GO Molecular Function

Before you make a GO annotation

• Gene Ontology (GO) annotations are used to describe the normal (wild type) functions, processes and cellular components or locations of a gene product (protein or RNA).
• Molecular Function is the basic activity performed by a gene product, such as "protein serine/threonine kinase activity", "transporter" or any other activity that occurs at the molecular level. As a general rule, molecular functions correspond to single step activities performed by individual gene products. A gene can have multiple molecular functions.
• Gene products may be annotated with multiple molecular function terms.
• Whenever possible, we want to connect the molecular function of a gene to other GO terms or gene products through annotation extensions:
  • The cellular component where that function happens (e.g. the cytoskeletal protein-membrane anchor activity of cdc15 takes place at the medial cortex).
  • The biological process in which this molecular function is involved (e.g. that cdc15 activity is involved in the mitotic actomyosin ring assembly).
  • The cell cycle phase during which it occurs (Cell cycle phases are also GO biological processes).
  • The gene products targeted by the molecular function (all the proteins that Cdc15 anchors)
    
  • The cellular response to stimulus in which that molecular function is involved (e.g. hsf1 is a heat-shock transcription factor, so we can connect its "transcription regulatory region nucleic acid binding" molecular function to the "cellular response to heat")
  • The DNA region where a gene product binds. For instance, in the example below we connect the DNA binding activity of the transcription factor with HSE (Heat Shock Element, a term from the Sequence Ontology) to indicate the type of sequences where DNA binding happens.
    

Video summary

Making an annotation

On the Quick Links list, click on GO molecular function to open a window that requires you to indicate:

• Gene: the gene that shows the molecular function. See how to add genes.
• Term name: a GO term describing the molecular function.
  • Start typing a molecular function in the search box. If you do not find the precise function you are looking for, choose a broad term (e.g. catalytic activity, molecular adaptor, transporter) that can be refined later.
  • Click the chosen term, and verify that the displayed definition describes the phenotype you want to annotate. There is sometimes a "Comment" section with extra tips for annotation.
  • If the blue button reads Next, click it and see if you can find a more specific term that the one you originally selected. If so, select it and do as before.
  • Otherwise, click Finish.
  • If you do not find the term you require, select a broader term, and request a new one clicking on Suggest a new term on the right side of the text box.
• Annotation extension: this field appears once you have selected a GO term. Always click the Add button to see if you can specify:
  • Links to gene products: extensions such as anchors, transports, phosphorylates, etc. link the molecular function of a gene with the gene products that are substrates of that activity. Some gene products should be linked to themselves (e.g. pom1 phosphorylates pom1)
  • Links to biological processes:
    • involved in biological process to indicate that the function takes part in a particular cellular process.
    • happens during to indicate that the function occurs during a cell cycle phase or cellular response to stimulus.
  • Links to a cellular component: physical location to indicate that the function occurs at a specific location or protein complex.
  • Links to sequence ontology terms: to indicate the type of transcript or DNA regions a gene product binds to.
  • Modified form: sometimes, only a certain modified form of the gene product (e.g. phosphorylated) exhibits the activity. This is very valuable information, but requires a PR ontology term to exist for the modified version of the protein, which is rare. You can include this information in the comment section (e.g. write: "phosphorylated form").
  • You can make several annotations with the same molecular function and gene, with different extensions:
    • To link it to several gene products (e.g. different substrates of a kinase).
    • To indicate that a gene kinase activity phosphorylates a protein inside the nucleus during mitosis, and a different one in the cytoplasm during interphase.
  • You can find some useful biological examples in the Before you make a GO annotation box.
• Evidence code: the type of experiment where the phenotype was observed.
• Comment: it's very useful for us if you indicate the figure or table where this phenotype comes from.