MicroRNA doking onto mRNA

Question

[zahir]

Hi everyone, I want to show the post-transcription interaction of MicoRNA with mature mRNA. I am looking for a server that can show this interaction and if not, then could anyone tell me about the interaction of MicroRNA with DNA? thanks for your time and attention

[Farbod]

Dear Zahir, Hi,

Do you have any transcriptomic data of the species you are working with?

And maybe you are interested in some integrated analysis (e.g: 1 and 2) which is more complicated in non-model species.

~ Best

[zahir]

I dont have transcriptomic data but i know the microRNA and the gene sequences where it binds. The problem is, I could not find an online server that can be used to show the hybridization of microRNA with my gene mRNA. Could anybody suggest me any tool/sof or server plz?

[Farbod]

Hi,

Please kindly put your comment and responds in the "add a reply" section, instead of "adding new answer". Thanks

[zahir]

Second, could I used the transcriptomic data where my gene is upregulated for microRNA targeting?

Answer 1

[stephanie.hilz]

Are you interested in simply predicting which mRNAs a miRNA interact with (i.e. predicted targets of an miRNA)? Or are you looking to further determine whether there is a significant change in expression (including potential post-transcriptional regulation) of those targets?

Regardless, a good starting point might be to get lists of predicted target mRNAs for your miRNA. There are a number of tools available to do this, including: TargetScan: http://www.targetscan.org/vert_71/ PicTar: http://pictar.org miRanda: http://www.microrna.org/microrna/home.do

If you give me more details on exactly what you are interested in doing, I can try to help a bit more.

[zahir]

Yes, I have but of different stage of differentiation where my gene is upregulated. The micrRNA which i want to show the hybridization with my mRNA is up-regulated at different stage of differentiation where my gene is down-regulated.

Answer 2

[Farbod]

Hi,

Please search for miRNA in the "Integration with other data types" section at this paper.

[zahir]

Can I use ChIP seq data for finding microRNA targets or vice versa?