regarding miRNA cluster visualization

[Anusha Angajala]

Dear Sir or Madam,

I have a list of miRNAs as bellow differential expressed in my experiment. Kindly please help me to do followings.

1. How can I get chromosomal location for list of miRNAs. Currently, I am trying to get the location by miRbase one by one manually. If I can get all by one single search that would be good.

2. I am unable to see their location or tracks and map them to chromosome.

Any advice would be very helpful.

https://www.sciencedirect.com/science/article/pii/S0165037812006523#fig0005

https://www.nature.com/articles/s41598-018-33712-4.pdf

List of DEGs

hsa-mir-129-2

hsa-mir-129-1

hsa-mir-135b

hsa-mir-584

hsa-mir-455

hsa-mir-20a

hsa-mir-4661

hsa-mir-20b

hsa-mir-17

Thank you so much,

Anusha.

[Conner Powell]

Dear Anusha,

Thank you for using the UCSC Genome Browser and for your question about determining chromosomal location for miRNAs.

To obtain chromosomal locations for miRNAs, we recommend using the sno/miRna track which contains data about the microRNAs from the miRBase at the Wellcome Trust Sanger Institute(WTSI).

To obtain the chromosomal locations for miRNAs from the sno/miRna track, you can use the following steps:
1. Navigate to the Table Browser, https://genome.ucsc.edu/cgi-bin/hgTables.
2. Make the following selections:

clade: Mammal
genome: Human
assembly: Dec. 2013 (GRCh38/hg38) 
group: Genes and Gene Predictions
track: sno/miRNA
table: wgRna
region: genome

3. Next to 'identifiers (names/accessions)', click 'past list' or 'upload list' based on your preference.
4. Submit your list of miRNA
5. Click 'get output'.

You can also use the following link to access wgRna track on the Table Browser: https://genome.ucsc.edu/cgi-bin/hgTables?hgta_doMainPage=1&hgta_group=genes&hgta_track=wgRna&hgta_table=wgRna. Then complete steps 3-5 mentioned above.

Your output should look similar to this:

#bin    chrom    chromStart    chromEnd    name    score    strand    thickStart    thickEnd    type
2152    chr1    205448301    205448398    hsa-mir-135b    0    -    0    0    miRNA
1722    chr5    149062312    149062409    hsa-mir-584    0    -    0    0    miRNA
1563    chr7    128207871    128207943    hsa-mir-129-1    0    +    0    0    miRNA
1280    chr8    91205484    91205559    hsa-mir-4661    0    +    0    0    miRNA
1456    chr9    114209433    114209529    hsa-mir-455    0    +    0    0    miRNA
1608    chrX    134169808    134169877    hsa-mir-20b    0    -    0    0    miRNA
917    chr11    43581393    43581483    hsa-mir-129-2    0    +    0    0    miRNA
1281    chr13    91350604    91350688    hsa-mir-17    0    +    0    0    miRNA
1281    chr13    91351064    91351135    hsa-mir-20a    0    +    0    0    miRNA

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Conner Powell

UCSC Genomics Institute, Quality Assurance and Support Analyst 

[Anusha Angajala]

Dear Dr.Conner Powell,

Thanks so much for replying to my message. It is quite helpful.I am able to obtain the chromosomal location for list of miRNAs.

Kindly, please advice, how can I make a map like this for list of miRNAs?

My plan is to make a figure instead of having coordinates for these miRNAs. This may help with visualization for location.

hsa-mir-127

hsa-mir-889

hsa-mir-495

hsa-mir-323a

hsa-mir-382

hsa-mir-485

hsa-mir-377

hsa-mir-134

hsa-mir-431

hsa-mir-379

hsa-mir-345

hsa-mir-496

hsa-mir-299

hsa-mir-655

hsa-mir-654

hsa-mir-539

hsa-mir-487b

hsa-mir-370

hsa-mir-369

hsa-mir-758

hsa-mir-154

hsa-mir-411

hsa-mir-494

hsa-mir-432

hsa-mir-493

hsa-mir-376c

hsa-mir-376b

---

From: Conner Powell <ccpo...@ucsc.edu>
Sent: Wednesday, March 13, 2019 5:32:03 PM
To: Anusha Angajala
Cc: gen...@soe.ucsc.edu
Subject: Re: [genome] regarding miRNA cluster visualization

 

[Luis Nassar]

Hello Anusha,

While I don't believe we have any way to replicate an image exactly like that one, I will go over some options which may be what you are looking for.

The first option is creating a custom track with your miRNA identifiers, and then exporting an image of the Genome Browser track data. If you follow the steps outlined in the previous Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables) response above, but before you get output you first change the output format to custom track, you will see a new page where you can give the custom track a name, description, etc. When you are ready, you can then click get custom track in Genome Browser, and your data will be visualized as a data track. Here is an example of the miRNAs visualized on chromosome 14: http://genome.ucsc.edu/s/Lou/hg38_MLQ16. This image can be exported by mousing over the "View" bluebar menu above, and selecting PDF/PS.

The second option is a tool, hgGenome(https://genome.ucsc.edu/cgi-bin/hgGenome), which can show you the density of objects present across the genome. Here is a link that will show you the example of where all the genes are located on the GENCODE track (http://genome.ucsc.edu/cgi-bin/hgGenome?hgS_doOtherUser=submit&hgS_otherUserName=Lou&hgS_otherUserSessionName=hg38_GenomeGraph). If you would like to generate a similar visual for your data, you will want to create a custom track as outlined above, and then use the bluebar menu above to go to Tools -> Genome Graphs, which should lead you to this page (http://genome.ucsc.edu/cgi-bin/hgGenome). From there you can select import, then change group to Custom Tracks, and you should see your miRNA custom track.

Selecting submit then selecting this new track from the graph menu should produce a density graph accross the genome. In this case, the identifiers are only located on a small section of chromosome 14.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

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To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/DM6PR19MB27005702CEEA664CD1D34E70DF1E0%40DM6PR19MB2700.namprd19.prod.outlook.com.