Dear Friends
Hi
I am working about gene expression. I have gotten fold change so high. for example: 80000 fold, but I do not understand why. please tell me about why it is so high.
thanks so much
Allahdou
Haveing almost no expression under control condition and some expression under treatment conditions will give you an arbitrary high fold-change. In the limiting case that the expression under control condition tends to zero, the fold-change tends to infinity. "Fold-change" is not a very useful mesaure is such cases where the expression under one condition is almost zero, and it simply inadequate in cases where the expression is exactly zero.
Are you using qRT-PCR and pfaffl method quantification? If the response is Yes, each cycle is 1 log of differences. If you have crazy differences could be mathematical problems (see previous response), technical problems (bad quality of the sample or not good primers, that leads to very late cycles or very early, both are in non confidence areas of the amplification curve). If you provide more information regarding what samples are you comparing, CT of your gene of interest and CT of your houskeeping gene probably we could figure out the reason of your results.
What is the source of the gene expression data? Microarray, RNA-Seq, qPCR? Microarrays are notorious for vastly over estimating induction of highly induced genes as the detector simply gets saturated with signal well outside the range it can reliably measure. In such cases, you can be confident that your gene was highly induced, but not by how much. With RNA-Seq, a bad normalization scheme or skewed count distribution can be problematic as well.
Jochen Wilhelm
Dear Sir,
Sometimes I have also faced the same problem and experienced 500-600 fold increases using Real-Time PCR platform (SYBR Green chemistry). So, what method is scientifically correct to check the expression pattern for those very lowly expressed genes in control.
With regards,
Koner
- Badges
- Science topic
- Similar topics
- Biological Science
- Genetics
- Gene Expression