Bioinformatic Interpretation of Gene Expression in Genecard

Question

[Shicheng Guo]

Hi All,

How to interpret the gene expression Figure from Genecard website. Enclosed is the gene expression of LDHA gene.

From the microarray and SAGE dataset, it seems this gene is median expressing, however, from RNAs-eq, it seems this gne is high expressing gene?

http://www.genecards.org/cgi-bin/carddisp.pl?gene=LDHA&keywords=LDHA

How to deal with this disparities?

Thanks.

Answer 1

[Ibrahim Tanyalcin]

Dear,

Due to the technical differences, comparing them on an absolute scale might not be the best way to go. I would first try to normalize them within each other and then compare them. Just to exemplify, within each case, take the min and max and then normalize:

new Value = scaleFactor*((value-min)/(max-min))+offsetFactor

This is just mapping. If you take scaleFactor as 1 and offset as 0, you will end up with values between 0 and 1 (you can also use other transformations/mappings but try the obvious one first). Then maybe comparing these values might be easier and more informative.