What's New in SGD in 2005

December 15, 2005

• The SGD full-text literature search capability (powered by Textpresso) has been expanded to include 31,000 yeast-related full-text journal articles. The full-text literature search can be accessed via the Full-text search link on the home page, as a link on the SGD Search Options contents page and from the Literature pulldown menu on the right side of all Locus Summary pages, where the search form is prefilled with the ORF or gene name.

December 7, 2005

• The "Comparison Resources" pull-down menu (located on the right hand side of Locus Summary pages) now includes links to the Yeast Gene Order Browser, a tool used to visualize the syntenic context of protein coding genes from S. cerevisiae, S. castellii, C. glabrata, A. gossypii, K. lactis, K. waltii, and S. kluyveri. This tool was developed by Kevin Byrne and Ken Wolfe (Trinity College, Dublin, Ireland), as described in Byrne and Wolfe, 2005.

November 22, 2005

• The Model Organism BLASTP Best Hits resource now includes Candida albicans (CGD) and Schizosaccharomyces pombe (S. pombe GeneDB) in the list of model organisms whose predicted protein sequences have been compared to S. cerevisiae predicted protein sequences. This resource can be accessed from the "Comparison Resources" pull-down menu of the Locus Summary page and also from the Homology & Comparisons page. BLASTP Best Hits results are also available for download from SGD's FTP site.

November 4, 2005

• The format of several sequence files on SGD's ftp site has been updated. All updated files are located in: http://www.yeastgenome.org/download-data/sequence

The following changes have been made:
1. Header lines in files found in the orf_dna, orf_protein, rna, and other_features subdirectories have been expanded:

• old 8-digit SGDIDs replaced with current 10-digit SGDIDs (the same number but with additional padding zeros)
• a detailed description of the feature, enclosed in quotes, is now included at the end of the header line

2. The content and header line format of the intergenic/NotFeature.fasta file have been changed:

• the intergenic sequences and coordinates listed no longer overlap with the flanking genes
• the header line lists the flanking genes
• the header format has been changed to be more consistent with those found in other sequence files

November 4, 2005

• Over the course of the next several months, SGD curators will be updating the systematic sequence to correct verified errors in sequencing and/or annotation. The files on our ftp site will be updated on a weekly basis. Comprehensive information about changes to the systematic sequence can be found in the Table of Sequence Updates. Sequence/annotation change details are also described in the "Locus History" pages for affected features.
• Between 2005-10-31 and 2005-11-04, changes were made affecting three features: SAE3/YHR079C-A , UTH1/YKR042W, and TRF5/YNL299W.
• Between 2005-11-07 and 2005-11-11, sequence and/or annotation changes were made affecting four features (APE3/YBR286W, SOL3/YHR163W, YHL026C, YPT11/YNL304W), and four new features were added (SNR161/snR161, YBR056C-B, YBR201C-A, YGL194C-A).
• Between 2005-11-14 and 2005-11-18, eight new features were added: YCL048W-A, YDR461C-A, YDR374W-A, YDR119W-A, YDL007C-A, YKL023C-A, YKL065W-A, and YLR146W-A.
• Between 2005-11-21 and 2005-11-23, sequence and/or annotation changes were made affecting four features (NHP2/YDL208W, LSM6/YDR378C, SPG1/YGR236C, SEC28/YIL076W), and two new features were added (YIL102C-A, YPR145C-A).
• Between 2005-11-28 and 2005-12-02, sequence and/or annotation changes were made affecting 12 features (YER030W, RSM18/YER050C, AMA1/YGR225W, YGR226C, YJL046W, GLG1/YKR058W, CDC21/YOR074C, TMA46/YOR091W, MDM32/YOR147W, MCT1/YOR221C, MIP1/YOR330C, JIP5/YPR169W), and one new feature was added (SNR80/snR80).
• Between 2005-12-12 and 2005-12-16, sequence and/or annotation changes were made affecting 5 features (PTM1/YKL039W, UTP11/YKL099C, YKL137W, OAZ1/YPL052W, YPL052W-A ).

October 24, 2005

• SGD has sent out the quarterly newsletter to colleagues designated as contacts in SGD. An HTML version of the newsletter is available. If you would like to receive this letter in the future please use the Colleague Submission/Update form to let us know.

October 24, 2005

• A new microarray dataset, "Effects of glycosylation defects on gene expression" (Cullen et al. 2004), has been added to Expression Connection. This study compares the expression profiles of all genes in cells undergoing a conditional protein glycosylation defect induced in a pmi40-101 mutant by growing cells in medium lacking mannose and comparing to cells grown in media supplemented with mannose. A second experiment identifies those genes whose expression in the glycosylation mutant is dependent on the transcription factor Ste12p.
• 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 menu located on the right side of the Locus Summary or by clicking on the Expression Summary histogram. Datasets in Expression Connection are also available for download from SGD's ftp site.

October 13, 2005

• The SGD "Quick Search" (located at the top of most SGD pages) has been enhanced to accept PubMed IDs (e.g., 15608219) and Gene Ontology (GO) IDs (e.g., GO:0007117). An exact match to a PubMed ID will display information about how the paper is curated for the Literature Guide, while an exact match to a GO ID will display information about the GO term and what genes have been annotated to that GO term at SGD. Note that the PubMed ID search only works on publications that have been added to SGD.

October 13, 2005

• The "Comparison Resources" pull-down menu (located on the right hand side of Locus Summary pages) now includes links between S. cerevisiae genes and Candida albicans homologs identified at the Candida Genome Database (CGD). Thanks to Gavin Sherlock and Martha Arnaud for providing homology determinations using software developed by Inparanoid.

October 3, 2005

• SGD displays Protein Domains and Motifs predicted by comparing S. cerevisiae protein sequences against sequences in the InterPro Database using the InterProScan program (Quevillon E et al. (2005)). The InterPro Database intergrates motif and domain information from Prosite, PRINTS, SMART, ProDom, TIGERFAMs and PIR Superfamily databases. Protein Domains/Motifs can be accessed from the Locus Summary page or Homology and Comparisons Contents pages. InterProScan results for all S. cerevisiae proteins are also available for download from SGD's FTP site

August 8, 2005

• A new "Regulatory Role" section has been added to the locus pages for many known transcriptional regulators. This section displays DNA-binding motifs for these transcription factors and provides links to predicted regulatory modules in which they may be involved [as predicted by Segal et al. (2003)] . DNA-binding sites for 102 transcriptional regulators [as mapped by Harbison et al.(2004)] have also been added as a "Regulatory regions and binding sites" track to the GBrowse map viewer, and an expanded thumbnail of this viewer now appears in the "Sequence Information" section of the locus page. The GFF file for these binding sites is available from the ftp site. Please see the SUM1 locus page for an example of the new transcription factor data.

July 29, 2005

• SGD has sent out the quarterly newsletter to colleagues designated as contacts in SGD. An HTML version of the newsletter is available. If you would like to receive this letter in the future please use the Colleague Submission/Update form to let us know.

July 27, 2005

• Abstracts of the XXIIth International Conference on Yeast Genetics and Molecular Biology to be held in Bratislava, Slovakia are available in advance of the meeting. All abstracts can be queried via an online search form available at SGD.

July 27, 2005

• Jef Boeke's lab, in collaboration with others, designed a microarray based on the tags (or barcodes) used to uniquely identify the individual mutant strains in the yeast knockout collection; these arrays have been used successfully by the SLAM (Synthetic Lethality Analyzed by Microarray) project. Because these arrays will likely be generally useful to the research community for a variety of other types of experiments, a buyer's consortium has been established to enable researchers to purchase the arrays through Agilent Technologies; academic researchers will receive a special discount. Please note that neither the SLAM project, its scientists, nor members of the consortium receive compensation of any kind as a result of sales of these arrays. To join the consortium, go to the barcode home page; for more information (e.g. protocols, materials, etc) about these arrays, see the SLAM home page at Johns Hopkins University.

July 8, 2005

• Navigation tabs have been added in order to provide easier access to different types of information currently available for genes and chromosomal features. These tabs are hyperlinked to pages already accessible via pull-down options on the right hand side of a Locus page. A colored tab indicates the page being viewed. The navigation tabs can be found at the top of the following pages: Locus page, Locus History, Literature Guide, Gene Ontology evidence and references, Phenotype details and references, Interaction details and references, Expression Summary, and Protein Info.

June 16, 2005

• Primer sequences previously distributed by Invitrogen/Research Genetics have been remapped to the current S. cerevisiae genome sequence and added to the GBrowse map viewer. Information about individual primer sequences as well as predicted PCR products from unique primer pairs can be viewed as tracks in Gbrowse. In addition, the GFF file for these primers and PCR products is available from the ftp site.

June 1, 2005

• A new microarray data set, "Exploration of essential gene functions via titratable promoter alleles" (Mnaimneh, S., et al. (2004)) has been added to Expression Connection. This study measures expression of each S. cerevisiae gene under depletion conditions for each of 215 essential gene products. Thanks to Tim Hughes for assistance with this data set.
• 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. Data sets in Expression Connection are also available for download from the SGD ftp site.

April 28, 2005

• MIPS and SGD have re-examined the systematic names of 22 small ORFs which were incorrect at one or both databases. These systematic names have now been updated, with a total of 12 systematic names changed at SGD and 13 systematic names changed at MIPS (3 systematic names were corrected at both databases). All systematic names used at either database will remain associated with the appropriate ORF, either as systematic names or as aliases. All SGDIDs and coordinates remain unchanged. A summary of these corrections has been posted at SGD, and individual changes are also described in the "Locus History" section for each ORF. Please note that researchers should not publish systematic names for newly discovered protein coding ORFs without prior consultation with SGD; see the Systematic Names - Protein Coding ORFs for more information.

April 27, 2005

• We have added over 15,000 genetic and physical interactions provided by the GRID interaction d atabase 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 web 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.

April 15, 2005

• 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.

March 21, 2005

• International Conference on Yeast Genetics and Molecular Biology will occur this summer in Bratislava, Slovak Republic from August 7-12. The deadline for submission of abstracts is April 1st (abstract form). Reduced registration fees are available for those that register before April 1st (registration form).

March 4, 2005

• 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.

February 22, 2005

• 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.

February 9, 2005

• 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 et al., 2004). 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.

February 2, 2005

• The PSI-BLAST results page (previously called the "Sequence Similarity Query") now displays the results of a PSI-BLAST analysis for every S. cerevisiae protein sequence against UniProt's UniRef90 dataset. A new download option has been added to this resource so that sequences of interest can be downloaded in FASTA format.

January 31, 2005

• SGD sends out its quarterly newsletter to colleagues designated as contacts in SGD. An HTML version of the newsletter is available. If you would like to receive this letter in the future please use the Colleague Submission/Update form to let us know.

January 28, 2005

• SGD has created a Lab Strains summary page describing strains commonly used by yeast researchers, such as S288C, SK1, Sigma 1278B and W303. We will continue to add information on genotypes and important phenotypes for these backgrounds and others. If you have information that should be included, please send an e-mail with the information and a reference, if possible, to yeast-curator@genome.stanford.edu.

January 20, 2005

• The Locus page has been updated to display the references that have been used as citations for the Description, Name Description, and Gene Product. The citation number will be listed after the information if references are available. These references, along with the references used in the Summary Paragraph, are listed at the bottom of the Locus page.

January 5, 2005

• New search criteria have been added to the Advanced Search tool, including interaction and expression data as well as feature qualifiers (Dubious, Verified, Uncharacterized).
• Results from two studies (Troyanskaya et al. (2003) PNAS 100:8348-53 and Lee et al. (2004) Science 306:1555-8) that predict functional interactions between genes have been added to the SGD ftp site.

January 1, 2005

• The 2005 Nucleic Acids Research Database issue is now available. This issue includes a paper (html|pdf) by the SGD staff describing the following new tools at SGD:
• Fungal BLAST (for nucleotide and protein searches against fungal sequences available at GenBank)
• Model Organism BLASTP Best Hits (for links to curated information about sequences conserved in other organisms)