Question: what is difference between HG-U133A and HG-U133B array ? which one to use ?
gravatar for aaponcseku
5.0 years ago by
aaponcseku10 wrote:

I am working on NCI-60 database for data mining purpose. In NCBI I found miRNA expression profiles (link). But for mRNA of each cell lines I found 2 kinds of expression profile array in NCBI (link) categorized as Affymetrix HG-U133A and HG-U133B. They also overlap many mRNA probes and their expression values. I can't understand which one to use or how ? What is the difference ?

gene rna-seq R genome • 5.5k views
ADD COMMENTlink modified 3.6 years ago by jmfriedman710 • written 5.0 years ago by aaponcseku10
gravatar for cpad0112
5.0 years ago by
cpad011214k wrote:

This PDF from Affymetrix clarifies the difference between 133A, 133 B and 133 plus. As for using the datasets, look at this question: Combining Two Platforms Affy Hgu133A And Hgu133B. It seems 60 samples are analyzed using both the chips.

copy/pasted from Affymetrix website:

The HG-U133A Array includes representation of the RefSeq database sequences and probe sets related to sequences previously represented on the Human Genome U95Av2 Array. The HG-U133B Array contains primarily probe sets representing EST clusters.
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by cpad011214k
gravatar for jmfriedman7
3.6 years ago by
jmfriedman710 wrote:

One big difference (for studies about cancer) is that the HG-U133B array appears to include gene for PD-L1 (annotated as CD274) but this gene appears to be absent from the annotation for the HG-U133A array; maybe I have just not found the right annotation since there can be multiple names for this gene. For older data sets, this PD-L1 gene was not yet recognised to be of importance. The related gene PD-1 appears to be in both arrays.

On the other hand, HG-U133B seems to contain many fewer lines in the annotation file and so maybe fewer genes. I suggest you check for known proteins of interest, to make sure that no important ones are missing, in case you want to compare known actors with newly found ones.

ADD COMMENTlink written 3.6 years ago by jmfriedman710
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