ready made or customize miRNA microarray chip - (Jul/26/2009 )

Dear all,

I'm a master student. I'm new in miRNA. I like to characterize the unknown function of the present miRNA (with unknown function). the question of mine is all microRNAs on the ready made miRNA microarray chip are functionally known? because I like to compare cancer tumor and normal adjacent cells using microarray method and look for the differential expression of miRNA, then select one miRNA for further study on it function. or should i customize a micrarray for my study? another question is the commercial ready made microRNA microarray include all found miRNAs (functionally known and functionally unknown) in human?Thank you!!!!
-Hui Hui-

Well, to be on the chip, the sequence must be known. Either it's a validated miRNA based upon several criteria, or (for example the Ambion array) have some some predicted miRNA probes on the chip. Many of the miRNAs on these chips have unknown function, however, which I think is that you are interested in. If you wanted to find novel miRNAs (without known function) then I'd suggest you look into high throughput sequencing technologies such as 454 and Solexa.

Or, since so many microarray studies have been done on tumor samples, you could see if the tumor type that you're working with has already been analyzed by another group and use their data set to find some miRNAs that they didn't look at. That way you won't need to do the array at all, and can get straight to functional studies.

thank you very much!!