miRNA binding site database

[papori]

Hi all,

I am looking for a downloadable database/csv that include the miRNAs, plus the genomic coordinates (Grch37) of the known/published binding sites.

I guess this sounds trivial, but honestly i didn't find up-to-date db..

Thanks,
Pap

[GenoMax]

You need to do some work to see if any of these are up to date and/or downloadable.

http://www.ncrna.org/KnowledgeBase/link-database/mirna_target_database

http://en.wikipedia.org/wiki/MicroRNA_and_microRNA_target_database

http://mirdb.org/miRDB/

http://mirbase.org/ (for known miRNA).

[papori]

Thanks GenoMax!
I didnt find there this info in the links..
But, i guess the comination from few DB's give me this..
I will update..

[rbagnall]

From UCSC, a table of microRNA binding sites as predicted by Target scan:

ftp://hgdownload.soe.ucsc.edu/golden...etScanS.txt.gz

which looks like this:

chr1 879822 879830 SAMD11:miR-504 90 +
chr1 900599 900606 KLHL17:miR-299/299-3p 26 +
chr1 900605 900612 KLHL17:miR-124/506 7 +
chr1 900933 900941 KLHL17:miR-19 82 +
chr1 901054 901061 KLHL17:miR-137 14 +
chr1 990829 990836 AGRN:miR-144 10 +

hg19 coordinates, gene symbol:microRNA, target scan score (higher score = better match) , strand

[papori]

From UCSC, a table of microRNA binding sites as predicted by Target scan:

ftp://hgdownload.soe.ucsc.edu/golden...etScanS.txt.gz

which looks like this:

chr1 879822 879830 SAMD11:miR-504 90 +
chr1 900599 900606 KLHL17:miR-299/299-3p 26 +
chr1 900605 900612 KLHL17:miR-124/506 7 +
chr1 900933 900941 KLHL17:miR-19 82 +
chr1 901054 901061 KLHL17:miR-137 14 +
chr1 990829 990836 AGRN:miR-144 10 +

hg19 coordinates, gene symbol:microRNA, target scan score (higher score = better match) , strand

Thanks!!! this is exactly what i looked for!

I downlod the file and these are the first 6 lines:

591 chr1 879822 879830 SAMD11:miR-504 90 +
591 chr1 900599 900606 KLHL17:miR-299/299-3p 26 +
591 chr1 900605 900612 KLHL17:miR-124/506 7 +
591 chr1 900933 900941 KLHL17:miR-19 82 +
591 chr1 901054 901061 KLHL17:miR-137 14 +
592 chr1 990829 990836 AGRN:miR-144 10 +
...

Thanks for your fields explanation, but do you know what is the first field? 591/592 etc..

Thanks,
Pap

[rbagnall]

I think that is part of the indexing by USCS for faster searching. You can ignore it.

[GenoMax]

According to TS miRNA sites table schema the first field is "indexing field to speed chromosome range queries".

@papori: Remember that all UCSC databases/files are 0-based.

[papori]

According to TS miRNA sites table schema the first field is "indexing field to speed chromosome range queries".

@papori: Remember that all UCSC databases/files are 0-based.

Thanks GenoMax!