Please explain the bimodal pattern of expression in real time PCR. What is meant by it?
Very nice question,
we most of time observe this effect
eg. gene A shows up regulated level in test but the fold changes comes sometime 2 to 10 fold
statistics will consider it as high standard deviation and reject but actual reality is as we go on further new biological replicates we tend to observe this bi-modality if it exist,
I feel we need to observe trend or pattern consistency to make valid conclusion about gene expression
Ref: PNAS, 107.51 (2010): 22096–22101. PMC. Web. 29 Oct. 2017.
Bimodal gene expression (the distribution of gene products that has two maxima) is a cause of phenotypic diversity in genetically identical cell populations, and it is critical for population survival in a fluctuating environment
this is when expression system occurs by two modes leading to diversity of cells and possibly increased survival rates
Very nice question,
we most of time observe this effect
eg. gene A shows up regulated level in test but the fold changes comes sometime 2 to 10 fold
statistics will consider it as high standard deviation and reject but actual reality is as we go on further new biological replicates we tend to observe this bi-modality if it exist,
I feel we need to observe trend or pattern consistency to make valid conclusion about gene expression
Ref: PNAS, 107.51 (2010): 22096–22101. PMC. Web. 29 Oct. 2017.
Bimodal gene expression (the distribution of gene products that has two maxima) is a cause of phenotypic diversity in genetically identical cell populations, and it is critical for population survival in a fluctuating environment
Hi Vijesh, well-asked question, but has numerous aspects to workout. Bimodality in a gene expression is due to the massive heterogeneity prevails in its expression. This bimodality or asymmetry whenever you observe in qPCR, so should have some idea about the overall possibilities to rule out properly, before raising the final claim that you have a bimodal gene expression and these may include;
Primer dimers, non-specific amplifications, mutations, SNPs of heterozygous nature, methylation patterns in DNA, splice variants presence (one of the main reason of a gene's bimodal behavior), existence of asymmetrical distribution of GC content in single product.
So, these bimodals are actually sequence specific and occurs because of two different Tms (melting points) in the sequence.
Bimodal or two-component expression genes are served as excellent candidates for disease biomarkers and this phenomenon has been observed in many cancers, where a bimodal expression of a gene may induce new disease phenotypes. Both modes (peaks) of a certain gene's expression may also correspond to different subtypes of a disease. Bimodality, therefore, is often an unexpected but well significant property of a gene's expression.
So, in a bimodal expression, we either have two distinct levels of transcript abundance (as in splice variant case) OR just the single transcript abundance (possibly due to difference in GC content along the desired gene sequence).
It has also been found that bimodal genes tend to cluster into small groups of 4 to 6 genes with synchronized expression, especially in breast cancer.
Regards....
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