Dataset Information

Up-to-date catalogues of yeast protein complexes.

ABSTRACT: Gold standard datasets on protein complexes are key to inferring and validating protein-protein interactions. Despite much progress in characterizing protein complexes in the yeast Saccharomyces cerevisiae, numerous researchers still use as reference the manually curated complexes catalogued by the Munich Information Center of Protein Sequences database. Although this catalogue has served the community extremely well, it no longer reflects the current state of knowledge. Here, we report two catalogues of yeast protein complexes as results of systematic curation efforts. The first one, denoted as CYC2008, is a comprehensive catalogue of 408 manually curated heteromeric protein complexes reliably backed by small-scale experiments reported in the current literature. This catalogue represents an up-to-date reference set for biologists interested in discovering protein interactions and protein complexes. The second catalogue, denoted as YHTP2008, comprises 400 high-throughput complexes annotated with current literature evidence. Among them, 262 correspond, at least partially, to CYC2008 complexes. Evidence for interacting subunits is collected for 68 complexes that have only partial or no overlap with CYC2008 complexes, whereas no literature evidence was found for 100 complexes. Some of these partially supported and as yet unsupported complexes may be interesting candidates for experimental follow up. Both catalogues are freely available at: http://wodaklab.org/cyc2008/.

SUBMITTER: Pu S

PROVIDER: S-EPMC2647312 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Up-to-date catalogues of yeast protein complexes.

Pu Shuye S Wong Jessica J Turner Brian B Cho Emerson E Wodak Shoshana J SJ

Nucleic acids research 20081218 3

Gold standard datasets on protein complexes are key to inferring and validating protein-protein interactions. Despite much progress in characterizing protein complexes in the yeast Saccharomyces cerevisiae, numerous researchers still use as reference the manually curated complexes catalogued by the Munich Information Center of Protein Sequences database. Although this catalogue has served the community extremely well, it no longer reflects the current state of knowledge. Here, we report two cata ...[more]

PMID: 19095691

Similar Datasets

Project description:If perturbing two genes together has a stronger or weaker effect than expected, they are said to genetically interact. Genetic interactions are important because they help map gene function, and functionally related genes have similar genetic interaction patterns. Mapping quantitative (positive and negative) genetic interactions on a global scale has recently become possible. This data clearly shows groups of genes connected by predominantly positive or negative interactions, termed monochromatic groups. These groups often correspond to functional modules, like biological processes or complexes, or connections between modules. However it is not yet known how these patterns globally relate to known functional modules. Here we systematically study the monochromatic nature of known biological processes using the largest quantitative genetic interaction data set available, which includes fitness measurements for ?5.4 million gene pairs in the yeast Saccharomyces cerevisiae. We find that only 10% of biological processes, as defined by Gene Ontology annotations, and less than 1% of inter-process connections are monochromatic. Further, we show that protein complexes are responsible for a surprisingly large fraction of these patterns. This suggests that complexes play a central role in shaping the monochromatic landscape of biological processes. Altogether this work shows that both positive and negative monochromatic patterns are found in known biological processes and in their connections and that protein complexes play an important role in these patterns. The monochromatic processes, complexes and connections we find chart a hierarchical and modular map of sensitive and redundant biological systems in the yeast cell that will be useful for gene function prediction and comparison across phenotypes and organisms. Furthermore the analysis methods we develop are applicable to other species for which genetic interactions will progressively become more available.

Project description:Parathyroid carcinoma (PC) is a rare disease responsible for about 1% of primary hyperparathyroidism (PHPT) cases. PC usually has an indolent course, tough to differentiate from the benign causes of PHPT, and the only certain diagnosis is histologic. The gold standard surgical treatment is the en bloc resection associated with the homolateral thyroid loboistmectomy. The aim of this study was to underline the main differences between PC and benign PHPT, along with gathering epidemiological knowledge relative to PC in our region. Data from the regional cancer network (Rete Oncologica del Piemonte e della Valle d'Aosta) since 2007 have been reported, including 21 patients from three hospitals (AO S. Croce e Carle of Cuneo, AOU Città della Salute of Turin, and ASL Città di Torino). The incidence of the disease, gender, age at time of diagnosis, presence of renal and bone symptoms, serum calcium and PTH levels, surgical technique performed, and percentage of recurrence were analysed. PC data were than compared with a series of patients affected by benign PHPT, referred to ASL Città di Torino, Maria Vittoria Hospital, from 2007 to 2019. A PC incidence of 0.05 cases per 100,000 inhabitants was found in our region. Benign forms occurred more frequently in females (p=0.0002), while PC equally occurred in males and females and affected younger patients (p=0.026). Serum calcium and PTH levels were significantly higher in PC patients; accordingly, typical PHPT symptoms were more frequently reported in PC than in benign PHPT. In the PC group, the en bloc resection shows a 13 times lower risk for relapse compared with all the other surgical techniques. PC is equally gender distributed, and the average patients' age is in the fifth decade of life. It is usually functioning, with greater biochemical activity and multiple symptoms. A not-radical surgical resection is associated with a higher recurrence rate. A meticulous presurgical evaluation of PHPT patients showing PC's evocative features is mandatory to obtain a complete disease extirpation.

Dataset Information

Up-to-date catalogues of yeast protein complexes.

Publications

Up-to-date catalogues of yeast protein complexes.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure