CYGD: the Comprehensive Yeast Genome Database

Abstract

The Comprehensive Yeast Genome Database (CYGD) compiles a comprehensive data resource for information on the cellular functions of the yeast Saccharomyces cerevisiae and related species, chosen as the best understood model organism for eukaryotes. The database serves as a common resource generated by a European consortium, going beyond the provision of sequence information and functional annotations on individual genes and proteins. In addition, it provides information on the physical and functional interactions among proteins as well as other genetic elements. These cellular networks include metabolic and regulatory pathways, signal transduction and transport processes as well as co-regulated gene clusters. As more yeast genomes are published, their annotation becomes greatly facilitated using S.cerevisiae as a reference. CYGD provides a way of exploring related genomes with the aid of the S.cerevisiae genome as a backbone and SIMAP, the Similarity Matrix of Proteins. The comprehensive resource is available under http://mips.gsf.de/genre/proj/yeast/.

Genome‐scale metabolic model of methylotrophic yeast Pichia pastoris and its use for in silico analysis of heterologous protein production

“…pletely essential and was confirmed using the S. cerevisiae database [36]. While the results from the knockout simulation of the PpaMBEL1254 model were in good agreement with data found with S. cerevisiae, there is a possibility that these results are not true.…”

Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts

“…Thus, the set of reciprocal gene-loss loci seems biased towards those with functions most likely to be conserved between duplicates. This functional bias increases the potential contribution of reciprocal gene-loss loci to reproductive isolation, because 40% of the Class 3 loci are essential 19 in S. cerevisiae, compared with 20% of Class 4 loci (P , 10 210 , x 2 -test).…”

The Structural Assessment of Glycosylation Sites Database - SAGS – An Overall View on N-Glycosylation

“…Of particular importance is to use an as large as possible data set of sequences with known subcellular localization. On this line we found most useful LOCATE which curates all documented proteins sequences from mouse and human (Sprenger et al, 2008) and CYGD that comprise the documented localization in yeast (Güldener et al, 2005).…”