The Pathway Database
A pathway database is a clc object that contains information about pathways, specifically which functional terms are present in each pathway, e.g. for MetaCyc each pathway is associated with a set of EC numbers. These EC numbers form the basis for pathway calling from an abundance table or a differential abundance table.
The pathway database has three views:
- The Pathway table (
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- The Compound table (
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- The Enzyme table (
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The Pathway table
The pathway table is a list of all pathways in the database and it has two columns, Name and MetaCyc ID, giving the name of a pathway and its MetaCyc ID, which is also a link to the relevant online site. The pathway table has two buttons at the bottom- Open Pathway View: Opens a split view with a visualization of the selected pathways. Note that double clicking on a single line in the Pathway table is identical to selecting that line and clicking on Open Pathway View.
- Create New Pathway Database: Creates a new database only containing the selected pathways. This is useful, e.g. for constructing a species specific database
The Compound table
The compound table is a list of all compounds, including side compounds, in the database. This table has three columns,- Name: The name of the compound.
- MetaCyc ID: The compound's MetaCyc ID which is a link to the compound's description on the MetaCyc homepage.
- Cellular location: The location of the compound in the cell. Some names occur several times as their cellular locations are different, e.g. there are protons in the cytosol, outside of the cell and inside the lumen of some organelles.
- Open Pathway View from Selected Compound(s): Opens a split view with a visualization of the pathways in which the selected compounds occur. Note that double clicking on a single line in the Compund table is identical to selecting that line and clicking on Open Pathway View from Selected Compound(s).
- Create New Pathway Database: Creates a new pathway database containing only pathways in which the selected compounds occur.
The Enzyme table
The enzyme table is a list of all enzymes in the database. This table has three columns,- Name: the name of the Enzyme. Note that some names occur several times because they reference different genes.
- MetaCyc ID: the enzyme's MetaCyc ID which is a link to the enzyme's description on the MetaCyc homepage.
- Cellular location: the location of the enzyme in the cell. Some names occur several times as their cellular locations are different, e.g. there are protons in the cytosol, outside of the cell and inside the lumen of some organelles.
- Open Pathway View from Selected Enzyme(s): Opens a split view with a visualization of the pathways in which the selected enzymes occur. Note that double clicking on a single line in the Enzyme table is identical to selecting that line and clicking on Open Pathway View from Selected Enzyme(s).
- Create New Pathway Database: Creates a new pathway database containing only pathways in which the selected enzymes occur.