CGD Help: Locus Page

Contents

• Organization of the Locus page
• Basic Information
• Resources
• Additional Information

The CGD locus page is divided into three sections: BASIC INFORMATION, RESOURCES, and ADDITIONAL INFORMATION, as described below.

• Basic Information

The Basic Information section lists any names and aliases (synonyms, including allele names) for a particular locus, and indicates whether a name is standard or reserved. Additional information about gene names in CGD (including explanation of the standard format, systematic name format, and other gene identifiers used) may be found on the Nomenclature page. The Basic Information Section also includes the following additional information:

• Feature Type: The Feature Type section indicates what sort of gene or other genetic element resides on this chromosomal sequence (e.g., ORF, tRNA, or CEN). Information about the changes to ORFs from one genome assembly to the next is no longer displayed in this section; this information has moved to the Locus History.


• Description
  The Description field lists general information about the gene.


• Ortholog(s) and Best Hits
  This section provides orthologs and best hit mappings of C. albicans genes to C. dubliniensis and S. cerevisiae.

  The ortholog mappings between C. albicans and C. dubliniensis were provided to CGD by John Gamble and Matthew Berriman at the Wellcome Trust Sanger Institute. The C. dubliniensis orthologs are manually curated positional orthologs based on synteny (rather than on sequence similarity). Assembly 20 of the C. albicans SC5314 genome sequence was used for positional ortholog determination.

  The ortholog mappings between C. albicans and S. cerevisiae were generated using the InParanoid software (version 3.0) developed at the Karolinska Institutet. To run InParanoid, the haploid complement of C. albicans proteins from CGD was compared to the latest set of S. cerevisiae proteins from SGD (as of April 7th, 2008), and the set of C. elegans proteins from the Sanger Institute, in wormpep 188, was used as an outgroup. Stringent cutoffs were set: BLOSUM80 (instead of the default BLOSUM62), and an InParanoid score of 100%. In total, 3453 ortholog mappings met these criteria. BLAST version 2.2.18 was used by InParanoid. Note, that the ortholog pairings are automatically generated, with no curator intervention. Thus, there will occasionally be pairings that may not occur with a different scoring matrix. In the interest of automating the process, we do not intend to hand-curate the ortholog pairs at this time. Please also note that, in the Assembly 21-based mapping, orthologs are not computed or displayed for the C. albicans ORFs that were present in a prior assembly (Assembly 19 or 20) and subsequently deleted from Assembly 21. The orthologs of these ORFs are present in the archived Assembly 19 or 20-based mapping files. For C. albicans proteins that did not have an ortholog that meets these criteria, we used BLASTp, using the same parameters as were used by InParanoid (-F \"m S\" -M BLOSUM80) with an expectation value (E) of 1e-5 to identify their best hit in the S. cerevisiae protein complement. Best hits were identified for 1373 of the C. albicans proteins. Orthologs and Best Hits are displayed on the CGD Locus pages, and linked to the corresponding SGD Locus pages. In addition, all of this information is available in bulk in files that are available from the /Assem21orthologs/ download directory on the CGD web site. (If you are interested in the archived Assembly 19-based ortholog mapping (from August 15, 2005), or the Assembly 20-based ortholog mapping (from November 26, 2006), these are also available for download from our web site.



• Gene Ontology (GO) Annotations: Molecular Function, Biological Process, and Cellular Component
  The GO annotations describe a gene's molecular functions, its role in biological processes, and its presence in cellular components or complexes. Each annotation links to a page showing all genes annotated to the term in CGD. The GO annotations use a controlled vocabulary that allow powerful searches within CGD and across other databases. The "Gene Ontology" tab and the "GO evidence and references" link will display a page with more information about the GO assignments, including links to the references that support assignment of each GO term.


• Mutant Phenotype
  The Phenotype field lists the mutant phenotype for the gene. The "Phenotype" tab and "Phenotype details and references" links display a page with additional information about the phenotypes, including references and additional notes.


• Pathways
  The Pathways field lists any biochemical pathways in which the gene product is predicted to participate. Each pathway name is hyperlinked to the corresponding pathway diagram.


• Chromosomal Location
  The Chromosomal Location field indicates the location of the gene in Assembly 21 and Assembly 20 of the C. albicans genome. The coordinates of each exon and intron are listed, with the relative position of these regions with respect to the feature, and to the chromosome. Also displayed are the dates on which the most recent updates to the sequence coordinates and to the sequence itself were made. Dates that appear on many pages:
  • 2004-05-03: the Assembly 19 sequence paper, Jones et al. (2004) was first published online
  • 2000-07-06: C. albicans mitochondrial sequence was submitted to Genbank by Federspiel et al. Please note that the mitochondrial chromosome was not included in Assemblies 20 or 21, and therefore mitochondrially encoded genes have coordinates in Assembly 19, but not 20 or 21. Please see the Sequence Documentation for more information.
  • 2004-10-25: Assembly 19 sequences were loaded into CGD
  • 2006-09-12: Assembly 20 sequences from the NRC-BRI were loaded into CGD
  • 2007-09-13: Assembly 21 sequences from the NRC-BRI were loaded into CGD
  • 2007-09-19: Assembly 21 feature coordinates were mapped at CGD and loaded into the database
  Please note: Gaps have been introduced into some ORFs to make adjustments to the reading frame or to eliminate stop codons, in cases in which the annotator judged that the sequence was likely to be in error. These gaps called "Adjustments," rather than "Introns" on the Locus page of the affected ORFs in Assemblies 20 and 21. (All introns and adjustments are called "Gaps" in Assembly 19.) Some of the gaps have a length that is a negative number; that is, the coding sequence comprises two overlapping segments, such that some sequence is counted twice. The "adjustments" should be considered flags that indicate that resequencing of the area is advised.


• Contig Location(s)
  The Contig Location field lists the name of the contig (in Contig19 nomenclature, from Assembly 19 of the genomic sequence) and the base pair coordinates within the contig at which each allele resides. The name of each allele is a hyperlink to the GBrowse genome browser, which allows viewing and navigation of the contig.


• External Links
  This field provides links to other information sources for the gene.
  • "UniProt/Swiss-Prot" links to the corresponding UniProtKB records.
  • "Broad" links to the Candida comparative annotation site at the Broad Institute.
  • "BRI" links to the Annotation Working Group orf19 information on the C. albicans web site of the Biotechnology Research Institute of the National Research Council, Canada.
  • "Candida DB" links to the CandidaDB web site at the Institut Pasteur.
  • "CYGD" links to the Comprehensive Yeast Genome Database (CYGD) at MIPS
  • "Transcription Modules" links to the sets of co-regulated genes described by Ihmels et al. in "Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program." PLoS Genet. 2005 Sep;1(3):e39.
  • "Fungal Orthologs" links to the ortholog group pages at the Fungal Orthogroups Repository, described by Wapinski et al. (2007) in "Natural history and evolutionary principles of gene duplication in fungi." Nature, 449(7158):54-61.
  
  
• Primary CGDID
  This is an identifier that has been assigned to the locus at CGD.

• Resources

The Resources section provides resources for analysis and addtional information retrieval for a particular gene. The Resources section has the following information retrieval options:


• GBrowse Genome Browser:
  Allows you to view and navigate the chromosomes from Assembly 21 (or Assembly 20) of the genome sequence, and the contigs from Assembly 19. GBrowse may be accessed using the GBrowse map thumbnail views or the "Contig Location(s)" links. See the ACT1 Locus Page as an example. The three small maps on the right-hand side of the page correspond to the ACT1 ORF in Assembly 21 and, below, the two ACT1 alleles from Assembly 19. (A hyperlink to Assembly 20 GBrowse is also available; however, no map thumbnail view is displayed for Assembly 20.) Clicking on one of these will display a region of the chromosome or contig, with the selected ORF at the center and neighboring ORFs visible on either side. GBrowse is described in more detail on the GBrowse Help Documentation page.


• Literature:
• Literature Guide: retrieves CGD's Literature Guide page, which organizes papers about a gene by various topics.
• PubMed Search: searches PubMed for papers that mention a locus (or its aliases) as well as Candida albicans.
• Search Google Scholar: searches Google Scholar for papers that mention a locus (or its aliases) as well as "albicans."
• Search NCBI: searches Entrez at NCBI for papers that mention a locus (or its aliases) as well as "albicans."


• Retrieve Sequences:
  Retrieves, for the gene in Assembly 21 (or 20), or for each allele in Assembly 19, the Genomic DNA (with introns), the Exons-only Sequence (Coding Sequence of an ORF, or the sequence with exons removed of any non-translated feature) , the Genomic DNA with 1 kb of flanking sequence upstream and downstream of the gene (also includes any introns), or the ORF translation. For more details about the sequence datasets, please see the Sequence Documentation page.


• Sequence Analysis Tools:
  
  • BLAST options:
    Allow comparison of the genomic, coding, or ORF translation sequence to various C. albicans sequence datasets. For more detailed instructions for use of the BLAST tool, please see the BLAST Search Help page. For a detailed description of the search output, please see the BLAST Results Help page.
  • Design Primers:
    Recommends primers appropriate for either PCR or sequencing of a given sequence, within configurable parameters. For more information about this tool, please see the Web Primer tool help page.
  • Restriction Fragment Map:
    Generates a restriction map of a specified DNA sequence. The restriction map may include all enzymes, or a subset of enzyme types (3' overhangs, 5' overhangs, blunt ends, or enzymes that cut once or twice). For more information about this tool, please see the Restriction Analysis tool help page.


• Maps and Displays:
  The Flanking Features Table provides a tabular view of the other nearby features (ORFs, etc.) on the Assembly 21 chromosome, with brief descriptions of each neighboring feature and links to additional resources and information. By default, the table lists features within 5 kb flanking the locus; use the "Retrieve Features Left" or "Retrieve Features Right" options near the bottom of the page to include additional flanking region. The column labeled "Retrieve" provides links to the Locus page and to the Assembly 21 nucleotide sequence of each feature listed in the table. Documentation page).

• Additional Information

The Additional Information section has links to pages and features in CGD that provide further information about a locus.


• Locus History link and the Locus History tab: retrieve notes about the locus, including information about ways in which the sequence or annotation has changed from one genome sequence assembly to the next. The Locus History may also alert the user to contradictory information in the literature or to potentially confusing gene names. For reserved gene names, the Locus History includes the reservation date and expiration date. For ORFs in Assembly 20 that result from merges of Assembly 19 ORFs, the Locus History provides the names of the merged components. It also provides comments and notes about the locus that came from the original Assembly 20 files released by the Candida Annotation Working Group/Assembly 20 collaboration.


• Gene/Sequence Resources: tools for sequence display and analysis. For more detail, please see the Gene/Sequence Resource help document.


• Global Gene Hunter: links to the Global Gene Hunter search form, already filled out with the gene name (or ORF name, for ORFs that do not have a standard or reserved gene name) for the locus. For more detail, please see the Global Gene Hunter help document.



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