CYGD: the Comprehensive Yeast Genome Database

By U. Güldener, M. Münsterkötter, G. Kastenmüller, N. Strack, Jacques van Helden, C. Lemer, J. Richelles, Shoshana J. Wodak, J. García-Martínez, J. Pérez-Ortín and 10 more. Nucleic Acids Res., 2004

350 citations recorded by the source corpus.

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/.

Subfields: Food Science, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5a7efc181a8fa9beb410c9a4c85334343ca00c56

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Citations in the corpus

MPact: the MIPS protein interaction resource on yeast (2005, background): “Accordingly, only few databases of manually compiled PPIs exist. CYGD ( 10 ), DIP”
CFinder: locating cliques and overlapping modules in biological networks (2006, background): “Availability: CFinder (for Windows, Linux and Macintosh) and its manual can be downloaded from http://angel.elte.hu/clustering.”
Why Do Hubs Tend to Be Essential in Protein Networks? (2006, positive): “Caveats Our analysis is based on the PPI data in the Comprehensive Yeast Genome Database [13].”
CORUM: the comprehensive resource of mammalian protein complexes—2019 (2018, background): “To date, there are no reliable estimates about the total number of protein complexes in cells (complexome), but data from single cell organisms provide evidence that more than half of the gene products are involved in the formation of protein complexes (1).”
SIMAP—the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage (2013, background): “Other resources integrate SIMAP result lists directly in their online reports on proteins of interest as GeneCards (30) or CYGD (31).”
The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information (2010, background): “gov/genome/guide/human), the Mouse Genome Database (44), yeasts (45,46), etc.”
CORUM: the comprehensive resource of mammalian protein complexes (2007, background): “Combining information from manual annotation and high-throughput experiments reveals that 2733 (45%) of 6007 protein coding genes in yeast form components of protein complexes (6).”
Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System (2008, background): “org), the Yeast Protein Database [41], and the Munich Information Center for Protein Sequences database [42] and on literature searches.”
CORUM: the comprehensive resource of mammalian protein complexes—2009 (2007, background): “To date there are no reliable estimates about the total number of protein complexes in cells (complexome), but data from single cell organisms provide evidence, that more than half of the gene products are involved in the formation of protein complexes (2).”
Data Mining Techniques for the Life Sciences (2010, background): “RNAdb and NONCODE manually collect GenBank entries that correspond to noncoding RNAs.”