dictyBase Help: Literature Topics

Contents

• Description
• Organization of the Literature Topics Pages
  • Literature Topics Navigation: Left Hand Column
  • Literature Curation Summary
  • Specific Topic Pages
• PubMed Search
• The Literature Topics
  • Topic Descriptions
  • Topic Groupings
• Glossary Terms

Description

Literature Topics are a guide to the literature for a given gene and are derived from journal abstracts. dictyBase performs a search through all PubMed literature (dating back to 1966) for all papers mentioning the gene name and any synonyms. (See PubMed Search for more details on how that search is performed). dictyBase curators read the abstracts of those papers and assign the papers to one or more Topics that describe the kind of biological information contained in the abstracts. The Literature Topics are thus designed to help the user easily find the papers relevant to a given gene. Please note, however, that since often only abstracts are read, the Literature Topics are not a complete description of the information contained in the papers.

Organization of the Literature Topics Pages

• Literature Topics Navigation: Left Hand Column - The left hand column of all of Literature Topics pages lists the various categories of biological information that were found for that gene in the PubMed abstracts. There are 44 different topics that are currently in use. 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. 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.

• Literature Curation Summary - The Literature Curation Summary is the starting page to access the Literature Topics. Literature curation is an ongoing project at dictyBase. For some loci, we have not yet reviewed any or all literature. The Literature Curation Summary will give the curation status, with the numbers of both curated and uncurated references, the date of last curation, and the date of the last systematic search of PubMed. Any notes or information specific to the curation of the given gene will be found on this page. Clicking on 'Other Genes' will display a table of the other genes that are mentioned in the curated papers for the gene (Please note that this count excludes any paper that is associated with the topic "Genome-wide Analysis"). Other literature resources are also accessible from this page. These include a link to dictyBase's Gene Summary Paragraph, if available, and links to PubMed to search for references that mention the gene.

• 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 gene. For each reference there will be links to additional information for the reference, including the dictyBase Papers Entry, the PubMed citation and abstract (abstract not always available), and a link to the full text on the publisher's site if available. In graphics-enabled browsers, these links for additional reference information are represented by icons:
  

dictyBase Papers Entry:   PubMed Citation and Abstract:   Full Text on Publisher's Site: or a journal specific icon

PubMed Search

The systematic search of PubMed retrieves papers that mention a gene (or its synonyms) as a Gene Symbol or in the Abstract for "Dictyostelium". Additional papers may be contained in the Literature Topics if a curator manually added a paper to the literature curation for the given gene.

The Literature Topics

• Topic Descriptions:

  A paper is filed under one or more of the following topics if its abstract contains information about:
  
  
  • Adhesion
    Role of the gene product in cell-substrate -, or cell-cell adhesion.

  • Synonym
    Different names that are used for the genes or its gene product.

  • Archived Literature
    When there is extensive literature for a gene, a curator will mark a review or reviews as "Selected Review" and curate literature dating from one year prior to the date of the review. Earlier literature will be found in this topic.

  • Cell Cycle
    Cell cycle-related changes in the expression or activity of the gene product.

  • 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 listed under this topic.

  • Cell-type Localization
    Expression of the gene product in the multicellular organism as determined by gene-fusion or in situ hybridization experiments.

  • Chemotaxis/Motility
    Involvement of the gene product in cell movement in general, and in response to a chemical attractant.

  • Cytoskeleton
    Evidence for the protein being part of or having an effect on the cytoskeleton.

  • Development/Morphogenesis
    Studies of the gene product in morphogenesis, including all stages of multicellular development.

  • Disease Gene Related
    Homology between the Dictyostelium gene and a 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.)

  • Endocytosis
    Role of the gene product in the process of taking substances into the cell, including pinocytosis, 'macro-pinocytosis', and phagocytosis.

  • Function/Process
    The role the protein plays in the cell and what the protein is, i.e. what type of enzyme it is and if the protein functions as part of a large complex or a multi-subunit enzyme.

  • Genetic Interactions
    Interactions between loci identified by genetic means, including suppression, complementation, synthetic lethality, etc.

  • Genome-wide Analysis
    References dealing with systematic analyses of large numbers of genes, e.g. microarray studies comparing expression of all the genes in a genome in two different conditions, but not systematic sequencing papers.

  • Germination
    Role of the gene product in the ability to form spores and spore viability studies.

  • Growth
    Role and effect of the gene product on growth rates. Includes studies of the gene product during growth as a life cycle phase.

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

  • Mammalian Gene Related
    Sequence and/or functional homologs of mammalian genes.

  • Mapping
    Physical or genetic mapping results.

  • Mitosis
    Describes the gene product's involvement in cytokinesis or karyokinesis.

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

  • Non-Mammalian Gene Related
    Sequence and/or functional homologs of non-mammalian genes.

  • Other Features
    Items that appeared important to the curator but did not fit underneath a standard topic.

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

  • Protein Functional Domain
    Features of the hypothetical or real primary amino acid sequence of the gene product (functional domains, hydropathy analysis, ion-binding sites, active sites, homology regions, etc).

  • Protein-Nucleic Acid Interactions
    Any association with 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 encode RNAs that do not code for proteins, for instance tRNAs, ribosomal RNAs, etc., this topic includes interactions of those RNAs with proteins.

  • Protein/Nucleic Acid Structure
    The known structure of the gene product, including known structural location of specific residues. Predictions on the structure of the protein will also be filed under this topic tag.

  • Protein Physical Properties
    The molecular weight or amino acid composition of the real or hypothetical protein product.

  • 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 abstract cites evidence for indirect or direct interactions.

  • References Not Yet Curated
    References under this topic will have been associated with this gene by the systematic search of PubMed. However, they have not yet been examined by a dictyBase curator to confirm that they are relevant to this gene or to assign other topics.

  • Regulated By
    The regulation of the gene product regulation by another protein, metabolic conditions, chemical inhibitors, or other factors. This also includes auto-regulatory functions.

  • Regulatory Role
    The role that the gene plays in regulating the activity of other genes such as by acting as a transcription factor or regulatory kinase.

  • 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.).

  • Selected Review
    When there is extensive literature for a gene, a curator will mark a review or review as "Selected Review" and curate literature dating from one year prior to the date of the review. Earlier literature will be found in "Archived Literature".

  • Sexual Cycle
    Role of the gene product in the sexual cycle, including mating and meiosis.

  • Signal Transduction
    Description of the gene product being part of intra ­ or inter-cell signaling events.

  • Strains/Constructs
    Mutant strains and constructs developed for experimentation on the gene of interest.

  • Substrates/Ligands/Cofactors
    The 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
    How the the expression of the gene is controlled at the level of transcription, for example, what RNA polymerase is used, what transcription factors are needed, what other factors (such as metabolic conditions) affect transcription.

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

  
  
  

• Topic Groupings:

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

Associated Glossary Terms:

• Topic
• Literature Topics
• PubMed