Question: Is microarray gene expression analysis is dead ?
0
gravatar for cjgunase
2.8 years ago by
cjgunase30
United States
cjgunase30 wrote:

Is analyzing microarray data is considered obsolete? are there recent publications using gene expression data to construct large gene regulatory networks ?

microarray gene expression • 1.8k views
ADD COMMENTlink modified 2.8 years ago by genomicswolf20 • written 2.8 years ago by cjgunase30

I think it is still a method of choice for targeted gene expression analysis. Used more often in clinics. If I'm not wrong, CGH and SNPs are often studied using Array. This journal issue might be of help.

ADD REPLYlink written 2.8 years ago by Satyajeet Khare1.4k

For a comparison of microarray with RNA-seq, read this paper.

ADD REPLYlink written 2.8 years ago by Jean-Karim Heriche20k
3
gravatar for Marge
2.8 years ago by
Marge280
Italy
Marge280 wrote:

I don't think microarrays are dead, not yet, for a number of reasons.

Despite what WouterDeCoster says, I think they are still cheaper than RNAseq, allowing you more replicates for the same amount of money (so more reliable measurments).

It is definitely true that the landscape of what you profile is limited to what you spot on the array, but then for most applications people just collapse all reads mapping to a given gene even after doing the fancy RNAseq stuff.

I also think that analysis of RNAseq data is still much more challenging, in terms of computational resources as well as preparation of the analyst. Microarrays have been around for so long that there are many many tools to analyse them without much prior preparation. Space and RAM-wise, well: I can easily analyse from start to end a relatively large microarray dataset in my home laptop, but I definitely cannot do this for a large RNAseq dataset.

Here is an example of a recent publication in which expression profiling is microarray based: http://www.nature.com/nature/journal/v535/n7612/full/nature18637.html.

There are many more: not dead yet.

ADD COMMENTlink written 2.8 years ago by Marge280

I agree. There's just so many existing microarray studies out there to be mined, it can't be considered obsolete technology just yet.

ADD REPLYlink written 2.8 years ago by russhh4.6k
1
gravatar for WouterDeCoster
2.8 years ago by
Belgium
WouterDeCoster40k wrote:

Based on what I know about prices a microarray is not cheaper than RNA-seq (depending on desired number of reads of course), and RNA-seq is also more sensitive, giving you nucleotide level information and information about unannotated genes/transcripts. Therefore, I don't see a reason to use microarray over RNA-seq.

ADD COMMENTlink written 2.8 years ago by WouterDeCoster40k
1

Considering the availability of a Bioinformatician (also time in some cases) expertised in sequence analysis, I saw people still opting for Microarrays, but this is applicable for only few cases.

ADD REPLYlink written 2.8 years ago by venu6.2k
0
gravatar for lakhujanivijay
2.8 years ago by
lakhujanivijay4.2k
India
lakhujanivijay4.2k wrote:

Yes, to some extent, but NGS is still something which people are learning to gradually phase out microarrays. This threat was long known to microarray manufacturers. Read this article.

ADD COMMENTlink written 2.8 years ago by lakhujanivijay4.2k
0
gravatar for chen
2.8 years ago by
chen1.9k
OpenGene
chen1.9k wrote:

microarray application is narrowed, but it's still far to die

ADD COMMENTlink written 2.8 years ago by chen1.9k
0
gravatar for Irsan
2.8 years ago by
Irsan6.9k
Amsterdam
Irsan6.9k wrote:

In research, micro-arrays are on their return but in clinical diagnostics they are still used a lot, in particular array-CGH or SNP-arrays to determine germ line CNVs that predispose to disease.

ADD COMMENTlink written 2.8 years ago by Irsan6.9k

True, but the question is mainly about arrays for gene expression ;)

ADD REPLYlink written 2.8 years ago by WouterDeCoster40k

Oh yeah that's right, forgot about that...

ADD REPLYlink written 2.8 years ago by Irsan6.9k
0
gravatar for genomicswolf
2.8 years ago by
genomicswolf20
genomicswolf20 wrote:

Yes, in our laboratories it is completely dead, you know, if it is interesting to you. However, many institutions perform that every day.

ADD COMMENTlink written 2.8 years ago by genomicswolf20
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