A Complex-based Reconstruction of the Saccharomyces cerevisiae Interactome *S⃞
نویسندگان
چکیده
Most cellular processes are performed by proteomic units that interact with each other. These units are often stoichiometrically stable complexes comprised of several proteins. To obtain a faithful view of the protein interactome we must view it in terms of these basic units (complexes and proteins) and the interactions between them. This study makes two contributions toward this goal. First, it provides a new algorithm for reconstruction of stable complexes from a variety of heterogeneous biological assays; our approach combines state-of-the-art machine learning methods with a novel hierarchical clustering algorithm that allows clusters to overlap. We demonstrate that our approach constructs over 40% more known complexes than other recent methods and that the complexes it produces are more biologically coherent even compared with the reference set. We provide experimental support for some of our novel predictions, identifying both a new complex involved in nutrient starvation and a new component of the eisosome complex. Second, we provide a high accuracy algorithm for the novel problem of predicting transient interactions involving complexes. We show that our complex level network, which we call ComplexNet, provides novel insights regarding the protein-protein interaction network. In particular, we reinterpret the finding that "hubs" in the network are enriched for being essential, showing instead that essential proteins tend to be clustered together in essential complexes and that these essential complexes tend to be large.
منابع مشابه
Purification of Saccharomyces cerevisiae eIF4E/eIF4G/Pab1p Complex with Capped mRNA
Protein synthesis is one of the most complex cellular processes, involving numerous translation components that interact in multiple sequential steps. The most complex stage in protein synthesis is the initiation process. The basal set of factors required for translation initiation has been determined, and biochemical, genetic, and structural studies are now beginning to reveal details of their...
متن کاملSaccharomyces cerevisiae TFS9, a novel isolated yeast capable of high caffeine-tolerant and its application in biodecaffeination approach
There is a great call for using microbial bio-decaffeination approach to remove caffeinefrom caffeinated products and industrial wastes. We aimed in this study to screen strainsof yeasts which exhibit high caffeine tolerance and to investigate the bio-degradation ofcaffeine under growth conditions. Sixteen yeast strains were isolated from the cultivatedtea soils collected from sites of northern...
متن کاملمهار رشد رده سرطانی K562 با استفاده از دیواره سلولی استخراج شده از پروبیوتیک‌های Saccharomyces cerevisiae و Saccharomyces boulardi به همراه نانو ذرات روی
Background: Chronic myeloid leukemia is a common cancer in human, so the goal of this study was the use of natural compound such as cell wall obtained from Saccharomyces cerevisiae (S. cerevisiae) and Saccharomyces boulardi (S. boulardi) and zinc nanoparticles on the growth inhibition of K562 cell line. Methods: For cell wall preparation, both yeasts were cultured in a basic medium at a...
متن کاملEffect of Saccharomyces Cerevisiae Yeast and Butyrate Monoglycerides on Performance, Blood Parameters and Nutrients Digestibility in Holstein Suckling Calves
The aim of this study was to investigate the effects of saccharomyces cerevisiae yeast and butyrate monoglycerides on the performance, blood parameters and nutrients digestibility in suckling Holstein calves. For this experiment, 32 newly-born Holstein calves (average age 1-8 days; average weight 38±1 kg) were used in a completely randomized design with 2×2 factorial arrangement, 4 treatmen...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- Molecular & Cellular Proteomics : MCP
دوره 8 شماره
صفحات -
تاریخ انتشار 2009