dictyBase Help: Literature Topics

dictyBase Help: Literature Topics


Contents



Description

Literature Topics are a guide to the literature for a given gene and are derived from journal articles. dictyBase performs a weekly search for papers containing the terms Dictyostelium or discoideum. When dictyBase curators read those papers they assign one or more Topics that describe the kind of biological information contained in the paper. The Literature Topics are thus designed to help the user easily find the papers relevant to a given gene.

Organization of the Literature Topics Pages

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 papers curated. These topics are described in detail below. A topic will be missing from the list of Literature Topics if none of the curated papers has made reference to that kind of information. This column functions as a navigation bar between the individual topics, which, when clicked, are entered as a filter. The term the list is filtered for appears in a red box above the references and the filter can be cleared with a button to the right. In addition, the reference list can be filtered for any word string that is entered in a text box.

The Literature Topics

  • Topic Descriptions:

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

    • Adhesion
      Role of the gene product in cell-substrate -, or cell-cell adhesion.
    • Antibodies
      New antibodies have been published in this paper.
    • 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.
    • 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.
    • Phtotaxis/Thermotaxis
      Phototaxis or thermotaxis of the slug has been investigated in this study.
    • Phylogenetic Analysis
      Phylogenetic analysis has been performed for this gene in this study.
    • 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.
    • Sporulation/Germination
      Role of the gene product in the ability to form spores and spore viability studies.
    • 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.
    • Synonym
      Different names that are used for the genes or its gene product.
    • 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 into groups of related topics. Here are the groupings:
Genetics/Cell Biology
  • Adhesion
  • Cell Cycle
  • Cellular Location
  • Chemotaxis/Motility
  • Cytokinesis
  • Endocytosis
  • Function/Process
  • Genetic Interactions
  • Mitosis
  • Mutants/Phenotypes
  • Phototaxis/Thermotaxis
  • Signal Transduction
Nucleic Acid Information
  • DNA/RNA Sequence Features
  • Mapping
  • RNA Levels and Processing
  • Transcriptional Regulation
  • Translational Regulation
Protein Information
  • Protein Funtional Domain
  • Protein-Nucleic Acid Interactions
  • Protein/Nucleic Acid Structure
  • Protein Physical Properties
  • Protein-Protein Interactions
  • Post-Translational Modifications
  • Substrates/Ligands/Cofactors
  • Regulated By
  • Regulatory Role
Life Cycle
  • Cell Type Localization
  • Development/Morphogenesis
  • Sporulation/Germination
  • Growth
  • Sexual Cycle
Related Genes/Proteins
  • Disease Gene Related
  • Mammalian Gene Related
  • Non-Mammalian Gene Related
  • Phylogenetic Analysis
Research Aids
  • Antibodies
  • Genome-wide Analysis
  • Other Features
  • Strains/Constructs
  • Synonym
  • Techniques and Reagents
Curated Literature
  • Reviews
Additional Information
  • Archived Literature
  • References Not Yet Curated

Associated Glossary Terms:


Home| Contact dictyBase| SOPs| Site Map  Supported by NIH (NIGMS and NHGRI)