Question: miRNA Probe IDs
0
gravatar for snufkin002
3.0 years ago by
snufkin0020
snufkin0020 wrote:

Hey, 

I'm new to the world of computational genetics, and trying to get the hang of analysing this sort of data. I've got a list of miRNA probe IDs of the form A_25_P00012226 and CRINCR2000004659, for example, and I'm trying to figure out how to obtain the miRNA ID (like hsa-mir-210, for example), so that I can use this with mirbase to get the predicted cognate targets. Is there an R package that can help with this task? 

Any help would be much appreciated, and please let me know if I should clarify anything.

Thank you!

mirna microarray mirbase.db • 563 views
ADD COMMENTlink modified 3.0 years ago by Dario Strbenac1.5k • written 3.0 years ago by snufkin0020

It's helpful if you say what platform you are working on. We can always google the IDs you provide, but any extra steps we have to do in order to help you decreases the probability of anybody wanting to do so.

I did google those IDs, and at least one looks like an Agilent miRNA array ID. And unfortunately we don't have a ready made package for that array. Your best bet would be to download whatever annotation file Agilent makes available and use that to do the annotations.

ADD REPLYlink written 3.0 years ago by James W. MacDonald51k

Thank you for your answer!

ADD REPLYlink written 3.0 years ago by snufkin0020
Answer: miRNA Probe IDs
2
gravatar for Dario Strbenac
3.0 years ago by
Dario Strbenac1.5k
Australia
Dario Strbenac1.5k wrote:

Unfortunately, Agilent doesn't place their microarray designs in convenient locations such as GEO Browser. You will need to register for Agilent's eArray website. Once registered and logged in, you can obtain the probe design files for their commercial arrays.

Also, beware that microRNA probes bind more miRNAs than what you are interested in. For this reason, Agilent designs multiple probes for each miRNA. For example, hsa-mir-300 has four probes on a particular microarray that I've worked with:

A_25_P00012884: AGAGAGAGTCTGC
A_25_P00012885: AGAGAGAGTCTGCC
A_25_P00012886: AGAGAGAGTCTGCCC
A_25_P00012887: AGAGAGAGTCTGCCCT

It's the same probe sequence, but each probe differs in length by 1 nucleotide to another probe. The shorter the probe is, the more specific it is to the miRNA it is designed for and the less unwanted miRNAs it binds. But, there's no information about what other miRNAs each probe binds to and in what proportion. The proportion of incorrect binding also varies from one experiment to the other, because in some experiments, the cells don't express the cross-hybridising miRNAs but in other experiments, they do. Microarrays aren't a good technology for measuring miRNAs because of cross-hybridisiation problems. miRNA-seq would give clear results since there is no problematic hybridisation involved.

You should read the manufacturer's technical overview to understand the limitations of miRNA microarrays before commencing your analysis of them.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Dario Strbenac1.5k

Thank you for your answer as well! That's really helpful.

In consolidating the data to gain an expression matrix for each miRNA in the case of multiple probes, what is typically done? Some sort of mean? Or is simply one probe chosen? 

ADD REPLYlink written 3.0 years ago by snufkin0020

The values for different probes related to a particular miRNA are typically added up, but different research groups do it differently. You'd only average if they were designed to measure the same molecule, which they are not. You have to hope that very few miRNA will bind to incorrect probes, although there's not way to know if it's happening rarely or often. I suppose that you'll find out how much of a problem the unspecific binding is when you try to experimentally validate them using another technique. An interesting study that nobody has done before (not even the manufacturer) is to purchase certain miRNAs and make spike-in mixtures of them to evaluate the binding performance. Unfortunately, there isn't much motivation for it, because most researchers are doing miRNA-seq these days.

Note that there are also 10 replicates of each individual probe. You could average these.

ADD REPLYlink written 3.0 years ago by Dario Strbenac1.5k
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