Is there any bioinformatics software/ resource which gives the names of Transcription factors controlling a microRNA or vice versa?
Hi Sunitha
This is a yet unpublished tool that we developed. Take a look. Basically it uses several applications to predict TFs binding sites in already described miRNA promoters.
http://mirnatools.eu/TFmiRNA/loops.html
Please let me know what do you think and if you find this useful. Best
Paco
Hi Sunitha
This is a yet unpublished tool that we developed. Take a look. Basically it uses several applications to predict TFs binding sites in already described miRNA promoters.
http://mirnatools.eu/TFmiRNA/loops.html
Please let me know what do you think and if you find this useful. Best
Paco
Dear Sunitha and others,
Please share here any other miRNS -target database you know and better, or more relevant than these. So lets go through my collection.
First of all I suggest our integrated database which contains miRNA-gene and TF-miRNA data. www.signalink.org
miRNA-target:
http://www.targetscan.org/ #putative sometimes to many miRNA target
http://mirecords.biolead.org/index.php #integrated database lot of predicted targets from different databases
http://mirtarbase.mbc.nctu.edu.tw/ #good manually curated database
http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index #good, big, manually curated, but sometimes unavailable and hard to download.
TF-miRNA:
Target sites: http://mirstart.mbc.nctu.edu.tw/ I do not know this one but looks fancy.
http://www.isical.ac.in/~bioinfo_miu/TF-miRNA.php #Simple useful, but there are some non TF proteins also.
Transmir, the other TF-miRNA database is not currently available.
P.s. THX Paco to your database.
Hi Sunitha
I think that tools to detect transcriptional regulation of microRNAs are still limited and not very well validated. Here are some attempts using motif discovery approach that could help you:
PuTmiR (v1.1), http://www.isical.ac.in/~bioinfo_miu/TF-miRNA1.php predicts TF-miRNA interactions using predicted conserved TFBS within 20kb around the TSS of 721 annotated microRNAs (while 1870 are annotated in miRBase v20). Note they provide as PuTmiR v2 a list of TF-miRNA (176 TFs, 330 miRNAs) but without any score and no information about the novelty .
MIR@NT@N, http://maia.uni.lu/mironton.php uses prediction of the TFBS in the 10kb region upstream of the microRNAs (720 miRNAs, 146 TFs).
Best
Dear Paco, Dezso Modos & Rekins Janky
Thank you so much for the input. I had gone through all the links/ tools suggested.
PuTmiR & miRStart gives the results of miRNA TSS. So, are these TSS validated ones or predicted ones?
Even when we are going to find the TFs, given the TSS, it will be based on motif search pattern, and then we need to validate the results to get the exact results, right?
@ Paco, Nice collection of datas.
@ Dezso Modos, I went through Signalink. Good tool. But I think, miRNA- TF interaction can be obtained only for those 8 listed pathways. Is my understanding correct?
I think, MIR@NT@N will also be useful for me.
ChIPBase is another resource which I have found out, which gives the experimentally verified results, of a TF interacting with a particular microRNA and the TF's interaction with the genes, which is based on Chip-seq experiments. Any other suggestions on resources like ChIPBase?
TransmiR is presently not available and it was not updated too.
Thank you.
Best
Suni
I think you can find useful information on mirBase.
A data bank that can solve your query. www.mirbase.org
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