I need enzyme concentration and metabolites concentration values to en-corporate these values in my model and do some simulation.

I searched through some database

yeast metabolome database http://www.ymdb.ca/ brenda and other enzyme databases for enzmye conc and also did some literature search

but couldn't find much of data

where possibly i can get these data ?? is there any other way to do simulation without data.


1 Answer 1


You should take a look at SGD (the Saccharomyces Genome Database), and in particular YeastCyc. Some protein information pages at SGD give estimates of molecules per cell taken from this Nature paper.

Added later in response to some comments:

The question asks about levels of metabolites and of enzymes, not of transcripts. Microarray data can be, at best, only a guide to levels of proteins. Estimating the levels of metabolites from microarray data is a complete non-starter since there are entire layers of regulation that will be ignored. Just to give one example of a pitfall in this approach: you could have high levels of transcript from which you could you could infer high levels of enzyme, but that enzyme could be inactivated by a post-translational modification.

  • $\begingroup$ can't find much of data on YeastCyc and even $\endgroup$ Jun 21, 2013 at 4:11
  • $\begingroup$ try approximating from microarray or RNAseq data.. they are available in GEO and SRA $\endgroup$
    Jun 21, 2013 at 4:16
  • $\begingroup$ Can you elaborate or cite a paper how to estimate concentration of metabolites mainly present in this pathwayubiquinone synthesis from microarray RNAseq data. If any body have done similar thing and documented it please let me know. $\endgroup$ Jun 21, 2013 at 4:37

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