microRNA cluster queries

[Cook, Michael (NIH/NCI) [E]]

Hello,

 

I was wondering whether there is any easy way to query whether any of ~100 microRNAs are part of a microRNA cluster and then download the information for each of the identified clusters (the queried microRNA name, the microRNA cluster name, and the other (possibly non-queried) microRNAs that are part of that cluster)?

 

Thanks for any and all advice.

 

Best wishes,

 

Michael

 

[Brian Lee]

Dear Michael,

Thank you for using the UCSC Genome Browser and your question about looking at microRNA in the browser.

Here is a session of some microRNA data that you might be interested to explore: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hg38_microRNA

It features a track of microRNAs from snoRNABase and miRBase and also a recently added Pubic Hub of microRNAome expression (for inquiries, please contact Marc Halushka at halu...@jhmi.edu).

When looking at data in the UCSC Genome Browser you can also upload custom tracks, in the simplest form as BED (Browser Extensible Data) where three columns define a chromosome a start and an end (a forth column can annotate a name, fifth provide a score, and a sixth strand: http://genome.ucsc.edu/FAQ/FAQformat.html#format1).

If you transferred your 100 microRNAs into BED regions, like these below, you could add such a custom track, that you could paste or upload on the Custom Track page (accessed under "My Data" top blue menu bar, and then "Custom Tracks" option).

track name=MyRNAs description="example mRNAs on chr9" 

chr9 90023451 90023469

chr9 91636277 91636296 

chr9 92292461 92292484

chr9 92527991 92528012

chr9 93819367 93819382

chr9 94175962 94175983

...

With your custom regions loaded you could then use another tool called our Table Browser to intersect the regions with the other data loaded or our Data Integrator tool to return your custom regions with additional fields from other tracks that co-located in those regions.

With custom regions loaded, you could go to the Data Integrator tool (under the top Tools menu) and then select the custom track (named MyRNAs) and then find the sno/miRNA track under the "Genes and Gene Predictions" track group and "Non-coding RNA (wgRna) track. At this point if you clicked "get output" you would get all the fields from both of these tables of data. By clicking the "Choose fields" in the "Output Options" you could select all the information from our custom track and then only select the "name" from the wgRNA track. This would result in something like the following:

chr9 90023451 90023469 hsa-mir-4290

chr9 91636277 91636296 

chr9 92292461 92292484 SNORA84

chr9 92527991 92528012

chr9 93819367 93819382 hsa-mir-4291

chr9 94175962 94175983 hsa-let-7a-1

Only the custom regions that overlapped with a named item in wgRNA would result in the 4th column receiving a name annotation. You could further add those results as a new custom track like the below:

track name=DataInteg description="results from data integrator using wgRna track" 

chr9 90023451 90023469 hsa-mir-4290

chr9 92292461 92292484 SNORA84

chr9 93819367 93819382 hsa-mir-4291

chr9 94175962 94175983 hsa-let-7a-1

And visualize that result. For example, here is a session where you can see some results from a Data Integrator query for just a region chr9:89,793,222-95,453,222 (you can perform this across the entire genome for your data): http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hg38_microRNA_question

What it shows is an example load of microRNAs on chr9 that was then cross-checked with the snoRNABase/miRNA track, you can see with added yellow highlights that some of the data didn't have named hits, but does appear to be in the microRNAome hub. One could repeat these steps and instead use the hub's "Primary cells (hub_176129_primary_cells)" table as the track to perform the Data Integration against. You could also use the Data Integrator to extract other data to a file and then locally manipulate the results.

Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further questions and reply to gen...@soe.ucsc.edu messages will be archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee

UC Santa Cruz Genomics Institute

Training videos & resources: http://genome.ucsc.edu/training/index.html

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