how to know/predict a specific gene is regulated by miRNA - (Dec/12/2006 )
I would like to ask a question.
how to know/predict a specific gene is regulated by miRNA
Is there a software used for it, especially for plant
Hy, rye ...
Look into "miRNA target prediction".
For example: miRanda, PicTar
Another nice feature site: http://regrna.mbc.nctu.edu.tw/
But I am not really sure, what you are looking for, after reading your post in the "miRNA databases" thread.
Thank you monstercoccus
In fact, what I need is a way to find out whether specific mRNA transcript can be regulated by miRNA (contain miRNA target site), I did find the option in the link your provide ( http://regrna.mbc.nctu.edu.tw), while it can only applied for human, mouse and rat, not for plants…
To find out whether a mRNA is a microRNA target, you first need to scan the mRNA especially the 3'UTR region to see if there are decent targets which should at least have 8 seed sequence matches. The online program recommended by monstercoccus is a nice one. There are several other similar programs on the web too. Once you have found a target with high confidence, it doesn't necessarily mean that the target is a really one. What people usually do is to insert the target site into the 3'UTR region of a report gene and do a report assay to see the inserted target has any influence on the report activity. There are many different strategies to perform this type of experiment such as you can mutate the target sequence, transfect a synthetic microRNA which is supposed to bind to the target. Personally I think even the microRNA affects the report gene by binding to the target on the 3UTR, it does not necessarily mean the microRNA works the same way in vivo. That is why only a few microRNA targets have been verified although one microRNA is predicted computationally to have hundreds of targets.
Can you let me know what other websites out there that can predict miRNA targets for a gene for human?
There are many microRNA target prediction program on the web. Here is a collection of them:
Thank you pcrman