Question: identification of miRNA for zebrafish genes
0
gravatar for rajasekargutha
2.6 years ago by
India
rajasekargutha20 wrote:

how to identify predicted miRNAs for target genes from zebrafish. is there any online databases for this?

snp rna-seq next-gen genome • 970 views
ADD COMMENTlink modified 2.5 years ago by Chirag Nepal2.2k • written 2.6 years ago by rajasekargutha20
2

I don't understand, do you want to find novel miRNAs, conserved miRNAs or predict their targets? To identify novel miRNAs, you might want to look at miRDeep2. To find conserved miRNAs, you will be better off by aligning your sequences against miRBase And last but not least, there is already target predictions for zebrafish, in TargetScanFish

Hope it helps :)

ADD REPLYlink written 2.6 years ago by biofalconch390
1

We were trying to get OP to do some work :)

While everyone wants to be super helpful on Biostars we are trying to get new Biostars users to think/do some research themselves instead of handing them ready information/search results.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by genomax67k
1

Did you look for any resources on google? Please try this: http://bfy.tw/8V5o

If there is something I have missed, please clarify the question.

ADD REPLYlink written 2.6 years ago by Gjain5.3k

i have searched but i didnt get

ADD REPLYlink written 2.6 years ago by rajasekargutha20
1

Unless your search works in a different dimension than we are in the very first hit I saw was for the thing you are asking about. TargetScanFish.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by genomax67k
1
gravatar for Chirag Nepal
2.5 years ago by
Chirag Nepal2.2k
Copenhagen
Chirag Nepal2.2k wrote:

To identify predicted target genes of zebrafish miRNAs, have a look here http://www.targetscan.org/fish_62/

If you want to correlate the expression of miRNA promoters and predicted target genes (the ones you get from above data), you can use zebrafish CAGE-seq datasets to see how miRNA/target genes correlate across developmental stages.

Have a look here http://nar.oxfordjournals.org/content/early/2015/12/15/nar.gkv1354.full Annotation of Zebrafish pri-miRNAs promoters and CAGE-seq detected active Drosha processing events.

You also have access to histone modifications and RNA-seq data from same stages. You can visualize data from UCSC custom track here: http://genome-euro.ucsc.edu/cgi-bin/hgHubConnect?hgsid=218695066_W0Xr4VlL7iBMcdhAvDjYAfPTS5Na

Click "Promoterome CAGE and nucleosome positioning" to visualize tracks on UCSC browser.

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Chirag Nepal2.2k
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