CGD Help: Literature Guide

Contents

• Description
• Organization of the Literature Guide
  • Literature Curation Summary
  • Literature Topics Navigation: Left Hand Column
  • Specific Topic Pages
• PubMed Search
• The Literature Topics
  • Topic Descriptions
  • Topic Groupings
• Go to a Literature Guide page

Description

The Literature Guide categorizes literature into different topics, helping you sift through the papers about a given gene to find the particular information that you need. CGD performs a search through all PubMed literature for all papers mentioning that locus and any aliases. (See PubMed Search for more details on how that search is performed). CGD curators read the abstracts of those papers, review the full text when available, and assign the papers to one or more Topics that describe the kind of biological information contained in the abstracts. Please note, however, that since sometimes only abstracts are read, the Literature Topics are not necessarily a complete description of the information contained in the papers.

Organization of the Literature Guide

• Literature Curation Summary - The Literature Curation Summary is the starting page to access the Literature Topics. All the papers associated with a given gene are listed on this page, and the topics addressed by them are available in the left hand column.

  Other literature resources are also accessible from this page, including links to PubMed to search for references that mention the locus.

  Literature curation is an ongoing project at CGD. For some loci, we have not yet reviewed all of the literature. The Literature Curation Summary will give the curation status, with the numbers of both curated and uncurated references, and the date of last curation.

• Literature Topics Navigation: Left Hand Column - The left hand column of all of Literature Guide pages lists the various categories of biological information that were found for that locus in the PubMed abstracts. Many of these topics are described in detail below. A topic will be missing from the list of Literature Topics if no abstract has made reference to that kind of information for the given locus. This column functions as a navigation bar between the individual topics and additional information including the Literature Curation Summary. Your location within the Literature Topics is indicated within the left hand column by an arrow pointing to the topic name, which will now show as red text rather than as a hyperlink.

• Specific Topic Pages - Clicking on the name of a specific topic listed in the left hand column will give you a list, on the right hand side of the page, of all the references annotated to that topic for the given locus. For each reference there will be links to additional information for the reference, including, when available, the CGD Papers page, the PubMed citation, a link to the full text on the publisher's site, and web supplements.

PubMed Search

We search PubMed for papers associated with Candida keywords, including species and gene names. We then screen and curate these papers for CGD. Please let us know if you think our search has missed a paper.

The Literature Topics

• Topic Descriptions:

  A paper is filed under one or more of the following topics if it contains information about:

  • Adherence
    factors affecting adherence, either in vivo or in vitro.

  • Alias
    assignment of a particular gene name, whether it's the CGD standard name or another name (alias).

  • Animal Model
    studies of infections in animal model systems.

  • Biofilms
    involvement in biofilm formation or maintenance.

  • Cell Growth and Metabolism
    information pertaining to aspects of growth and growth phases, division, DNA replication,and metabolic pathways or processes. In particular, this topic can be used for studies of growth and metabolism that are not specific for any particular gene.

  • Cell wall properties/components
    information about cell wall and involvement of cell wall in virulence.

  • Cellular Location
    where in the cell the protein does what it does; information on the transport of the protein and regulation of its compartmentalization is also listed under this topic.

  • Clinical Data
    clinical studies in humans.

  • Comparative genomic hybridization
    involves DNA-DNA hybridization to assay for chromosomal rearrangements or SNP detection.

  • Computational analysis
    analysis that utilizes bioinformatics/computational methods (i.e. a "dry" set of experiments that may be based on previously determined wet lab results).

  • Cross-species Expression
    any experiment in which a gene from another species is expressed in a Candida cell, or vice-versa; this category also includes experiments addressing cross-species complementation.

  • Disease Gene Related
    homology between the Candida gene and a human gene that is disease-related.

  • DNA/RNA Sequence Features
    overall DNA sequence and DNA sequence features (promoters, exons, introns, etc.) and RNA sequence features (splice sites, poly-A sites, etc).

  • Epidemiological data
    studies about frequency and dissemination of Candida-caused diseases in host populations.

  • Evolution
    studies that discuss Candida evolution in general, as well as evolutionary studies of specific Candida genes. (Note that studies of related genes in other species or organisms may warrant assignment of the topic "Fungal Related Genes/Proteins" or "Non-Fungal Related Genes/Proteins").

  • Function/ Process
    the role the gene product plays in the cell, and the molecular function of the gene product.

  • Fungal Related Genes/ Proteins
    fungal homologs (both functional and sequence homologs) as well as members of a fungal gene or protein family.

  • Genetic Interactions
    interactions between loci identified by genetic means, including suppression, complementation, synthetic lethality, etc; this topic does not include cross-species complementation experiments, as these are covered by the category "cross-species expression".

  • Genomic co-immunoprecipitation study
    involves large-scale co-immunoprecipitation of proteins cross-linked to DNA or RNA in order to characterize protein-DNA or protein-RNA interactions using genomic techniques (for example ChIP on Chip experiments).

  • Genomic expression study
    includes microarray/chip/serial analysis of gene expression (SAGE) or other genome-wide techniques to assay gene expression on a genomic scale.

  • Host response
    studies of host processes induced by interaction with Candida.

  • Industrial Applications
    use of Candida in industrial processes.

  • Large-scale genetic interaction
    includes large-scale screens for genetic interactions including Synthetic Genetic Analysis (SGA), Diploid-based Synthetic Lethality Analysis on Microarrays (dSLAM), and other types of genetic interaction screens that use genomic techniques.

  • Large-scale phenotype analysis
    involves any large-scale phenotype analysis that utilizes genomic techniques or a systematic analysis of a collection of genes, e.g. genes on a single chromosome or genes expressed preferentially in specific cells.

  • Large-scale protein detection
    includes two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), mass spectrometry, immunodetection schemes and other studies that measure or examine protein levels on a large-scale; includes identification, detection, and expression of proteins.

  • Large-scale protein interaction
    includes large-scale two hybrid, phage display and other large-scale protein-protein interaction experiments.

  • Large-scale protein localization
    involves methods for determining the subcellular distribution of a large number of proteins.

  • Large-scale protein modification
    includes large-scale identification of various types of protein modifications, such as phosphorylation.

  • List of all Curated References
    list of all references annotated to any topic for this gene.

  • Mapping
    physical or genetic mapping results.

  • Mating
    involved in mating and parasexual cycle.

  • Mutants/ Phenotypes
    mutations, including deletions, of the gene and resulting phenotypes.

  • Non-Fungal Related Genes/ Proteins
    homologs, both functional and structural, from organisms other than fungi, as well as identification of members of a gene or protein family that are homologous to the fungal gene.

  • Nucleic acid-Nucleic acid interactions
    associations between DNA and/or RNA species.

  • Other Features
    items that appear to be significant, but which do not fit underneath a standard topic.

  • Other genomic analysis
    other large-scale analyses not described by the other large-scale genomics topics , for example, genomic/chromosomal sequencing , small molecule protein-binding assays, using microarray technology to identify replication origins or ribosome abundance, etc.

  • Phenotypic Switching
    factors that affect phenotype switching, for example between white and opaque phase..

  • Post-Translational Modifications
    how the protein is modified following translation, including regulatory and non-regulatory modifications, such as phosphorylation, attachment of sugars, etc.

  • Protein Domains/ Motifs
    identified domains and sequence motifs.

  • Protein Physical Properties
    the molecular weight or amino acid composition of the real or hypothetical protein product; also characterization of enzyme kinetics.

  • Protein Processing
    posttranslational maturation of proteins.

  • Protein/Nucleic Acid Structure
    the structure of the gene product, including known structural location of specific residues and structural predictions.

  • Protein-Nucleic Acid Interactions
    any association between a protein and DNA or RNA including direct binding or associating with other DNA- or RNA-binding proteins; this topic also includes information on binding sites; for genes that do not code for proteins, for instance tRNAs, ribosomal RNAs, etc., this topic includes interactions of those RNAs with proteins.

  • Protein-Protein Interactions
    physical interactions that have been demonstrated between proteins by methods such as two-hybrid analysis, cross-linking studies, coimmunoprecipitation, etc., or when the paper cites evidence for indirect or direct interactions.

  • Regulation (Other)
    regulation that is not included under one of the other topics.

  • Regulation (Unspecified)
    observed regulation, when the type of regulation is not described.

  • Regulation of Activity
    includes regulation of enzymatic activity.

  • Regulation of Protein Degradation
    controlled degradation of a protein as a regulatory mechanism.

  • Regulation of RNA Degradation
    controlled degradation of an RNA as a regulatory mechanism.

  • Regulatory Role
    regulation by the gene product, as opposed to regulation of the gene product; this topic is assigned when the gene product itself acts as a regulator.

  • Related Species
    literature pertaining to specified Candida species.

  • Reviews
    literature reviews that refer to the gene.

  • RNA Levels and Processing
    the RNA prior to translation (levels of RNA in the cell, stability, structure, splicing, etc.).

  • Sensitivity/response to drugs/other treatments
    effects of drugs on expression of the gene or activity of the gene product, genes or proteins responsible for drug resistance; mutations that lead to changes in drug susceptibility.

  • Signal Transduction
    involvement of the gene product in a signal transduction pathway.

  • Strains/ Constructs
    mutant strains and constructs developed for experimentation on the locus of interest.

  • Strain/species typing/detection
    methods of detecting and differentiating between Candida species and/or strains.

  • Substrates/ Ligands/ Cofactors
    substrates or ligands of the protein, including cofactors that regulate the protein's activity.

  • Techniques and Reagents
    novel techniques used in studying the gene as well as any reagents other than constructs that might help in experimentation, including antibodies, chemical inhibitors, and purified protein.

  • Transcriptional Regulation
    regulation of mRNA transcription.

  • Translational Regulation
    regulation of the translation of the mRNA into protein.

  • Variant Alleles
    information about sequence variation among alleles of the locus.

  • Virulence
    role of the gene product in infection of the host.

• Topic Groupings:

  To assist you in finding the topic in which you are most interested, we have grouped the Literature Topics (and the Literature Curation Summary) into groups of related topics. Here are the groupings: