ArrayXPath
 |PathMeSH |Pathway mapping |Help |ChromoViz |Registration |Contact us
E-Mail:   Password:     
Input to ArrayXPath
 

Input to ArrayXPath is a common tab-delimited text file for a (clustered) gene-expression profile: 
<Probe ID>-<Cluster ID>-[<Expression level at conditioni>]. 

  1. The first row must contain column heading (i.e., ID, ClusterID, condition1, condition2, ...).
  2. The first column must contain either GenBank accession, UniGene ID, LocusLink ID, SwissProt ID, TrEMBL ID, or official gene symbol. Affymetrix probe identifiers can also be used.
  3. The second column has cluster IDs. 
    * When you also want to visualize filtered-out profiles before clustering, put 'NA' as the cluster ID for the filtered probes.
  4. The third to i-th columns are optional and contain expression levels across experimental conditions. 

ArrayXPath dose not perform cluster analysis. The input format is designed primarily for partitional clustering algorithms (i.e., K-means and Self-Organizing Maps) but clustering results from hierarchical algorithms (i.e., dendrogram) may be applied by choosing a threshold carefully.

How to use ArrayXPath

  1. Download and install  SVG Viewer plug-in from Adobe
    (ArrayXPath has been tested in Adobe SVGViewer 3.0 and MS-Internet Explorer 5.0 or higher. MS-Windows XP users may not have to install SVG plug-in.)
  1. Submit your gene-expression cluster data (see input to ArrayXPath). You can choose the correct taxonomy (i.e. Hs, Mm or Rn) and statistical testing. 
     (The process is computationally expensive and may take several minutes depending on the input data size.)
    (Please try example data sets below)
  1. Browse the matched pathways with statistical scores (i.e. q-values, multiple-testing corrected).

  1. Select the pathway of your interest.
Each node has link to gene information page by the GRIP (Genome Research Informatics Pipeline) engine at SNUBI.


  1. Browse the pathway color-coded with gene-expression levels.

  1. Example output 
    10 clusters from the Human HeLa cell-cycle data analyzed by ArrayXPath.
    50 clusters from the Mouse kidney data analyzed by ArrayXPath.

Last Updated (14, February, 2005)  powered by SNUBI