Comprehensive Yeast Genome Database
Names
More detailed information about this field from each metasource.
Comprehensive Yeast Genome Database
metasource: Fairsharing.org
version: FAIRsharing.org: CYGD; Comprehensive Yeast Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.831m3y; Last edited: June 25, 2021, 2:44 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
CYGD
metasource: Fairsharing.org
version: FAIRsharing.org: CYGD; Comprehensive Yeast Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.831m3y; Last edited: June 25, 2021, 2:44 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Comprehensive yeast genome database (CYGD)
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:15.729097
cygd
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:15.729097
Names
More detailed information about this field from each metasource.
Comprehensive Yeast Genome Database
metasource: Fairsharing.orgversion: FAIRsharing.org: CYGD; Comprehensive Yeast Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.831m3y; Last edited: June 25, 2021, 2:44 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
CYGD
metasource: Fairsharing.orgversion: FAIRsharing.org: CYGD; Comprehensive Yeast Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.831m3y; Last edited: June 25, 2021, 2:44 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Comprehensive yeast genome database (CYGD)
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:15.729097
cygd
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:15.729097
Other names: CYGD, Comprehensive yeast genome database (CYGD), cygd
Names
More detailed information about this field from each metasource.
Comprehensive Yeast Genome Database
metasource: Fairsharing.orgversion: FAIRsharing.org: CYGD; Comprehensive Yeast Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.831m3y; Last edited: June 25, 2021, 2:44 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
CYGD
metasource: Fairsharing.orgversion: FAIRsharing.org: CYGD; Comprehensive Yeast Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.831m3y; Last edited: June 25, 2021, 2:44 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Comprehensive yeast genome database (CYGD)
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:15.729097
cygd
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:15.729097
This source may no longer be available. No known URL could be resolved successfully.
A major part of this information gets extracted by manual annotation from the yeast literature, and results of the systematic functional analysis projects as well as cross-references to other in-house or external databases (NCBI, PIR, PEDANT, EMBL) provide complementary material. In addition information and links to related ascomycetous species are added as far as genomic information is available. This resource has been marked as Uncertain because its project home can no longer be found. Please get in touch if you have any information about this resource.
Description
More detailed information about this field from each metasource.
A major part of this information gets extracted by manual annotation from the yeast literature, and results of the systematic functional analysis projects as well as cross-references to other in-house or external databases (NCBI, PIR, PEDANT, EMBL) provide complementary material. In addition information and links to related ascomycetous species are added as far as genomic information is available. This resource has been marked as Uncertain because its project home can no longer be found. Please get in touch if you have any information about this resource.
metasource: Fairsharing.orgversion: FAIRsharing.org: CYGD; Comprehensive Yeast Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.831m3y; Last edited: June 25, 2021, 2:44 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:15.729097
Webpage:
http://mips.gsf.de/genre/proj/yeast/index.jspWebpage
More detailed information about this field from each metasource.
http://mips.gsf.de/genre/proj/yeast/index.jsp
metasource: Fairsharing.orgversion: FAIRsharing.org: CYGD; Comprehensive Yeast Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.831m3y; Last edited: June 25, 2021, 2:44 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
http://www.helmholtz-muenchen.de/en/ibis/institute/groups/fungal-microbial-genomics/resources/cygd/index.html
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:15.729097
Licence:
Name: Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0Licence name
More detailed information about this field from each metasource.
Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0
metasource: Fairsharing.orgversion: FAIRsharing.org: CYGD; Comprehensive Yeast Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.831m3y; Last edited: June 25, 2021, 2:44 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Licence URL
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http://opendatacommons.org/licenses/pddl/1.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: CYGD; Comprehensive Yeast Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.831m3y; Last edited: June 25, 2021, 2:44 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
CYGD: the Comprehensive Yeast Genome Database
PMID: 15608217
metasource: Fairsharing.org
version: FAIRsharing.org: CYGD; Comprehensive Yeast Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.831m3y; Last edited: June 25, 2021, 2:44 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
http://dx.doi.org/10.1093/nar/gki053
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:15.729097
Publications
More detailed information about this field from each metasource.
CYGD: the Comprehensive Yeast Genome Database
PMID: 15608217
metasource: Fairsharing.org
version: FAIRsharing.org: CYGD; Comprehensive Yeast Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.831m3y; Last edited: June 25, 2021, 2:44 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
http://dx.doi.org/10.1093/nar/gki053
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:15.729097
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CYGD: the Comprehensive Yeast Genome Database
PubMed citations: 136.
136 articles citing: CYGD: the Comprehensive Yeast Genome Database
The relative impact of evolving pleiotropy and mutational correlation on trait divergence. PMID:34864966
Complex Portal 2022: new curation frontiers. PMID:34718729
Databases for Protein-Protein Interactions. PMID:34236665
Predicting gene phenotype by multi-label multi-class model based on essential functional features. PMID:33914130
Identification and evolutionary analysis of the nucleolar proteome of Giardia lamblia. PMID:32228450
Hidden in plain sight: what remains to be discovered in the eukaryotic proteome? PMID:30938578
CORUM: the comprehensive resource of mammalian protein complexes-2019. PMID:30357367
An effective approach to detecting both small and large complexes from protein-protein interaction networks. PMID:29072136
Identifying protein complexes in PPI network using non-cooperative sequential game. PMID:28827597
YMDB 2.0: a significantly expanded version of the yeast metabolome database. PMID:27899612
Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions. PMID:26729909
Identifying novel protein phenotype annotations by hybridizing protein-protein interactions and protein sequence similarities. PMID:26728152
Qualitative and Quantitative Protein Complex Prediction Through Proteome-Wide Simulations. PMID:26492574
A density-based clustering approach for identifying overlapping protein complexes with functional preferences. PMID:26013799
Modularity in the evolution of yeast protein interaction network. PMID:25914446
Clustering PPI data by combining FA and SHC method. PMID:25707632
SLDR: a computational technique to identify novel genetic regulatory relationships. PMID:25350940
Construction and analysis of the protein-protein interaction networks based on gene expression profiles of Parkinson's disease. PMID:25170921
ABC and IFC: modules detection method for PPI network. PMID:24991575
The genome sequence of the highly acetic acid-tolerant Zygosaccharomyces bailii-derived interspecies hybrid strain ISA1307, isolated from a sparkling wine plant. PMID:24453040
Prediction of gene phenotypes based on GO and KEGG pathway enrichment scores. PMID:24312912
Genetic robustness and functional evolution of gene duplicates. PMID:24288370
Protein function prediction by collective classification with explicit and implicit edges in protein-protein interaction networks. PMID:24267980
FunCoup 3.0: database of genome-wide functional coupling networks. PMID:24185702
SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage. PMID:24165881
Brain iron homeostasis: from molecular mechanisms to clinical significance and therapeutic opportunities. PMID:23815406
Evolutionary rate heterogeneity of core and attachment proteins in yeast protein complexes. PMID:23814130
The role of protein interactions in mediating essentiality and synthetic lethality. PMID:23638160
Improved method for protein complex detection using bottleneck proteins. PMID:23566214
The roles of whole-genome and small-scale duplications in the functional specialization of Saccharomyces cerevisiae genes. PMID:23300483
Network rewiring is an important mechanism of gene essentiality change. PMID:23198090
An overview of computational life science databases & exchange formats of relevance to chemical biology research. PMID:22934944
An overlapping module identification method in protein-protein interaction networks. PMID:22595001
Genomic insights into the different layers of gene regulation in yeast. PMID:22567375
PINALOG: a novel approach to align protein interaction networks--implications for complex detection and function prediction. PMID:22419782
Transparent mediation-based access to multiple yeast data sources using an ontology driven interface. PMID:22372975
An integrated framework to model cellular phenotype as a component of biochemical networks. PMID:22190923
HKC: an algorithm to predict protein complexes in protein-protein interaction networks. PMID:22174556
YMDB: the Yeast Metabolome Database. PMID:22064855
Endophytic life strategies decoded by genome and transcriptome analyses of the mutualistic root symbiont Piriformospora indica. PMID:22022265
Prediction of body fluids where proteins are secreted into based on protein interaction network. PMID:21829572
Network archaeology: uncovering ancient networks from present-day interactions. PMID:21533211
Actin-binding protein ABP140 is a methyltransferase for 3-methylcytidine at position 32 of tRNAs in Saccharomyces cerevisiae. PMID:21518805
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. PMID:21472436
Assembling a protein-protein interaction map of the SSU processome from existing datasets. PMID:21423703
Predicting protein phenotypes based on protein-protein interaction network. PMID:21423698
iWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions. PMID:21130772
Identifying protein complexes from interaction networks based on clique percolation and distance restriction. PMID:21047377
Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function. PMID:20852068
The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. PMID:20624719
YeastWeb: a workset-centric web resource for gene family analysis in yeast. PMID:20624324
Functional characterization and topological modularity of molecular interaction networks. PMID:20122208
Cooperativity within proximal phosphorylation sites is revealed from large-scale proteomics data. PMID:20100358
Searching for functional gene modules with interaction component models. PMID:20100324
Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data. PMID:20066130
Finding regulatory DNA motifs using alignment-free evolutionary conservation information. PMID:20047961
PutidaNET: interactome database service and network analysis of Pseudomonas putida KT2440. PMID:19958481
Matrix factorization for recovery of biological processes from microarray data. PMID:19897089
CORUM: the comprehensive resource of mammalian protein complexes--2009. PMID:19884131
Modeling structure-function relationships in synthetic DNA sequences using attribute grammars. PMID:19816554
Functionally guided alignment of protein interaction networks for module detection. PMID:19797409
Reconstructing a network of stress-response regulators via dynamic system modeling of gene regulation. PMID:19787074
Cyanobacterial contribution to the genomes of the plastid-lacking protists. PMID:19664294
Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation. PMID:19502427
Database resources in metabolomics: an overview. PMID:19418229
POINeT: protein interactome with sub-network analysis and hub prioritization. PMID:19379523
Enumeration of condition-dependent dense modules in protein interaction networks. PMID:19213739
Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation. PMID:19156128
Mechanistic characterization of the sulfur-relay system for eukaryotic 2-thiouridine biogenesis at tRNA wobble positions. PMID:19151091
Reconstruction of biochemical networks in microorganisms. PMID:19116616
An evolutionary and structural characterization of mammalian protein complex organization. PMID:19108706
Towards structured output prediction of enzyme function. PMID:19091049
Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data. PMID:18986551
Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PMID:18959479
Assessment of protein set coherence using functional annotations. PMID:18937846
Do amino acid biosynthetic costs constrain protein evolution in Saccharomyces cerevisiae? PMID:18937004
TFIIIC binding sites function as both heterochromatin barriers and chromatin insulators in Saccharomyces cerevisiae. PMID:18849469
Modifying the DPClus algorithm for identifying protein complexes based on new topological structures. PMID:18816408
Identifying gene regulatory modules of heat shock response in yeast. PMID:18811975
Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots. PMID:18791227
The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism. PMID:18687109
A proteomics analysis of yeast Mot1p protein-protein associations: insights into mechanism. PMID:18596064
Microarray data mining: a novel optimization-based approach to uncover biologically coherent structures. PMID:18538024
OREST: the online resource for EST analysis. PMID:18463135
MassNet: a functional annotation service for protein mass spectrometry data. PMID:18448467
A map of human protein interactions derived from co-expression of human mRNAs and their orthologs. PMID:18414481
Deletion of many yeast introns reveals a minority of genes that require splicing for function. PMID:18287520
Fuzzy association rules for biological data analysis: a case study on yeast. PMID:18284669
Prediction of protein-protein interactions using protein signature profiling. PMID:18267299
MIPS: analysis and annotation of genome information in 2007. PMID:18158298
The fungus Ustilago maydis and humans share disease-related proteins that are not found in Saccharomyces cerevisiae. PMID:18096044
CORUM: the comprehensive resource of mammalian protein complexes. PMID:17965090
Direct selection on genetic robustness revealed in the yeast transcriptome. PMID:17878946
Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina. PMID:17868481
Propagation of large concentration changes in reversible protein-binding networks. PMID:17699619
Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data. PMID:17683565
A data integration approach for cell cycle analysis oriented to model simulation in systems biology. PMID:17678529
False positive reduction in protein-protein interaction predictions using gene ontology annotations. PMID:17645798
In search of the biological significance of modular structures in protein networks. PMID:17542644
Reconstruction of human protein interolog network using evolutionary conserved network. PMID:17493278
Improved functional prediction of proteins by learning kernel combinations in multilabel settings. PMID:17493250
A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution. PMID:17298675
Plasticity of genetic interactions in metabolic networks of yeast. PMID:17284612
Genome survey sequencing of the wine spoilage yeast Dekkera (Brettanomyces) bruxellensis. PMID:17277171
Consistent patterns of rate asymmetry and gene loss indicate widespread neofunctionalization of yeast genes after whole-genome duplication. PMID:17194778
Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes. PMID:17158152
A traveling salesman approach for predicting protein functions. PMID:17147783
An inventory of yeast proteins associated with nucleolar and ribosomal components. PMID:17067374
PhenomicDB: a new cross-species genotype/phenotype resource. PMID:16982638
MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics. PMID:16753052
Why do hubs tend to be essential in protein networks? PMID:16751849
Fold designability, distribution, and disease. PMID:16680196
Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. PMID:16642040
LS-NMF: a modified non-negative matrix factorization algorithm utilizing uncertainty estimates. PMID:16569230
Protein protein interactions, evolutionary rate, abundance and age. PMID:16533385
Complex genetic interactions in a quantitative trait locus. PMID:16462944
Discovery of Time-Delayed Gene Regulatory Networks based on temporal gene expression profiling. PMID:16420705
iVici: Interrelational Visualization and Correlation Interface. PMID:16420674
A systematic approach to infer biological relevance and biases of gene network structures. PMID:16407322
FGDB: a comprehensive fungal genome resource on the plant pathogen Fusarium graminearum. PMID:16381910
The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. PMID:16381908
MPact: the MIPS protein interaction resource on yeast. PMID:16381906
SIMAP: the similarity matrix of proteins. PMID:16381858
High-dimensional and large-scale phenotyping of yeast mutants. PMID:16365294
The activity reaction core and plasticity of metabolic networks. PMID:16362071
Characterization of the yeast ionome: a genome-wide analysis of nutrient mineral and trace element homeostasis in Saccharomyces cerevisiae. PMID:16168084
Role of essential genes in mitochondrial morphogenesis in Saccharomyces cerevisiae. PMID:16135527
Munich information center for protein sequences plant genome resources: a framework for integrative and comparative analyses 1(W). PMID:16010004
Data mining tools for the Saccharomyces cerevisiae morphological database. PMID:15980577
AVID: an integrative framework for discovering functional relationships among proteins. PMID:15929793
Dynamical remodeling of the transcriptome during short-term anaerobiosis in Saccharomyces cerevisiae: differential response and role of Msn2 and/or Msn4 and other factors in galactose and glucose media. PMID:15870279
Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. PMID:15693947
A Drosophila protein-interaction map centered on cell-cycle regulators. PMID:15575970
Large-scale exploration of growth inhibition caused by overexpression of genomic fragments in Saccharomyces cerevisiae. PMID:15345056
No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions. PMID:15096275
Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome. PMID:12799350 - http://dx.doi.org/10.1093/nar/gki053
Tags:
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More detailed information about this field from each metasource.
genome
metasource: Fairsharing.org
version: FAIRsharing.org: CYGD; Comprehensive Yeast Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.831m3y; Last edited: June 25, 2021, 2:44 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:15.729097
model organisms
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:15.729097
comparative genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:15.729097
Tags
More detailed information about this field from each metasource.
genome
metasource: Fairsharing.orgversion: FAIRsharing.org: CYGD; Comprehensive Yeast Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.831m3y; Last edited: June 25, 2021, 2:44 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
molecular interactions, pathways and networks
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:15.729097
model organisms
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:15.729097
comparative genomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:15.729097
genome molecular interactions, pathways and networks model organisms comparative genomics
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