Topics for the exercise

Protein co-variation

Here we use protein co-variation as an estimate of protein complex formation. We explore proteomics data consisting of relative abundance estimates of the proteomes of cancer patients, as quantified through multiplexed mass spectrometry

CORUM protein complex database

As a comparison with our proteomics data, we use the CORUM database that describes the composition of protein complexes in mammalian organisms. The composition of each complex is supported by experimental evidence. As a start, we first load the CORUM database for human protein complexes.

Proteogenomics data from CPTAC

After establishing a collection of experimentally determined human protein complexes using CORUM, we need a source of protein abundance measurements to estimate the covariation of protein abundance amongst complex members. As a source of protein abundance estimates we will use the proteogenomics data generated by the CPTAC consortium. CPTAC publishes large-scale clinical, genome, transcriptome and proteome data of cancer patients. Some of the analysed CPTAC data has been conveniently collected at linkedomics, which we use to load the data into our VM’s storage.