Question: RNA-seq vs. Microarray
gravatar for mangfu100
5.6 years ago by
Korea, Republic Of
mangfu100740 wrote:

Hi all.

I am studying bioinformatics for my research and I have some questions regarding RNA seq vs. Microarray for gene expression level.

When considering their pros and cons, I think that RNA-seq has more good advantages over Microarray. For example, RNA is available for all species and also can check novel transcribed regions because RNA-seq platform doesn't require pre-defined procedures for checking gene expression level.

And also RNA has good advantages which are alternative splicing and to identify fusion genes. However, I didn't get the reason why RNA-seq has such two good points (alternative splicing, fusion genes) over Microarray techniques.

Could you explain the reason for me? 

sequencing next-gen alignment • 6.3k views
ADD COMMENTlink modified 5.6 years ago by Devon Ryan97k • written 5.6 years ago by mangfu100740
gravatar for Devon Ryan
5.6 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

The two things you aren't sure about are due to microarrays only being able to detect exactly what they were designed for. In the case of fusion genes, to detect that on a microarray you'd have to have a probe spanning the fusion point. Similarly, for alternative splicing, you can only detect what you've designed probes for. That's one of the biggest gains with RNAseq, you can find things that you didn't explicitly want to look at beforehand.

I should note that the only real downside to RNAseq is that signals from genes/transcripts/etc. are competitive. So if you ever want to deconvolve signals originating from multiple sources (e.g., you have heterogenous samples and are interested in differential expression due to something within each of the sources rather than simply between treatment groups) then this is simpler with microarrays (i.e., things like independent component analysis are simpler).

ADD COMMENTlink modified 5.6 years ago • written 5.6 years ago by Devon Ryan97k

Hi Devon, could you clarify the second part (downside) a little more? What feature of RNA-Seq makes the signals competitive?

ADD REPLYlink written 4.1 years ago by ebrudermanver80

Competitiveness is an innate part of sequencing (unless you have really low input and don't amplify it much), cluster number is small compared to the number of fragments available to bind to them.

ADD REPLYlink written 4.1 years ago by Devon Ryan97k
gravatar for fashiondesignrussian
5.6 years ago by
fashiondesignrussian60 wrote:

These are completely different techniques, they supplement each other in some ways, but they are different in nature. Microarray`s expression catches some time moment of a predefined gene set and sequence analysis can cover the entire genome, however, processing and annotation is prone to losing the truth.

You can find free books on topic on and and on amazon and abebooks, of course.

ADD COMMENTlink written 5.6 years ago by fashiondesignrussian60
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