Metabolomics → Visualization

Metabolomic Functions:





UCSD Biochemical Genetics Laboratory

Metabolomic Functions

Welcome to Visual Biochemical Genetics.

Explore metabolic pathways, and visualize your biochemical results
You can view our lab's results superimposed on a collection of metabolic pathways, to indicate which metabolites are outside of reference ranges.  We have imported a nearly complete set of pathways from the KEGG collection, and are continually extending local maps to emphasize the compounds we measure on our metabolomics platforms.  We are also working with the UCSD Biomolecular and Proteomic Mass Spectrometry Facility

Results of both metabolomics (HMDB) and proteomics (Uniprot) can be entered together.  Our lab will provide you with data which can be pasted directly into the software below.   Choose the data and the network below, and then view the map (note: clicking rectangles in maps also links to other maps, so the entire kegg-space can be explored).. 

Newer Software:
  • Enter Omics Data:

    Enter your data in standard format, and then visualize.
    Data must be arranged in three columns: 1) identifier (HMDB or Uniprot), 2) fold-change, 3) significance (p- or q-value).
    Data may be pasted from comma-separated (CSV) format, space-delimited, or tab-delimited format (as from pasted Excel worksheets).
    You will see a listing of pathways in which the specified metabolites are found, and links to display the data superimposed on the pathways.

  • Find Identifiers:

    Find HMDB identifiers to enter -omics data.
    Data is simple arranged in one column, specifying chemical names or identifiers.
    Data may be pasted from comma-separated (CSV) format, space-delimited, or tab-delimited format (as from pasted Excel worksheets).
    You will see a listing of identifiers or synonyms for the specified metabolites, and links to display information.




Old Software:
  • Choose the map:

    Select the map from the listing.
    <Test>Select the map from the listing.</Test>
    You have selected map:  No map selected.<Default is MapUCSD>

  • Choose your dataset (optional):

    Select the sample, specifying the UCSD Biochemical Genetics sample number for your data from the list of recent runs.
    You have selected dataset:  No data selected.<Default is NoData>

  • Visualize the data on the map:

    View the map.
    <Test>View the map</Test>