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. ORFs and noncoding RNA genes are assigned the additional qualifiers, Verified, Uncharacterized, or Dubious. At first these qualifiers were applied only to ORFs in CGD; as of January 2011, noncoding RNA features are also included. Features are labeled as Verified if there is experimental characterization that indicates that a functional gene product is produced (as defined by curated Gene Ontology terms with experimental evidence codes, i.e., evidence codes other than IEA, ISS, RCA, ISA, ISM, ISO, NAS). Uncharacterized ORFs or RNA genes do not currently have curated experimental characterization. Upon publication that provides experimental evidence that an Uncharacterized feature produces a product, the feature will be reclassified as Verified. Dubious genes are unlikely to encode a product, as they appear indistinguishable from random non-coding sequence based on comparative analysis, they show no significant homology to an S. cerevisiae gene (by the same criteria used to determine Best Hits and Orthologs at CGD), and they have no experimental characterization. Only features that are included in the current sequence assembly are assigned one of these ORF qualifiers.


• Description
  A concise summary of the biological role and molecular function of the gene, and any other particularly salient information. Genes without experimental characterization may have descriptions that discuss orthology to genes in other organisms, as described in more detail.


• Ortholog(s) and Best Hits
  This section provides ortholog and best hit mappings.

  Please note, regarding the issue of orthology and shared function:
  We use the standard evolutionary definition of orthology: genes descended from a common ancestral gene sequence. This definition does not require that the genes are functionally equivalent after the speciation event, although it will often be the case.

  A detailed description of the methodology used to generate the ortholog and best hit mappings is posted here.



• 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.

  As described here, the evidence code "ND", or "Not Determined" is used with annotations to the three root terms "molecular_function unknown", "biological_process unknown", or "cellular_component unknown" and signifies that a curator has examined the literature and that as of the date of the annotation to the unknown term, there were either no publications concerning that gene, or there was no information in any available publications that allowed a curator to make an annotation to a specific term in that ontology.



• 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.


• Sequence Information
  The Sequence Information field indicates the location of the gene in the 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 C. albicans pages:
  • 2004-05-03: the C. albicans 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
  • 2008-10-07: Assembly 20 was moved to archival storage and access has been removed from Locus Summary pages, GBrowse and most sequence analysis tools.
  • 2008-11-07: A large set of Assembly 21 chromosome sequence and annotation updates were loaded into the database, based on work done in collaboration between CGD and the Broad Institute, MIT.
  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 Assembly 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.
  • "Entrez Gene" and "Entrez RefSeq Nucleotide" link to NCBI 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.
  • "C. dubliniensis ortholog" links C. albicans Locus pages to the corresponding ortholog page at GeneDB. These 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.
  • "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 chromosome or contig sequences. GBrowse may be accessed using the GBrowse map thumbnail views or the links in the Sequence Information section. See the C. albicans 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. 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.
• Full-text lit. search, gene name(s): links to the Textpresso tool with the search box pre-filled with the standard and systematic name of the gene. Textpresso supports searches of the full text of Candida albicans papers in CGD.
• Full-text lit. search, gene name(s) and aliases: links to the Textpresso tool with the search box pre-filled with the standard name, systematic name and all aliases of the gene. Textpresso supports searches of the full text of Candida albicans papers in CGD.
• 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 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.
  Sequences are displayed by default in FASTA format. Several other sequence formats are available as hyperlinks on the page displaying the sequence, or via the Gene/Seq Resources tool. The other formats include, GCG, No header, Decorated FASTA and Numbered sequence.


• 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.



• Locus Summary Notes

The Summary Paragraph section is displayed on some Locus Summary Pages. It contains a brief overview of published information regarding a locus, composed by CGD curators. Gene Summary Paragraphs contain references and may link to further information.

• References Cited on this Page

This section lists the references used to curate information displayed in the Standard Name, Alias, Description, Name Description, and the Summary Paragraph fields. Note that this section is not a comprehensive listing of publications relevant to this gene. To retrieve a list of all publications annotated to this gene, select the "Literature" tab at the top of the page.


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