
By Clinking Alingnment button, you can see how this contig are assembled.

Download KegArray for your PC's OS.
You can upload your local data, but also can retrieve microarray data stored in GenomeNet (mainy from Synechocystis and Bacillus subtilis).
Select ex0000142, for example, then array image and scatter plot will be launched.
You can change Ratio threshold and/or Intensity threshold.
Clicking Search button will lead you to the pathway map search result with specified set of genes.
You can also upload metabolomics data from the Compounds panel. Sample data.

Last updated: 26 June, 2012