Is analyzing microarray data is considered obsolete? are there recent publications using gene expression data to construct large gene regulatory networks ?
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.
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.
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.
microarray application is narrowed, but it's still far to die
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.
Yes, in our laboratories it is completely dead, you know, if it is interesting to you. However, many institutions perform that every day.
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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.
For a comparison of microarray with RNA-seq, read this paper.