Nucleic Acids Research, 2004, Vol. 32, Database issue D311-D314
© 2004 Oxford University Press
Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms
Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305-5120, USA and 1 Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton University, Washington Road, Princeton, NJ 08544, USA
*To whom correspondence should be addressed. Tel: +1 650 723 7541; Fax: +1 650 723 7016; Email: cherry{at}genome.stanford.edu
Received September 11, 2003; Accepted September 15, 2003
 |
ABSTRACT |
|---|
 TOP ABSTRACT INTRODUCTIONFUNGAL ALIGNMENT VIEWERSEQUENCE SIMILARITY QUERY TOOLOTHER NEW TOOLSSUMMARYREFERENCES |
|---|
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/), a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, has recently developed several new resources that allow the comparison and integration of information on a genome-wide scale, enabling the user not only to find detailed information about individual genes, but also to make connections across groups of genes with common features and across different species. The Fungal Alignment Viewer displays alignments of sequences from multiple fungal genomes, while the Sequence Similarity Query tool displays PSI-BLAST alignments of each S.cerevisiae protein with similar proteins from any species whose sequences are contained in the non-redundant (nr) protein data set at NCBI. The Yeast Biochemical Pathways tool integrates groups of genes by their common roles in metabolism and displays the metabolic pathways in a graphical form. Finally, the Find Chromosomal Features search interface provides a versatile tool for querying multiple types of information in SGD.
|
INTRODUCTION |
|---|
|
TOPABSTRACTINTRODUCTIONFUNGAL ALIGNMENT VIEWERSEQUENCE SIMILARITY QUERY TOOLOTHER NEW TOOLSSUMMARYREFERENCES |
|---|
The Saccharomyces Genome Database (SGD) collects and organizes biological information about genes and proteins of the yeast Saccharomyces cerevisiae from the scientific literature, and presents this information on individual Locus Pages for each yeast gene. In addition to collecting detailed information about S.cerevisiae genes and proteins, SGD is continuing to develop new ways for users to visualize the relationships of yeast genes to one another and to similar genes and proteins from different species. The new tools described below help place individual genes in a larger biological context, using flexible interfaces that allow users to choose the format in which results are presented, or to use the results generated by one tool as a starting point for analysis with another tool.
|
FUNGAL ALIGNMENT VIEWER |
|---|
|
TOPABSTRACTINTRODUCTIONFUNGAL ALIGNMENT VIEWERSEQUENCE SIMILARITY QUERY TOOLOTHER NEW TOOLSSUMMARYREFERENCES |
|---|
The Fungal Alignment Viewer (Fig. 1), accessible from the Comparison Resources pulldown menu in the right-hand column of the Locus Page, displays available sequences from other fungal genomes that have similarity to a predicted protein sequence from S.cerevisiae. At the top of the viewer is a dendrogram showing the relationships between the sequences, as determined using ClustalW (1). The next portion of the viewer displays the ClustalW alignment itself, with a control menu. The default display option is to include all available fungal protein sequences in the alignment. Colored highlighting provides easy visualization of the degree of sequence conservation: amino acid residues identical in all sequences are highlighted in yellow; those sharing strong similarity in pink; and those sharing weak similarity in green. All sequences are displayed at the bottom of the page. Each is also available on an individual page, in either FASTA or GCG format, by clicking on the name of that sequence in the alignment.
|
The selection control menu above the alignment allows the user to regenerate the alignment using custom parameters. The left side of the menu allows selection from the available sequences, while the right side of the menu allows selection of various alignment types: protein, DNA from the open reading frame (ORF), the upstream flanking DNA, the downstream flanking DNA, or the ORF DNA plus upstream and downstream flanking regions. This provides a quick and easy way to customize the alignment for specific sequences or regions of interest, or to remove partial sequences from the alignment.
Currently the Fungal Alignment Viewer provides access to sequences from several other Saccharomyces genomes, including those of four closely related sensu stricto species (Saccharomyces paradoxus, Saccharomyces mikatae, Saccharomyces kudriavzevii and Saccharomyces bayanus) and two more distantly related sensu lato species (Saccharomyces castellii and Saccharomyces kluyveri). The genomes of S.paradoxus, S.mikatae and S.bayanus were sequenced at 6–8x coverage by the Fungal Genome Initiative at the Whitehead Institute (2). The genomes of S.mikatae, S.bayanus, S.kudriavzevii, S.castellii and S.kluyveri were sequenced at 2–4x coverage by Mark Johnston’s group at Washington University (3). The availability of sequence data from the closely related sensu stricto species allows the evaluation of conservation in non-protein coding features such as regulatory elements, while data from the more distantly related sensu lato species are valuable in the analysis of sequence conservation in protein sequences and domains. The Fungal Alignment Viewer will be a dynamic resource not limited to the data currently available. Current plans include the addition of sequences from Schizosaccharomyces pombe, Candida albicans and other fungi as sequence information becomes available.
An additional tool, the Synteny Viewer (not shown; also accessible from the Comparison Resources pulldown menu), visualizes the conserved order of genes amongst the three sensu stricto species sequenced by the Fungal Genome Initiative (2), indicating orthologs and paralogs where determined, and showing the contigs from each sequenced genome aligned with the chromosomal sequence of S.cerevisiae, as held by SGD. These fairly complete genomes from species closely related to S.cerevisiae provide detailed information about individual gene sequences and about genome organization and evolution as a whole. Individual features shown for the sensu stricto species are hyperlinked to the Fungal Alignment Viewer when related sequences are available.
This combination of sequence data from both sensu stricto and sensu lato Saccharomyces species is a powerful resource for investigation of the Saccharomyces genome, providing information about genome organization as well as identifying residues and regions crucial for the function of specific proteins. The Fungal Alignment Viewer and the Synteny Viewer provide users with versatile web interfaces for analyzing these data.
|
SEQUENCE SIMILARITY QUERY TOOL |
|---|
|
TOPABSTRACTINTRODUCTIONFUNGAL ALIGNMENT VIEWERSEQUENCE SIMILARITY QUERY TOOLOTHER NEW TOOLSSUMMARYREFERENCES |
|---|
The Sequence Similarity Query tool displays sequences from any species that are related to a given protein from S.cerevisiae. Each protein sequence in SGD is used as a query for the PSI-BLAST (Position-Specific Iterated BLAST) program (4) against the most recent version of the non-redundant (nr) protein sequence data set (5) at NCBI (6). This data set contains the sum of all unique entries from all species for which sequence data exist, compiled from the Swiss-Prot, PIR, PDB and GenPept Databases. The PSI-BLAST program identifies families of related proteins using an iterative BLAST procedure that groups related hits into families. An initial pass using BLAST identifies the strongest hits to the query sequence. Subsequent iterations use information from both the initial query sequence and all accumulated hits to generate a query for BLAST to find additional related sequences. The process can be allowed to run until no new additional sequences are identified. This iterative procedure often finds protein relationships that are not identified in single-pass methods (4), making it highly effective for identifying protein families. In the first run of this analysis at SGD,
60% of S.cerevisiae proteins identified similar proteins from Homo sapiens, Mus musculus, Arabidopsis thaliana, S.pombe, Drosophila melanogaster, Caenorhabditis elegans and Neurospora crassa. The data in this tool will be updated quarterly by running PSI-BLAST against NCBI’s most up-to-date version of the nr protein sequence database. Accessible from the Comparison Resources pulldown menu in the right-hand column of the Locus Page, the Sequence Similarity Query resource produces a graphical summary of results (Fig. 2), as well as options for generating alignments for any sequence with more than one hit in the nr protein data set. The taxonomic distribution of all hits is presented as a color-coded bar graph with the following major taxonomic categories: Archaea, Eubacteria, Viruses, Fungi (Ascomycetes), Fungi (Basidiomycetes), Fungi (other), Animals (mammals), Animals (other vertebrates), Animals (other), Green plants, Other eukaryotes and Unclassified/unknown. The relationships between the sequences, including the initial query sequence, are diagrammed in a dendrogram with the same color coding as that in the bar graph.
|
The Sequence Similarity Query resource provides multiple options for viewing alignments of hits to the query sequence. In the ‘Align by Best Hits’ section, one can select sequences of interest from the top 10 hits (i.e. lowest E-values). The ‘Align by Species’ section allows one or more groups of sequences to be selected by species. Both sections provide options for constructing either a multiple alignment of all selected sequences or pairwise alignments of each sequence against the query from S.cerevisiae. Pages displaying the alignment of selected sequences include links to download the GenBank accession numbers of all sequences included.
|
OTHER NEW TOOLS |
|---|
|
TOPABSTRACTINTRODUCTIONFUNGAL ALIGNMENT VIEWERSEQUENCE SIMILARITY QUERY TOOLOTHER NEW TOOLSSUMMARYREFERENCES |
|---|
Two other major new features at SGD provide new types of information about S.cerevisiae genes and proteins, and facilitate more detailed searches of the database. The Metabolic Pathways tool visualizes S.cerevisiae metabolic pathways and the genes involved in them. The Chromosomal Features Search is a versatile tool that provides many advanced options for querying the database.
Using the MetaCyc Database of metabolic reactions (7) and the Pathway Tools software created by Peter Karp’s group (8), SGD has generated metabolic pathway information for S.cerevisiae. Metabolic pathways are represented graphically and can be viewed at multiple levels of detail, from general summaries to detailed diagrams showing the chemical structures of each compound. Enzymatic activities shown on each pathway diagram are linked to the SGD Locus Pages of the proteins involved, and conversely, SGD Locus Pages are linked to all relevant pathway diagrams. The pathways are being curated at SGD to provide an up-to-date resource specific to the metabolic pathways present in S.cerevisiae.
The Find Chromosomal Features search provides advanced options for finding a gene or genes based on one or more criteria, including feature type (e.g. ORF, tRNA); protein molecular weight, length or pI; chromosomal location; the presence of introns; and associated Gene Ontology terms (9,10). The results page indicates numbers of hits for each step of the query to help the user refine the query, if necessary, and displays all results in a tabular form with links to the individual Locus Pages of all genes that satisfy the query. The list of results can be analyzed directly with other tools, including the GO Term Finder, the GO Term Mapper or Expression Connection, or it can be downloaded as a tab-delimited file.
|
SUMMARY |
|---|
|
TOPABSTRACTINTRODUCTIONFUNGAL ALIGNMENT VIEWERSEQUENCE SIMILARITY QUERY TOOLOTHER NEW TOOLSSUMMARYREFERENCES |
|---|
SGD has developed several new tools to increase ease of access to information about genes and proteins from S.cerevisiae and related proteins of other species. Two new tools provide information about related sequences. The Fungal Alignment Viewer displays alignments of S.cerevisiae protein or DNA sequences with those of other fungi. The Sequence Similarity Query tool provides information about all currently available protein sequences similar to a given protein sequence from S.cerevisiae. Visualization of metabolic pathways has been added, providing a unified source of information about the biochemical pathways in yeast. Finally, the Find Chromosomal Features search provides greater search capabilities of the basic gene and protein information already available at SGD. These tools will facilitate the use of S.cerevisiae as a model organism and reference for comparison with other species.
|
REFERENCES |
|---|
|
TOPABSTRACTINTRODUCTIONFUNGAL ALIGNMENT VIEWERSEQUENCE SIMILARITY QUERY TOOLOTHER NEW TOOLSSUMMARYREFERENCES |
|---|
- Chenna,R., Sugawara ,H., Koike,T., Lopez,R., Gibson,T.J., Higgins,D.G. and Thompson,J.D. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res., 31, 3497–3500.
[Abstract/Free Full Text] - Kellis,M., Patterson,N., Endrizzi,M., Birren,B. and Lander,E.S. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature, 423, 241–254.[CrossRef][Medline]
- Cliften,P., Sudarsanam,P., Desikan,A., Fulton,L., Fulton,B., Majors,J., Waterston,R., Cohen,B.A. and Johnston,M. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science, 301, 71–76.
[Abstract/Free Full Text] - Altschul,S.F. and Koonin,E.V. (1998) Iterated profile searches with PSI-BLAST—a tool for discovery in protein databases. Trends Biochem. Sci., 23, 444–447.[CrossRef][Web of Science][Medline]
- Altschul,S.F., Boguski,M.S., Gish,W. and Wootton,J.C. (1994) Issues in searching molecular sequence databases. Nature Genet., 6, 119–129.[CrossRef][Web of Science][Medline]
- Wheeler,D.L., Church,D.M., Federhen,S., Lash,A.E., Madden,T.L., Pontius,J.U., Schuler,G.D., Schriml,L.M., Sequeira,E., Tatusova,T.A. and Wagner L. (2003) Database resources of the National Center for Biotechnology. Nucleic Acids Res., 31, 28–33.
[Abstract/Free Full Text] - Karp,P.D., Riley,M., Paley,S.M. and Pellegrini-Toole,A. (2002) The MetaCyc Database. Nucleic Acids Res., 30, 59–61.
[Abstract/Free Full Text] - Karp,P.D., Paley,S. and Romero,P. (2002) The Pathway Tools software. Bioinformatics, 18, S225–S232.[Abstract]
- The Gene Ontology Consortium. (2001) Creating the gene ontology resource: design and implementation. Genome Res., 11, 1425–1433.
[Abstract/Free Full Text] - Dwight,S.S., Harris,M.A., Dolinski,K., Ball ,C.A., Binkley,G., Christie,K.R., Fisk,D.G., Issel-Tarver,L., Schroeder,M., Sherlock,G., Sethuraman,A., Weng,S., Botstein,D. and Cherry,J.M. (2002) Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res., 30, 69–72.
[Abstract/Free Full Text]
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  C.-H. Kuo and H. Ochman Deletional Bias across the Three Domains of Life Gen Biol Evol, July 10, 2009; 2009(0): 145 - 152. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Moreno-Ruiz, G. Ortu, P. W. J. de Groot, F. Cottier, C. Loussert, M.-C. Prevost, C. de Koster, F. M. Klis, S. Goyard, and C. d'Enfert The GPI-modified proteins Pga59 and Pga62 of Candida albicans are required for cell wall integrity Microbiology, June 1, 2009; 155(6): 2004 - 2020. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Gerlee, T. Lundh, B. Zhang, and A.R.A. Anderson Gene divergence and pathway duplication in the metabolic network of yeast and digital organisms J R Soc Interface, March 18, 2009; (2009) rsif.2008.0514v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. A Reeves, D. Talavera, and J. M Thornton Genome and proteome annotation: organization, interpretation and integration J R Soc Interface, February 6, 2009; 6(31): 129 - 147. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. A. Reeves, K. Eilbeck, M. Magrane, C. O'Donovan, L. Montecchi-Palazzi, M. A. Harris, S. Orchard, R. C. Jimenez, A. Prlic, T. J. P. Hubbard, et al. The Protein Feature Ontology: a tool for the unification of protein feature annotations Bioinformatics, December 1, 2008; 24(23): 2767 - 2772. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Yosef, R. Sharan, and W. S. Noble Improved network-based identification of protein orthologs Bioinformatics, August 15, 2008; 24(16): i200 - i206. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Pitre, C. North, M. Alamgir, M. Jessulat, A. Chan, X. Luo, J. R. Green, M. Dumontier, F. Dehne, and A. Golshani Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences Nucleic Acids Res., August 1, 2008; 36(13): 4286 - 4294. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. J. Hickman and F. Winston Heme Levels Switch the Function of Hap1 of Saccharomyces cerevisiae between Transcriptional Activator and Transcriptional Repressor Mol. Cell. Biol., November 1, 2007; 27(21): 7414 - 7424. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Li, S. Zhang, Y. Wang, X.-S. Zhang, and L. Chen Alignment of molecular networks by integer quadratic programming Bioinformatics, July 1, 2007; 23(13): 1631 - 1639. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Yang and S. Altman A noncoding RNA in Saccharomyces cerevisiae is an RNase P substrate RNA, May 1, 2007; 13(5): 682 - 690. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Z. Zhang, J. R. Hesselberth, and S. Fields Genome-wide identification of spliced introns using a tiling microarray Genome Res., April 1, 2007; 17(4): 503 - 509. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Yoneya and H. Mamitsuka A hidden Markov model-based approach for identifying timing differences in gene expression under different experimental factors Bioinformatics, April 1, 2007; 23(7): 842 - 849. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Kitagawa, H. Hoshida, and R. Akada Genome-Wide Analysis of Cellular Response to Bacterial Genotoxin CdtB in Yeast Infect. Immun., March 1, 2007; 75(3): 1393 - 1402. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. P. Byrne and K. H. Wolfe Consistent Patterns of Rate Asymmetry and Gene Loss Indicate Widespread Neofunctionalization of Yeast Genes After Whole-Genome Duplication Genetics, March 1, 2007; 175(3): 1341 - 1350. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Garcia, X. Darzacq, T. Delaveau, L. Jourdren, R. H. Singer, and C. Jacq Mitochondria-associated Yeast mRNAs and the Biogenesis of Molecular Complexes Mol. Biol. Cell, February 1, 2007; 18(2): 362 - 368. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. B. Arnaud, M. C. Costanzo, M. S. Skrzypek, P. Shah, G. Binkley, C. Lane, S. R. Miyasato, and G. Sherlock Sequence resources at the Candida Genome Database Nucleic Acids Res., January 12, 2007; 35(suppl_1): D452 - D456. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Hollunder, M. Friedel, A. Beyer, C. T. Workman, and T. Wilhelm DASS: efficient discovery and p-value calculation of substructures in unordered data Bioinformatics, January 1, 2007; 23(1): 77 - 83. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Ng, B. Bursteinas, Q. Gao, E. Mollison, and M. Zvelebil Resources for integrative systems biology: from data through databases to networks and dynamic system models Brief Bioinform, December 1, 2006; 7(4): 318 - 330. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. A. Kavanaugh, J. A. Fraser, and F. S. Dietrich Recent Evolution of the Human Pathogen Cryptococcus neoformans by Intervarietal Transfer of a 14-Gene Fragment Mol. Biol. Evol., October 1, 2006; 23(10): 1879 - 1890. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Flannick, A. Novak, B. S. Srinivasan, H. H. McAdams, and S. Batzoglou Graemlin: General and robust alignment of multiple large interaction networks Genome Res., September 1, 2006; 16(9): 1169 - 1181. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Kim, K. Melen, M. Osterberg, and G. von Heijne A global topology map of the Saccharomyces cerevisiae membrane proteome PNAS, July 25, 2006; 103(30): 11142 - 11147. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. J. Penkett, J. A. Morris, V. Wood, and J. Bahler YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W330 - W334. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J. Herrgard, B.-S. Lee, V. Portnoy, and B. O. Palsson Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae Genome Res., May 1, 2006; 16(5): 627 - 635. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. P. Samanta, W. Tongprasit, H. Sethi, C.-S. Chin, and V. Stolc Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway. PNAS, March 14, 2006; 103(11): 4192 - 4197. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Bandyopadhyay, R. Sharan, and T. Ideker Systematic identification of functional orthologs based on protein network comparison Genome Res., March 1, 2006; 16(3): 428 - 435. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Amato, A. Ciaramella, N. Deniskina, C. D. Mondo, D. di Bernardo, C. Donalek, G. Longo, G. Mangano, G. Miele, G. Raiconi, et al. A multi-step approach to time series analysis and gene expression clustering Bioinformatics, March 1, 2006; 22(5): 589 - 596. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Cai, S. Kauffman, F. Naider, and J. M. Becker Genomewide Screen Reveals a Wide Regulatory Network for Di/Tripeptide Utilization in Saccharomyces cerevisiae Genetics, March 1, 2006; 172(3): 1459 - 1476. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. J. Robinson and E. R. S. Kunji Mitochondrial carriers in the cytoplasmic state have a common substrate binding site PNAS, February 21, 2006; 103(8): 2617 - 2622. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Dunin-Horkawicz, A. Czerwoniec, M. J. Gajda, M. Feder, H. Grosjean, and J. M. Bujnicki MODOMICS: a database of RNA modification pathways Nucleic Acids Res., January 1, 2006; 34(suppl_1): D145 - D149. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. L. Schneider, K. S. Pollard, R. Baertsch, A. Pohl, and T. M. Lowe The UCSC Archaeal Genome Browser Nucleic Acids Res., January 1, 2006; 34(suppl_1): D407 - D410. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. L. Chisholm, P. Gaudet, E. M. Just, K. E. Pilcher, P. Fey, S. N. Merchant, and W. A. Kibbe dictyBase, the model organism database for Dictyostelium discoideum Nucleic Acids Res., January 1, 2006; 34(suppl_1): D423 - D427. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. P. Byrne and K. H. Wolfe Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser Nucleic Acids Res., January 1, 2006; 34(suppl_1): D452 - D455. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Sims, B. Bursteinas, Q. Gao, M. Zvelebil, and B. Baum FLIGHT: database and tools for the integration and cross-correlation of large-scale RNAi phenotypic datasets Nucleic Acids Res., January 1, 2006; 34(suppl_1): D479 - D483. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Stark, B.-J. Breitkreutz, T. Reguly, L. Boucher, A. Breitkreutz, and M. Tyers BioGRID: a general repository for interaction datasets Nucleic Acids Res., January 1, 2006; 34(suppl_1): D535 - D539. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. S. Hinrichs, D. Karolchik, R. Baertsch, G. P. Barber, G. Bejerano, H. Clawson, M. Diekhans, T. S. Furey, R. A. Harte, F. Hsu, et al. The UCSC Genome Browser Database: update 2006 Nucleic Acids Res., January 1, 2006; 34(suppl_1): D590 - D598. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Liu, Z.-Z. Hu, J. Zhang, and C. Wu BioThesaurus: a web-based thesaurus of protein and gene names Bioinformatics, January 1, 2006; 22(1): 103 - 105. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Ohya, J. Sese, M. Yukawa, F. Sano, Y. Nakatani, T. L. Saito, A. Saka, T. Fukuda, S. Ishihara, S. Oka, et al. High-dimensional and large-scale phenotyping of yeast mutants PNAS, December 27, 2005; 102(52): 19015 - 19020. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Reihl and J. Stolz The Monocarboxylate Transporter Homolog Mch5p Catalyzes Riboflavin (Vitamin B2) Uptake in Saccharomyces cerevisiae J. Biol. Chem., December 2, 2005; 280(48): 39809 - 39817. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Jambunathan, A. W. Martinez, E. C. Robert, N. B. Agochukwu, M. E. Ibos, S. L. Dugas, and D. Donze Multiple Bromodomain Genes Are Involved in Restricting the Spread of Heterochromatic Silencing at the Saccharomyces cerevisiae HMR-tRNA Boundary Genetics, November 1, 2005; 171(3): 913 - 922. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Altmann and B. Westermann Role of Essential Genes in Mitochondrial Morphogenesis in Saccharomyces cerevisiae Mol. Biol. Cell, November 1, 2005; 16(11): 5410 - 5417. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. D. Karp, C. A. Ouzounis, C. Moore-Kochlacs, L. Goldovsky, P. Kaipa, D. Ahren, S. Tsoka, N. Darzentas, V. Kunin, and N. Lopez-Bigas Expansion of the BioCyc collection of pathway/genome databases to 160 genomes Nucleic Acids Res., October 24, 2005; 33(19): 6083 - 6089. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. A. Petti and G. M. Church A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae Genome Res., September 1, 2005; 15(9): 1298 - 1306. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Y. Pinter, O. Rokhlenko, E. Yeger-Lotem, and M. Ziv-Ukelson Alignment of metabolic pathways Bioinformatics, August 15, 2005; 21(16): 3401 - 3408. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Siepel, G. Bejerano, J. S. Pedersen, A. S. Hinrichs, M. Hou, K. Rosenbloom, H. Clawson, J. Spieth, L. W. Hillier, S. Richards, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes Genome Res., August 1, 2005; 15(8): 1034 - 1050. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Usadel, A. Nagel, O. Thimm, H. Redestig, O. E. Blaesing, N. Palacios-Rojas, J. Selbig, J. Hannemann, M. C. Piques, D. Steinhauser, et al. Extension of the Visualization Tool MapMan to Allow Statistical Analysis of Arrays, Display of Coresponding Genes, and Comparison with Known Responses Plant Physiology, July 1, 2005; 138(3): 1195 - 1204. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Natter, P. Leitner, A. Faschinger, H. Wolinski, S. McCraith, S. Fields, and S. D. Kohlwein The Spatial Organization of Lipid Synthesis in the Yeast Saccharomyces cerevisiae Derived from Large Scale Green Fluorescent Protein Tagging and High Resolution Microscopy Mol. Cell. Proteomics, May 1, 2005; 4(5): 662 - 672. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Kemmeren, T. T. J. P. Kockelkorn, T. Bijma, R. Donders, and F. C. P. Holstege Predicting gene function through systematic analysis and quality assessment of high-throughput data Bioinformatics, April 15, 2005; 21(8): 1644 - 1652. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Droit, G. G Poirier, and J. M Hunter Experimental and bioinformatic approaches for interrogating protein-protein interactions to determine protein function J. Mol. Endocrinol., April 1, 2005; 34(2): 263 - 280. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. B. Pereira-Leal and S. A. Teichmann Novel specificities emerge by stepwise duplication of functional modules Genome Res., April 1, 2005; 15(4): 552 - 559. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Sharan, S. Suthram, R. M. Kelley, T. Kuhn, S. McCuine, P. Uetz, T. Sittler, R. M. Karp, and T. Ideker From the Cover: Conserved patterns of protein interaction in multiple species PNAS, February 8, 2005; 102(6): 1974 - 1979. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 U. de Lichtenberg, L. J. Jensen, S. Brunak, and P. Bork Dynamic Complex Formation During the Yeast Cell Cycle Science, February 4, 2005; 307(5710): 724 - 727. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Meinel, A. Krause, H. Luz, M. Vingron, and E. Staub The SYSTERS Protein Family Database in 2005 Nucleic Acids Res., January 1, 2005; 33(suppl_1): D226 - D229. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Hermida, S. Brachat, S. Voegeli, P. Philippsen, and M. Primig The Ashbya Genome Database (AGD)--a tool for the yeast community and genome biologists Nucleic Acids Res., January 1, 2005; 33(suppl_1): D348 - D352. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. d'Enfert, S. Goyard, S. Rodriguez-Arnaveilhe, L. Frangeul, L. Jones, F. Tekaia, O. Bader, A. Albrecht, L. Castillo, A. Dominguez, et al. CandidaDB: a genome database for Candida albicans pathogenomics Nucleic Acids Res., January 1, 2005; 33(suppl_1): D353 - D357. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. B. Arnaud, M. C. Costanzo, M. S. Skrzypek, G. Binkley, C. Lane, S. R. Miyasato, and G. Sherlock The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information Nucleic Acids Res., January 1, 2005; 33(suppl_1): D358 - D363. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
U. Guldener, M. Munsterkotter, G. Kastenmuller, N. Strack, J. van Helden, C. Lemer, J. Richelles, S. J. Wodak, J. Garcia-Martinez, J. E. Perez-Ortin, et al. CYGD: the Comprehensive Yeast Genome Database Nucleic Acids Res., January 1, 2005; 33(suppl_1): D364 - D368. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Balakrishnan, K. R. Christie, M. C. Costanzo, K. Dolinski, S. S. Dwight, S. R. Engel, D. G. Fisk, J. E. Hirschman, E. L. Hong, R. Nash, et al. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD) Nucleic Acids Res., January 1, 2005; 33(suppl_1): D374 - D377. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Riffle, L. Malmstrom, and T. N. Davis The Yeast Resource Center Public Data Repository Nucleic Acids Res., January 1, 2005; 33(suppl_1): D378 - D382. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Chen, T. W. Harris, I. Antoshechkin, C. Bastiani, T. Bieri, D. Blasiar, K. Bradnam, P. Canaran, J. Chan, C.-K. Chen, et al. WormBase: a comprehensive data resource for Caenorhabditis biology and genomics Nucleic Acids Res., January 1, 2005; 33(suppl_1): D383 - D389. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Wiwatwattana and A. Kumar Organelle DB: a cross-species database of protein localization and function Nucleic Acids Res., January 1, 2005; 33(suppl_1): D598 - D604. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Ruepp, A. Zollner, D. Maier, K. Albermann, J. Hani, M. Mokrejs, I. Tetko, U. Guldener, G. Mannhaupt, M. Munsterkotter, et al. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes Nucleic Acids Res., October 14, 2004; 32(18): 5539 - 5545. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Pancoska, Z. Moravek, and U. M. Moll Rational design of DNA sequences for nanotechnology, microarrays and molecular computers using Eulerian graphs Nucleic Acids Res., August 27, 2004; 32(15): 4630 - 4645. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. V. ROSADO and J. DE LA CRUZ Npa1p is an essential trans-acting factor required for an early step in the assembly of 60S ribosomal subunits in Saccharomyces cerevisiae RNA, July 1, 2004; 10(7): 1073 - 1083. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. P. Kelley, B. Yuan, F. Lewitter, R. Sharan, B. R. Stockwell, and T. Ideker PathBLAST: a tool for alignment of protein interaction networks Nucleic Acids Res., July 1, 2004; 32(suppl_2): W83 - W88. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Yu, N. M. Luscombe, H. X. Lu, X. Zhu, Y. Xia, J.-D. J. Han, N. Bertin, S. Chung, M. Vidal, and M. Gerstein Annotation Transfer Between Genomes: Protein-Protein Interologs and Protein-DNA Regulogs Genome Res., June 1, 2004; 14(6): 1107 - 1118. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Tanay, R. Sharan, M. Kupiec, and R. Shamir Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data PNAS, March 2, 2004; 101(9): 2981 - 2986. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Bandyopadhyay, R. Sharan, and T. Ideker Systematic identification of functional orthologs based on protein network comparison Genome Res., March 1, 2006; 16(3): 428 - 435. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||