About - CYC2008 - Wodak Lab


For many years, the yeast protein complexes catalogued by the Munich Information Center of Protein Sequences (MIPS) database have been widely used to generate protein-protein interaction reference sets. Thanks to advances in proteomics techniques, many new yeast protein complexes have been identified in small-scale and large-scale experiments since the MIPS catalogue was compiled. Although this catalogue has served the community very well, it no longer reflects the current state of knowledge in the field. Using a guided curation approach, we have compiled CYC2008, a comprehensive catalogue of manually curated 408 heteromeric protein complexes in S. cerevisiae reliably backed by small-scale experiments from the literature.

CYC2008 provides an up-to-date reference set of yeast protein complexes for both experimental biologists who work on yeast protein complexes and computational biologists who are interested in predicting protein-protein interactions and protein complexes in yeast.

The CYC2008 catalogue can be downloaded, browsed and searched interactively. We use a searching strategy that allows complexes to be retrieved using a variety of key words. When searching by complex names, the user do not have to enter exact complex name; instead, all complexes that contain a searching word, e.g., "ribosomal", will be listed, and the user can select the intended one for further details. The complex can also be searched by gene names, Gene Ontology terms (GO slim) in the Biological Process and Cellular component categories, Pfam domain names, etc. Alternate gene IDs are obtained from iProClass.

Meanwhile, we also provide a list of 400 protein complexes derived from high-throughput Tandem Affinity Purification/Mass Spectrometry (TAP/MS) studies (See Pu et al, Proteomics 7, 944-60, 2007 for detail). Complexes in this list, denoted as YHTP2008 complex, are manually annotated with current literature citations if they share subunits with literature-reported complexes, and are marked as putative complexes if they are not yet characterized in any small-scale studies. This list is only for downloading, not for browsing and searching.

Related publications

19095691   Pu, S., Wong, J., Turner, B., Cho, E. & Wodak, S.J.
Up-to-date catalogues of yeast protein complexes.
Nucleic Acids Res. 2008 Dec 18

17370254   Pu, S., Vlasblom, J., Emili, A., Greenblatt, J. & Wodak, S.J.
Identifying functional modules in the physical interactome of Saccharomyces cerevisiae.
Proteomics 7, 944-60 (2007).