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Manchester Centre for Integrative Systems Biology

MCISB Public Databases


Omics

The MCISB contributed to a systems biology study of the effects of growth rate on the levels of gene expression, protein and metabolites in the yeast, Saccharomyces cerevisiae (Castrillo et al., 2007). This study was performed in order to understand how changes in the transcriptome, proteome and metabolome can regulate growth rate in organisms. These measurements were made in yeast which were grown in continuous culture under four nutrient limiting conditions, glucose, ammonium, phosphate and sulphate at three different growth rates. Common changes that were found in the transcriptome, proteome and metabolome were considered to be related in the regulation of growth rate.

The gene expression, protein and metabolite levels that were measured in this study have been stored in three separate, online databases:


Two types of access are provided to each of these databases. An HTML interface is provided for browsing the transcriptomic, proteomic and metabolomic data. MaxdBrowse was used to provide an HTML interface to the transcriptome data whilst that for the proteomics and metabolomics data was deployed using the Pierre software. In addition, Web Service interfaces are provided for programmatic access.


Yeast metabolism

The MCISB organised a jamboree meeting in April 2007 where several groups engaged in creating a consensus network of yeast. While reconciling the different reconstructions was a major focus, the team was also very interested in standardizing the naming of metabolites and following other standard annotation procedures (e.g. MIRIAM). The conclusions have been published in (Herrgård et al., 2008) and the data made available from the YeastNet database, which is implemented according to the B-Net schema. Further information is available here.