regarding miRNA location on AR binding sites
Anusha Angajala
Dear Sir or Madam,
I am interested in following miRNAs, breast cancer. I would like to map these miRNAs on genome and see if these are located near AR ( Androgen receptor ) binding sites. If I can map in TCGA breast cancer dataset, that would be great.
Kindly, advise how can I do it in UCSC genome browser?
Thanks so much in advance,
Anusha.
Thank you so much,
Anusha.
Luis Nassar
Hello Anusha,
We have miRNA data as well as some cancer datasets, however, I am not sure if these are what you are looking for.
We have a feature called track search which allows you to search for data with specific keywords. If you go to the hg38 Genome Browser (http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38), you will see a button track search just below the display graphic. Clicking on it will take you to a page titled: Search for Tracks in the Human Dec. 2013 (GRCh38/hg38) Assembly
You can search for specific kinds of data, such as 'tcga', and the results will be any data we have on that Browser that matches your search. In this case, you will see 9 search results, including various cancer datasets:
GDC Cancer mutations: 33 TCGA Cancer Projects Summary (Pan-Can 33)
Transcript-level Expression in 33 TCGA Cancer Tissues (GENCODE v23)
...
You may also search for miRNA which will lead to the the sno/miRNA data. If you have miRNA identifiers such as hsa-mir-17, hsa-mir-20a, etc, you can use the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) to see if the identifiers intersect with other data sets, or certain genomic positions. For more information on the Table Browser, see the documention (http://genome.ucsc.edu/cgi-bin/hgTables#Help). The specific settings I refer to are identifiers and intersection.
Another place to find relative information would be our public hubs (http://genome.ucsc.edu/cgi-bin/hgHubConnect). These are additional sources of data supplied by users. You can search for specific terms, such as 'binding site', and review the results. This leads to helpful data sets such as:
UniBind: A map of direct TF-DNA interactions from ChIP-seq and TF binding profiles
Lastly, let us know if you have any specific data sets that you would like to see in the Genome Browser. We support external data visualization through track hubs (http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html) and custom tracks (http://genome.ucsc.edu/cgi-bin/hgCustom).
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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