Overview

BioCarta and KEGG define their pathways in different ways.

• BioCarta displays gene interactions within pathways for cellular processes, such as apoptosis and cell cycle regulation, and includes diagrams of molecular assemblies.
• KEGG displays enzymes and intermediary compounds within metabolic and regulatory pathways, also includes diagrams of molecular assemblies, and connects one pathway with another. There are only a few pathways that are common to both BioCarta and KEGG.

As a result, the CGAP Pathway Searcher has been designed to primarily search the two sets of pathways separately.

What Exactly to Put In the Fields

• Keyword in Title of BioCarta and KEGG Pathways

  • Enter any word found in a title, for example signaling, complement, tRNA, or proline.
  • If you prefer, use the wild card (*) to help find pathways. For example, to find pathways involved in inflammation, type inflam* which will bring up "inflammatory response".

• Gene Identifier in BioCarta and KEGG Pathways

  • Enter a gene symbol such as BDP1 or RGS2, or one of the many alternate names for a gene. For example BDP1 is also known as TFC5, TFNR, TAF3B1, KIAA1241, KIAA1689, TFIIIB90, HSA238520, TFIIIB150. All gene symbols are taken from LocusLink.
  • In addition to the gene symbol, a LocusLink ID may be used, e.g., 10621.

• Enzyme or Compound in KEGG

  • If you know the name of the enzyme or compound enter it into the field, e.g., cyclin-dependent kinase 4 or glucose.
  • Click "Help" if you are not sure of the name. When the new window opens, type in part of the name using wildcard characters ('*') before and/or after the word, e.g., cyclin* or *kinase*. Hit "enter". A list of terms is returned in the results box. Click any term to have it inserted into your query field entry box. (Older browsers: click a term in the results box, then click your query field entry box.)
  • In addition to the enzyme name, an E.C. number may be used, e.g., 2.7.7.6, a LocusLink ID may be used, e.g., 10621, or a gene symbol may be used, e.g., GCK. However, the Help may not be used in these cases.
  • In addition to the compound name, a KEGG Compound Number may be used, e.g., C00074. However, the Help may not be used in this case.
  • To search for pathways that link two enzymes or compounds, enter the names of either two enzymes or two compounds, as described above.

The Pathway List Page - The Path Finder Results

The results of every Path Searcher query are returned on a Pathway List Page. The list contains one or more pathways that meet the selected search criteria, and each pathway is linked to its Pathway Graphic view. If the query was to search for pathways connecting two enzymes or compounds, the list would show the interactions between the given components.

The Pathway Graphic View

• BioCarta Pathways

  Each gene symbol that is associated with LocusLink is linked to its Gene Info page where related information about the gene from several NCI and NCBI databases is gathered.

• KEGG Pathways

  • Each enzyme in a KEGG diagram that can be associated via its E.C. number to a LocusLink number is color coded green and linked to its Gene Info page
  • Each compound in a pathway is linked to its own Compound Info Page where alternate names for the compound and its structure are displayed, along with the list of pathways in which the compound can be found.
  • If the query is for a single component within a pathway, each occurrence of that component will be encased in a multi-colored box (enzymes) or highlighted by a multi-colored disc (compounds).