SGD Help: Literature Guide

The Literature Guide, formerly called Gene_Info, categorizes literature into different topics, helping you sift through the papers about a given gene to find the particular information that you need. SGD performs a search through PubMed literature for all papers relevant to yeast genes and proteins. SGD curators read the full text or abstracts of those papers and assign the papers to one or more Topics that describe the kind of biological information contained in the papers.

Contents

  1. Organization of the Literature Guide
    1. Literature Curation Summary
    2. Literature Topics Navigation: Left Hand Column
    3. Specific Topic Pages
  2. Literature Collection
  3. The Literature Topics
    1. Topic Descriptions
    2. Topic Groupings

Organization of the Literature Guide

Literature Curation Summary

The Literature Curation Summary is the starting page to access the Literature Topics that have been associated with a given chromosomal feature. All the papers curated for the feature are listed on this page, and the topics addressed by these papers for that feature are available in the left hand column.

Other literature resources are also accessible from this page (see Additional Information at the bottom of the left-hand column). These include a link to SGD's Gene Summary Paragraph, if available for that feature, and links to PubMed to search for references that mention the locus. In addition, a link to the complete list of genome-wide analysis papers in SGD is included.

Literature curation is an ongoing project at SGD. For some loci, we have not yet reviewed all of the literature. The Literature Curation Summary shows the number of curated references and the date a paper was last curated for this feature.

Literature Topics Navigation: Left Hand Column

The left hand column of each Literature Guide page lists the various categories, or topics, of biological information that have been assigned by SGD curators to that feature based on results presented in the references. (Note that a topic will not appear in this list if no paper has been curated that provides information pertaining to that topic.) Each topic is hyperlinked to a page that lists all the references associated with that topic for that feature (see next section). Your location within the Literature Topics is indicated within the left hand column by an arrow pointing to the topic name, which appears as red text rather than as a hyperlink. The topics that are currently in use are described in detail below.

Specific Topic Pages

Clicking on the name of a specific topic listed in the left hand column leads to a page containing a list of all the references annotated to that topic for the given feature. For each reference there are links to additional information, including the SGD Curated Paper page, the PubMed citation, a link to the full text on the publisher's site, and web supplements.

Literature Collection

SGD gathers references via an automated search looks in PubMed records for papers whose titles or abstracts contain "yeast" or "cerevisiae". These papers are reviewed manually by SGD curators, and relevant papers are added to the database and linked to the appropriate genes during the curation process.

In addition, SGD users often let us know when we have missed a paper relevant to S. cerevisiae. Please contact us if you think a paper should be added to the database, by using our suggestion form or emailing sgd-helpdesk@lists.stanford.edu

The Literature Topics

As mentioned above, SGD curators read papers (usually the full text; occasionally just the abstract) and assign Literature Topics according to the biological information presented. Prior to April 2005, topics were assigned to the specific chromosomal features discussed in the paper and any information presented that did not pertain to a feature was not captured. However, a system of curation is now in use that allows curators to capture more general information about yeast that is not specific for any features (feature independent). Therefore, while most of the topics below apply to curation of a paper for specific features, several of the topics are ideal for more general feature-independent curation of the paper (such as "Evolution" or "Cell Growth and Metabolism").

As of January 28, 2013, all gene-associated publications were also assigned a gene-associated "Primary Literature," "Additional Literature" or "Reviews" Literature Topic. These Literature Topics provide a means for researchers to distinguish publications where the gene of interest is a principal focus of the publication (Primary Literature) from those in which that gene is addressed briefly but is not a principal focus for that research (Additional Literature). "Reviews" is a distinct category, as these publications generally do not contain original research.  At the same time, SGD curators stopped assigning the subject-specific Literature Topics described above. To find papers on a specific subject try a keyword search in SGD's full-text search tool, Textpresso.

Note that initial assignment of "Primary Literature" and "Additional Literature" topics was done in a semi-automatic fashion. If you see a paper listed in "Primary Literature" that would be better categorized as "Additional Literature" (or vice versa), please contact us by using our suggestion form or emailing sgd-helpdesk@lists.stanford.edu.

Topic Descriptions:

Additional Literature The associated gene is addressed briefly but is not a principal focus of the publication.
Alias Different names that are used for the gene.
Archived Literature When there is extensive literature for a locus, 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 under this topic.
Databases This topic includes papers that describe databases or particular features of databases that provide information useful for research in S. cerevisiae.
Cell Cycle Phase Involved Any characterization of a gene being involved in or regulated by the cell cycle. Cell cycle includes references to meiosis.
Cell Growth and Metabolism Information pertaining to aspects of yeast 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.
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.
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 one species is expressed in S. cerevisiae, or vice-versa. This category also includes experiments addressing cross-species complementation.
Disease Gene Related Homology between the yeast 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.)
Evolution Studies that discuss S. cerevisiae evolution in general, as well as evolutionary studies of specific S. cerevisiae 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 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.
Fungal Related Genes/Proteins Fungal homologs (both functional and sequence homologs) as well as members of a fungal gene or protein family. [Previous to 9/2002, this topic was called "Yeast Related Genes/Proteins," which was interpreted to include Saccharomyces cerevisiae and other yeast species (for instance, Saccharomyces carlsbergensis, Candida albicans, and Schizosaccharomyces pombe.) Papers curated after 9/2002 will be assigned according to the new, broader category, and older papers will be re-annotated on an ongoing basis.]
Genetic Interactions Interactions between loci identified by genetic means, including suppression, complementation, synthetic lethality, etc. This topic no longer includes cross-species complementation experiments, as these are now covered by the additional 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.
Industrial Applications The use of S. cerevisiae in industrial processes, such as winemaking, brewing, or baking.
Infection and Antifungals The involvement of S. cerevisiae in infection and illness, and the development/use of drugs to inhibit or cure such infections.
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 meiotic 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.
Mutants/Phenotypes Mutations, including deletions, of the gene and resulting phenotypes.
Non-Fungal Related Genes/Proteins Homologs, both functional and sequence, from organisms other than fungi, as well as identification of members of a gene or protein family that are homologous to the fungal gene. [Previous to 9/2002, this topic was called "Non-Yeast Related Genes/Proteins." Papers curated after 9/2002 will be assigned according to the newly defined category, and older papers will be re-annotated on an ongoing basis.]
Nucleic Acid Interaction Physical associations between nucleic acid species, including DNA:DNA, DNA:RNA, and RNA:RNA interactions.
Omics Includes large-scale analysis of some kind.
Other genomic analysis Uses 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.
Other large-scale proteomic analysis Uses other large-scale analyses not described by the other large-scale proteomics topics.
Primary Literature The associated gene is a principal focus of the publication.
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 Physical Properties The molecular weight or amino acid composition of the real or hypothetical protein product. Also characterization of enzyme kinetics or protein purification.
Protein Processing/Modification/Regulation Includes post-translational changes to a protein that may or may not affect its activity, including processing of the full-length product, modification (such as phosphorylation, prenylation, attachment of sugars or a GPI anchor, etc.), or direct regulation of activity.
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.
Protein Sequence Features 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 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.
Regulation Of The regulation of the gene product regulation by another protein, metabolic conditions, chemical inhibitors, or other factors.
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 review articles that refer to the gene.
RNA Levels and Processing The RNA prior to translation (levels of RNA in the cell, stability, structure, splicing, etc.). Compare to the "Transcription" topic below.
Selected Review When there is extensive literature for a locus, 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".
Strains/Constructs Mutant strains and constructs developed for experimentation on the locus 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.
Transcription 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. Cell-cycle dependent transcription is filed under the "Cell Cycle Phase Involved" topic.
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:

Curated Literature Additional Literature
All Curated References
Primary Literature
Reviews
Genetics/Cell Biology Cell Cycle Phase Involved
Cell Growth and Metabolism
Cellular Location
Function/Process
Genetic Interactions
Mutants/Phenotypes
Regulation of
Regulatory Role
Nucleic Acid Information DNA/RNA Sequence Features
Mapping
Nucleic Acid Interaction
RNA Levels and Processing
Transcription
Translational Regulation
Protein Information Protein Physical Properties
Protein Processing/Modification/Regulation
Protein Sequence Features
Protein-Nucleic Acid Interactions
Protein-Protein Interactions
Protein/Nucleic Acid Structure
Substrates/Ligands/Cofactors
Related Genes/Proteins Cross-species Expression
Disease Gene Related
Fungal Related Genes/Proteins
Non-Fungal Related Genes/Proteins
Research Aids Other Features
Strains/Constructs
Techniques and Reagents
Genome-wide Analysis Comparative genomic hybridization
Computational analysis
Genomic co-immunoprecipitation study
Genomic expression study
Large-scale genetic interaction
Large-scale phenotype analysis
Omics
Other genomic analysis
Proteome-wide Analysis Large-scale protein detection
Large-scale protein interaction
Large-scale protein localization
Large-scale protein modification
Other large-scale proteomic analysis
Other Topics Alias
Archived Literature
Evolution
Industrial Applications
Infection and Antifungals
Additional Information Literature Curation Summary
Gene Summary Paragraph
PubMed Search
Expanded PubMed Search
All genome-wide analysis papers

 

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