NCBI BioSystems Database
 
 
 
 
How to find the pathways in which a given gene or protein is involved
 
 

Search the NCBI BioSystems Database directly to retrieve biosystems that include the desired component

  • to search for biosystems that contain specific genes, you can use the Gene Name or Gene ID field. The biosystems that are retrieved have been associated with that gene through the method descibed in the data processing section of the BioSystems help document. (For example, search the BioSystems database for PTGS1[gn], or search for 5742[gid], to retrieve biosystems associated with the human prostaglandin-endoperoxide synthase 1 gene.)


  • to search for biosystems that contain specific proteins, you can use the Protein Name or Protein ID field. The biosystems that are retrieved have been associated with that protein through the method descibed in the data processing section of the help document. (For example, search the BioSystems database for prostaglandin endoperoxide synthase 1[pn], or search for NP_000953[pid], to retrieve biosystems associated with the human PTGS1 gene product.)
OR

Search the Entrez Gene or Entrez Protein database for the record of interest, then link to BioSystems records that include the gene or protein as a component

  • retrieve a record for a gene or protein of interest from the Entrez Gene or Entrez Protein database. (For example, retrieve the Gene record 5742: human PTGS1, or retrieve the protein sequence record for its gene product, NP_000953: prostaglandin G/H synthase 1 isoform 1 precursor [Homo sapiens].)


  • view the "Links" menu for the record and select the link for "BioSystems." (The menu has a label such as "Links" or "All links from this record" and is typically located in the right margin of the browser window.)


  • If you are looking at a Gene record, the "General Gene Information: Pathways from BioSystems" section of the record provides another way to view/link to the associated biosystems. (As an example, see GeneID 5742: human PTGS1: general gene information.)
    • Click on a biosystem of interest to view its record. The gene record from which you started will appear at the top of the "genes" folder tab for that biosystem and will be selected by default (i.e., its check box will be activated). You can then click on the "Highlight selected records in source database" to view the location of the gene within the pathway diagram, if that function is available for a given biosystem. (Currently, the highlight function is available only for KEGG records and the selected gene will be displayed with a red outline, as shown in an illustrated example. The gene name will also appear in red font, as may other gene names in the pathway diagram, indicating a link to the corresponding KEGG gene record. The red outline, however, will only appear around the gene(s) that were selected in the NCBI biosystem record.)

  • The biosystems that are retrieved have been associated with the gene or protein through the methods descibed in the data processing/create direct links section of the BioSystems help document.
 
 
 
 Revised 29 September 2014