SGD Help: Yeast Biochemical Pathways

Contents:

• Description
• Main Query Page
  • Query box
  • List of pathways
  • Browse ontologies
  • Links to summary information
• Advanced Query Form
• Viewing Yeast Biochemical Pathways Pages
  • Overview diagram
  • Pathways
  • Reactions
  • Enzymes
  • Compounds
  • Gene-reaction schematic
• Using the Expression Viewer

Description

Main query page

The main query page is organized into several sections that allow you to search the Yeast Biochemical Pathways dataset in different ways. The only dataset that is available is for the S. cerevisiae strain S288C, which is the reference strain at SGD.

Query box

• The query box is a keyword search of the information available in the biochemical pathways dataset at SGD. You can search for a protein name, a pathway, a reaction, a compound, or a gene. The keyword can be text or an E.C.#. It will automatically add a wildcard character to the beginning and end of your keyword. It does not support Boolean searches. The search is specific for the Yeast Biochemical Pathways dataset and will not search the rest of the database at SGD.
  
  
• If you search by genes, the result will be a Pathway Tools gene page containing a brief description of the gene and the reaction(s) catalyzed by the gene product. It will not automatically display the SGD locus page but if you click on the "Unification Link", you will be directed to the SGD locus page.
  
  
• If there is only 1 match to the keyword, it will be displayed immediately. If there is more than 1 match, all the results will be listed. If your keyword is not present in the match, the keyword matched a synonym.

List of pathways

• This option lists all the pathways present in the database. The pathways are divided into general categories that parallel the pathway ontology.
  
  
• If you click on the ontology category name, you will see a detailed ontology category page.
  
  
• If you click on a pathway name, you will be directed to the pathway page.

Browse ontologies

• The pathways, E.C.#, and compounds in the Pathway Tools are organized into an ontology. This allows users to see the relationship between different pathways, E.C.#, or compounds.
  
  
• Selecting one of these ontologies and clicking "Submit" will display the categories of the ontology that you can browse. You can browse the ontology by clicking on a name of a category. Each class will display the parents of that category as well as all children of that cateogory.
  
  
• The ontology of genes is a hierarchy of gene products. Since biological information about a gene product is captured at SGD using Gene Ontology (GO) terms, this ontology is not curated at SGD. Most of the gene products involved in biochemical pathways will be listed under the categories "unclassified" or "ORFs".

Links to summary information

• The summary page lists the statistics of the dataset, such as the number of pathways and number of enzymes in the dataset.
  
  
• The Overview Diagram shows the full metabolic map of the dataset. More information about the Overview Diagram is available below.
  
  
• The Expression Viewer allows you to overlay expression data onto the Overview diagram. More information about this tool is available below.
  
  
• The release notes describe information about the history of the dataset.
  
  
• The PathoLogic Pathway Analysis page contains links to web pages that provide a visual overview of the current dataset. The Pathway Report lists all pathways that have been created automatically or manually. The Missing Reactions Report lists all reactions that have not been associated with a gene product.
  
  

Advanced Query Form

The Advanced Query form allows you to retrieve specific types of information from the Yeast Biochemical Pathways. The data structure of the Yeast Biochemical Pathways is identical to EcoCyc and other datasets created using the Pathway Tools. The Pathway Tools provides an excellent help document for the Advanced Query.

Viewing Yeast Biochemical Pathways Pages

Every item on the pages is a hyperlink to a detailed page for that item. It will be underlined or appear as colored text.

• The blue reaction lines will direct you to the reaction page. Clicking on the E.C.# also takes you to the reaction page. The reaction page is described in detail below.
• The gold enzyme names will direct you to the enyzme page. The enzyme page is described in detail below.
• The purple gene names will direct you to the SGD locus page.
• The red compounds names will direct you to the compound page. The compound page is described in detail below.

Overview diagram

• The overview diagram displays all the biochemical pathways and reactions that have been created in the S. cerevisiae dataset.
  
  
• All shapes represent metabolic compounds of different classes. A legend is also available on the right side of the overview diagram.
  
  
  • Triangle: amino acid
  • Square: carbohydrate and derivatives
  • Diamond: proteins and modified proteins
  • Vertical ellipse: purines
  • Horizontal ellipse: pyrimidines
  • T: tRNA (not curated at SGD)
  • Circle: all other compounds
  • Filled in shape: phosphorylated compound
  
  
• Blue lines represent reactions that have been associated with a gene product. Reactions that have not been associated with a gene product are grayed out.
  
  
• The gray lines between metabolic compounds indicate where the same compound is present in a different reaction. For the sake of clarity, the gray lines are not exhaustive.
  
  
• The TCA cycle is shown in the center, with catabolic pathways on the right hand side and biosynthetic pathways on the left hand side. The flow of the pathway is from the top of the page to the bottom. On the far right side, reactions which are not part of pathways are listed.
  
  
• If you mouse over a compound, the name of the compound and the pathway it is in will appear on the bottom of your browser window. This will only work for Javascript-enabled browsers.
  
  
• If you click on a compound, the pathway containing that compound will be displayed.

Pathways

• Each pathway are shown on a single page.
  
  
• There are 5 levels of details to view the pathway. If the pathway contains many reactions, only intermediate compounds and reaction arrows are displayed initially. If the pathway contains only a few reactions, more detailed information, such as gene name and enzyme name, are shown as the default. You can use the "More detail" and "Less detail" buttons at the top of the page to browse the pathway detail.
  
  
• At the most detailed level to view the pathway, the compound structure for each intermediate in the pathway, the compound structure for all cofactors in the reaction, the gene name, and the enzyme name are displayed.
  
  
• Below the pathway diagram, the pathway ontology category containing the pathway are listed. In addition, any sub-pathways that make up the current pathway or any pathway that contains the current pathway are listed.
  
  
• Any synonyms for the pathway are listed.
  
  
• At the bottom of the page, an icon representing the current pathway appears in the overview diagram. The reactions are color coded based on how many pathways the reaction occurs in S. cerevisiae.

Reactions

• Each reaction is displayed on a single page that lists the E.C# of the reaction at the top of the page.
  
  
• The reaction page lists the following details of the reaction.
  
  
  • E.C. ontology category. For more information about the ontologies available through the Pathway Tools, please read the help section on viewing these ontologies.
  • Name of the enzyme that catalyzes the reaction
  • Gene name
  • Pathways that contain this reaction
  • The compounds and cofactors involved in the reaction
  • The ExPASy website that lists other gene products that catalyze the reaction. This hyperlink takes you to an external site.
    
    
• Below the reaction diagram, there is a gene-reaction schematic. More about the gene-reaction schematic is described below.

Enzymes

• The enzyme page lists the name of the enzyme, any synonyms or alternative enzyme names, the gene the codes for the polypeptide, the gene-reaction schematic (see below), the reaction(s) catalyzed by the enzyme, and the pathways that contain the current reaction.
  
  
• If the enzyme catalyzes multiple reactions, they will all be listed.

Compounds

• The compound page lists the common name of the formula, any synonyms, the empirical formula, the molecular weight, and the structure (if available).
  
  
• In addition, the Smiles string of the chemical compound is shown. Smiles is an alternative nomenclature to deescribe chemical structures.
  
  
• The bottom half of the page lists the reaction in which the chemical compound is used as well the pathways that contain the reaction.

Gene-reaction schematic

• The gene-reaction schematic is a visual representation of the relationship among a set of genes, enzymes, and reactions.
  
  
• The boxes on the left hand side represent the reactions, the boxes on the right hand side represent genes, and the circles in the middle represent polypeptides or protein complexes. Depending on which page you are viewing, the appropriate box or circle will be filled in.
  
  
• Each of the boxes and circles is a hyperlink to the reaction page, the enzyme page, or to the SGD locus page.
  
  
• The lines represent the relationship between these objects. A line from the gene to a circle indicates that the gene codes for that polypeptide. A line from a circle to another circle indicates the gene product is a subunit of that complex. A line from the circle to the reaction indicate the reaction is catalyzed by that polypeptide or protein complex.

Using the Expression Viewer

The Overview Expression Viewer is a feature of the Pathway Tools that allows you to superimpose expression data onto the metabolic Overview Diagram. With this feature, you are able to import a data file and display the absolute expression levels of metabolic enzymes, compare the expression of metabolic enzymes under different conditions, or create an animation of how expression levels change over time. The Pathway Tools provides a help document that includes information about file formats, analysis options, and interpreting results.

Since the Yeast Biochemical Pathways dataset only contains genes that are involved in metabolic pathways, only these genes in the dataset will be taken into consideration. In addition, if a metabolic enzyme has not been associated with a reaction, the results will not be shown on the Overview Diagram. As a consequence, the statistics produced by the Pathway Tools may be skewed.

At this time, only datasets available on your local machine (ie, your hard drive) can be used to run the Expression Viewer. If you are interested in a dataset available through Expression Connection at SGD, please contact us.

Warning: If you import a file containing thousands of data points, your query may time out or stall.

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