SGD Help: Literature Guide

SGD gathers references in three different ways.

• 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 some related strains (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.

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

• 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.

• 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.

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

• 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 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.). 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 below.

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