COXPRESdb  
version 4.0

COXPRESdb; co-expressed gene database



(last update) 2010.05.20

FAQ

About coexpression

  1. Can I search negative correlations of gene expression pattern to investigate gene regulation?

    2. No. We do not prepare the function to retrieve negative correlation for two reasons.
    1. Multiple probes are often available for a gene. To calculate gene-to-gene correlation between the genes with multiple probes, We use maxinum correlation among all possible probe combination for two genes of interest.
    2. In general, positive correlation is more useful to suggest gene function than negative correlation.

About network drawing

  1. How does NetworkDrawer select genes to draw gene network?

    2. The actual procedure of NetworkDrawer is as follows:
    • (1) Searching additional genes.
    • (1-1) Checking coexpressed (Top 3 MR) genes from query genes.
    • (1-2) Checking PPI genes from query genes. [option]
    • (1-3) Summarizing genes with at least two edges to the query genes.
    • (2) Making gene network of the genes to draw.

  2. How does COXPRESdb draw the gene network?

    3. We used "neato" function from Graphviz as follows:
    • (1) Prepare a dot file with following parameters.
      • overlap=orthoxy;
      • model=shortpath;
      • start="[regular][1]";
      • splines=true;
      • fontname=Helvetica;
      • node [height=.45, width=.4, fontname=Helvetica];
    • (2) Create a postscript file of gene network.
    • (3) Parse the postscript file for 2 purposes: (a) to decorate the network easy to see, and (b) to annotate it with KEGG annotation.
    • (For small network A)
      • (A-4) Convert the postscript fil to PNG file.
      • (A-5) Make clickable map on html.
    • (For google map network B)
      • (B-4) Convert the postscript fil to PNG files with various sizes.
      • (B-5) Split each of the PNG files into small rectangle PNG files with 256 x 256 picels.
      • (B-6) Use Google Maps API.

Miscellaneous

  1. Can I retrieve genes specifically expressed in the samples I specify?

    2. Sorry. We do not prepare such function.

  2. Is there any similar coexpression database with COXPRESdb?

    Yes. Many coexpression databases are available.