SGD Quarterly Newsletter, Spring 2005

About this newsletter:
This is the April 2005 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

Other relevant URLs mentioned in this newsletter are also at the bottom of the page. As always, please contact SGD with any comments or suggestions at: yeast-curator@genome.stanford.edu

Genome Snapshot of S. cerevisiae

SGD has created a Genome Snapshot page that provides the most up-to-date count of S. cerevisiae genomic features and a summary of Gene Ontology (GO) annotations. This page displays a pie-chart showing the number of Verified, Uncharacterized and Dubious protein coding genes, an inventory of all the genomic features by chromosome (breakdown of the number of protein coding ORFs, RNA coding genes, sequence length, etc.), a summary of GO annotations and the distribution of GO annotations for S. cerevisiae gene products by Process, Function and Component Ontologies. The Genome Snapshot page can be accessed from SGD's Home page under 'SGD Curation News' and from the Download Data and About SGD contents pages.

Full-text Literature Search

A full-text literature search capability has been added to SGD. The literature search tool is powered by Textpresso, a text-mining tool developed at Wormbase (Muller H, et al. (2004) PLoS Biol. 2(11):e309). Currently, the application contains about 14,000 pre-filtered, yeast-related full-text journal articles spanning the last 10 years. Queries may contain user-defined keywords, either alone, or in combination with optional category (grouping) terms. The full-text literature search can be accessed via the Full-text search link on the home page and is also available as a link on the SGD Search Options contents page.

PSI-BLAST Now Uses UniRef90 Data Set

The PSI-BLAST Results page (previously called the "Sequence Similarity Query") now displays the results of a precomputed PSI-BLAST analysis for every S. cerevisiae protein sequence against UniProt's UniRef90 data set. A new download option has been added to this resource so that sequences of interest can be downloaded in FASTA format. The PSI-BLAST Results can be accessed from the "Comparison Resources" pulldown menu on all Locus pages and from the Homology and Comparisons Page. More information about these data is included in the PSI-BLAST Help page.

Fungal Alignment Enhancements

The Fungal Alignment display has been updated with the following features: Faster retrieval of the default protein alignment; access to other, non-orthologous sequences; and more alternatives for sequence download, including the option of downloading multiple sequences without aligning them. The Fungal Alignment can be accessed from the "Comparison Resources" pulldown menu on all Locus pages and from the Homology and Comparisons Page. More information about this program is included in the Fungal Alignment Help page.

New Expression Connection Data Sets

Six new microarray data sets have recently been added to Expression Connection. We thank Astrid Haugen, Jennifer Collins, Jing Huang, Haico van Attikum, Olivier Fritsch, and Fred Winston for contributing their results and assisting us in loading the data. The new data sets are:

• Expression in the presence of small-molecule inhibitors of rapamycin (SMIRs) - Huang J, et al. (2004) PNAS 101(47):16594-9
• Expression analysis of snf/swi mutants - Sudarsanam P, et al. (2000) PNAS 97(7):3364-9
• Expression in response to arsenic (time and dose) and role of transcription factors in adaptation to arsenic-induced stress - Haugen AC, et al. (2004) Genome Biol 5(12):R95
• Gene regulation by Ino80 and Arp8 and Gene regulation by Ino80 and Arp8 in response to MMS - van Attikum H, et al. (2004) Cell 119(6):777-88

The Expression Connection tool allows users to search and compare expression patterns across multiple microarray experiments. A summary of expression changes for an individual ORF can be viewed by selecting "Expression Connection Summary" from the Functional Analysis pull-down located on the right hand side of the Locus page or clicking on the histogram. The data sets used in the Expression Connection tool are also available for download on the SGD ftp site.

Batch Download Expanded Data Types

The functionality of the Batch Download Tool has been updated to facilitate the retrieval of two new types of data:

1. Phenotypes in SGD's phenotypes.tab format
2. Genetic and Physical Interactions in a tab-delimited format

As with the other Batch Download options, these data can be retrieved using as input a list of gene names, feature names or SGDIDs. These newly available data types can be retrieved simultaneously with DNA sequences, protein sequences, and chromosomal coordinate information for the same input list. In addition, this tool now also allows retrieval of all the features within a chromosome without having to enter the beginning and end coordinates of the chromosome.

Analyze Gene List Enhancements

The Analyze Gene List module, available on the results pages of the Advanced Search tool, Expression Connection, Webminer and All Interactions, has been updated. It now links to the Batch Download tool and provides brief descriptions of the available options.

Correction of Systematic names

In partnership with Munich Information Center for Protein Sequences (MIPS), SGD has re-examined the systematic names of 22 small ORFs which were incorrect at one or both of our databases. In most cases, either MIPS or SGD changed to the systematic name used by the other database. In some cases, we chose to use a different name altogether, and the systematic name was changed at both databases. SGD has corrected the systematic names of 12 small ORFs and MIPS has corrected the systematic names of 13 small ORFs (3 systematic names were corrected at both databases). All SGDIDs and coordinates remain unchanged. All systematic names used at either database will remain associated with the appropriate ORF, either as systematic names or as aliases. A summary of these corrections has been posted at SGD. Please note that researchers should not publish systematic names for newly discovered protein coding ORFs without prior consultation with SGD; please see the Systematic Names Help page for more information on how newly discovered ORFs are assigned systematic names.

Addition of interaction data from GRID

We have added over 15,000 genetic and physical interactions provided by the GRID interaction database to SGD. The current GRID data set (downloaded on April 17 from the GRID download page) contains interactions curated from individual papers, high throughput studies, and the BIND and MIPS databases. These data can be viewed on the we on SGD Locus Pages, with links to pages that contain more detailed information about the interaction, such as the source of the information, the type of interaction, etc. In addition, the data are available for download from the SGD and GRID ftp sites. Thanks to Bobby-Joe Breitkreutz, Chris Stark, Teresa Reguly, and Mike Tyers for providing this resource to the community and for helping us load these data into SGD.

Community News

• May 11 - May 15, 2005 The Biology of Genomes, Cold Spring Harbor

Laboratory, Cold Spring Harbor, NY

• May 12 - May 14, 2005 Seventh International Yeast Lipid Conference,

University of Wales Swansea, UK

• May 21 - May 28, 2005 FEBS Advanced Lecture Course on Human Fungal

Pathogens: Molecular Mechanisms of Host-Pathogen Interactions and

Virulence, La Colle sur Loup, France

• June 10 - June 12, 2005 Conference on Numbers to the models:

Generating the data for Systems Biology, Goteborg, Sweden

• August 7 - August 12, 2005 XXII International Conference on Yeast

Genetics and Molecular Biology INCHEBA Exhibition & Fair Center,

Bratislava, Slovak Republic

• August 16 - August 21, 2005, Yeast Cell Biology, Cold Spring Harbor

Laboratory, Cold Spring Harbor, NY

• October 28 - November 1, 2005, Genome Informatics, Cold Spring

Harbor Laboratory, Cold Spring Harbor, NY

• November 12 - November 17, 2005, Comparative Genomics of Eukaryotic

Microorganisms: Eukaryotic Genome Evolution, Approaches with Yeasts and Fungi, Sant Feliu de Guixols, Spain

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