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Manchester Centre for Integrative Systems Biology

MCISB Pilot Project - Information Management for Yeast Systems Biology

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.

Data web services

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

Analysis and shim web services

The services below may be used for analysing the data within the pilot project.

Data analyses

Example analyses have been written using the data provided by the above Web Services to Maxd, PRIDE and MEMO. These analyses have been implemented as workflows which have been constructed using Taverna. This software has been adopted by MCISB as a tool for combining the use of MCISB and other third party databases with tools for analysing and integrating the data stored in these repositories.