Find Correlated Genes in Large Data Sets

If you are excited to find a gene showing the expression pattern you are looking for, it is time to find other genes that show similar profiles in the experiment.

In this example, we want to find other genes that correlate with NANOG in human ES and iPS cells. To do this in BxGenomicDB, simply select the NANOG gene, and click the correlation button will bring you to a new screen.

Find Correlated Genes

The correlation window will look like this. Note in 3. Correlation Values, you can choose if you want to see positive correlation (similar profiles as target gene), negative correlation (opposite profiles), or both.

After you click submit, wait for a while, and the system willl give you a list of hits ranked by correlation coefficiency. If you get no hits, try lower the cut off and submit again.

For each of the hits, you can review the correlation plot by click show plots at the last column. If you want to see the profile of the hits, just click the probe set ID.

In the case of NANOG, the top hit is a gene called FAM169A (soluble lamin-associated protein of 75 kDa), which shows very similar expression profile as NANOG and the correlation coefficiency is 0.93. You can click the picture at right to see the expression profiles of the two genes.

It will be interesting to follow up to investigate what biological roles FAM169A and lamin may play in stem cell differentiation.

As you can see, correlation tool can be very powerful to identify new targets for subsequent studies.

Correlation between NANOG and FAM169A

 

After you click submit, wait for a while, and the system willl give you a list of hits ranked by correlation coefficiency. If you get no hits, try lower the cut off and submit again.

For each of the hits, you can review the correlation plot by click show plots at the last column. If you want to see the profile of the hits, just click the probe set ID.