COXPRESdb

ver. 6.0


FAQ

About coexpression

  1. Can I search negative correlations of gene expression pattern to investigate gene regulation?
  2. Can I use tissue-specific coexpression data?

About NetworkDrawer

  1. How does COXPRESdb select genes to draw gene network?
  2. How does COXPRESdb draw the gene network?

Miscellaneous

  1. Can I retrieve genes specifically expressed in the samples I specify?
  2. Is there any similar coexpression database with COXPRESdb?




answer

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

Unfortunately, you cannot. 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.

answer

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

We know many users have a great interest on the tissue-specific coexpression data. However, we do not have a direct approach to construct them.
To construct tissue-specific coexpression data, we should select the microarray samples for the tissue. On the other hand, to construct reliable coexpression data, we should keep high variety of samples.
As one trial, we extracted genes expressed in a tissue from general coexpression data. Tissue specific-coexpression data on COXPRESdb is constructed like this.



answer

How does COXPRESdb select genes to draw gene network?

The actual procedure of NetworkDrawer is as follows:


answer

How does COXPRESdb draw the gene network?

We used "neato" function from Graphviz as follows:


answer

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

Sorry. We do not prepare such function.


answer

Is there any similar coexpression database with COXPRESdb?

Yes. Many coexpression databases are available.