Getting Started with CGD

This page presents answers to some basic questions that new users might ask about CGD. An overview of information about the CGD website can be found on the Help Resources page.

What types of information does CGD contain?

CGD is an organized collection of genetic and molecular biological information about Candida albicans, a yeast that is an opportunistic pathogen of humans, and about other Candida-related species, such as Candida glabrata. It contains information about genes and proteins; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information. The CGD Home page is the main entry point for the database.

CGD is aimed at scientists; collected information for the non-scientist about Candida albicans and other yeasts can be found at the Yeast Virtual Library. CGD curators cannot answer medical or health-related questions.

How is CGD organized?

An overview of the content and organization of CGD is presented in the sitemap.

The basic unit of CGD is the Locus Page (for an example, see RIM101). Each CGD gene or open reading frame has an individual Locus Page. Genetic loci that are not tied to a DNA sequence also have Locus Pages. All information relevant to a particular locus is either presented on or linked to the Locus Page. Tools for analysis and comparison of the locus are also accessible from the Locus Page.

Locus pages are accessible by using the Search Options form or by using the "Quick Search" box at the top of any CGD Locus or tool page. In addition, gene or protein names appearing anywhere in CGD are hyperlinked to the corresponding Locus Page.

Many other CGD pages, including tools, documentation, data submission forms, and others, are accessible from the CGD Home page.

How do I find information about a gene or protein of interest in CGD?

If you know the genetic or systematic name of the gene you are interested in, entering it in either the Quick Search box at the top of most CGD pages or in the Search Options form will bring you to that Locus Page (or to a list of genes, if the same name has been used for two or more).

Sometimes you may need to investigate genes or proteins without knowing their names. You can search for a class of similarly named genes using the wildcard character (e.g., searching for 'sap*' brings up SAP1, SAP2, SAP3...). Or, you can search with the name of a protein (e.g., actin) or protein complex (e.g., cytochrome c oxidase), or a Gene Ontology term (see next section) to bring up lists of the Locus Pages where this text occurs. Each gene name in the hit list resulting from the search is hyperlinked to the corresponding Locus Page.

The Locus Page is the central clearinghouse for all information specific to that gene and tools for its analysis, including:

How do I find groups of genes or proteins that share a function, role, or location?

Gene products in CGD are classified according to the Gene Ontology (GO) system of classification. Gene products are assigned GO terms that describe their molecular functions and subcellular locations, and the biological processes in which they are involved. The terms may be searched to find the set of proteins that have been annotated to a particular term. A detailed explanation of the GO system and how to use and search it is presented in a GO tutorial provided by the Saccharomyces Genome Database.

How can CGD help me interpret the results of large-scale experiments?

Lists of open reading frames and their characteristics are essential for keeping track of the results of any large-scale experiment. A variety of different tab-delimited text files containing data collected by CGD, listed on the Data Download index page, are freely available for downloading.

Interpreting the results of functional genomics experiments that identify large groups of genes with something in common (e.g., transcriptional coregulation, similar null phenotypes, etc.) presents a special challenge in integrating what is known about each gene to find the significance of the trends observed. Two tools at CGD facilitate such analysis. The GO Slim Term Mapper takes a list of genes and displays how many are annotated to each of the parent GO Slim terms, allowing visualization of the distribution of the input gene set over broad biological processes, biochemical functions, or subcellular localizations. The GO Term Finder tool also takes a list of genes as input, and identifies GO terms shared among members of the group. The difference between the two tools is that the GO Slim Term Mapper maps genes to broad parent GO terms, while the Term Finder identifies specific, granular terms shared by the group. The SGD GO tutorial provides details on the use of these tools.

How can CGD help me design experiments using Candida genes?

The Gene/Sequence Resources page presents a versatile array of tools allowing retrieval and analysis of any portion of the genome, or analysis of your own input sequence. Sequences may be retrieved from a specific region of the genome, given a genetic or systematic name, and may include sequence upstream and/or downstream of the region if desired. Alternatively, chromosomal coordinates may be specified to retrieve part or all of a chromosome. Finally, the user may start with his/her own input sequence. Once a sequence is retrieved or entered, tools allow its analysis in multiple different ways, including translation, restriction mapping, BLAST and FASTA analysis, and primer design. The user may select a desired format (GCG, FASTA, etc.) for the output of many of the tools. The oligonucleotide primer design and BLAST analysis tools are also available as direct links from the toolbar at the top of many CGD pages.

Additional tools and resources that facilitate sequence analysis and cloning may be accessed from the Search Options index page They include an assortment of search tools, including the Pattern Matching tool, which finds short sequences or sequence patterns in nucleotide or protein sequences.

What services does CGD provide?

By consensus of the research community, CGD serves as the official arbiter of C. albicans genetic nomenclature and maintains a gene name registry for new proposed gene names. CGD also maintains a web site for Candida Community News and a list of upcoming conferences.

How can I download data in bulk for use in a spreadsheet or other form?

All of CGD's data are freely available to the public for download. The CGD curators are available to assist researchers by creating custom files containing particular data of interest.

How can CGD help me participate in the Candida research community?

Several different kinds of information for the Candida research community are available through CGD. You can add your contact information to CGD's directory of colleagues, which can be searched by last name. You can also search or browse a list of Candida labs. CGD also maintains a list of upcoming conferences.

How can I find out what's new in CGD?

Current information about CGD is displayed on the CGD Home page. Additional community information is found on the Candida Community News page.

How can I get more help?

All CGD help resources are listed on the Help Resources page. The 'Help' button in the upper right corner of each tool and Locus page is linked directly to help documentation for that particular page.

For more general questions, the Frequently Asked Questions page is a good place to start. It includes common questions from CGD users.

The Saccharomyces Genome Database (SGD) Glossary page lists definitions of genetic, bioinformatic, and other terms used in CGD and in CGD.

A tutorial, provided by SGD, is available to illustrate the use of the GO tools.

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