From Microrna Prediction Databases To Microrna / Target Matrices

Question

[Some]

Hi there,

There are a lot of different microRNA prediction databases out there.

Since people apparently are using those a lot, I am wondering if they are inventing the wheel again and again every single time. Do you know sources/scripts/easy ways/downloads to get to this kind of matrix:

      | hsa-miR-X1 | hsa-miR-X2 | ....       |(all existing microRNAs)
______|____________|____________|____________|________________________
Gene1 |    1       |   0.51     |  ...       
______|____________|____________|____________
Gene2 |    0       |   1.24     |  ...
______|____________|____________|___________
Gene3 |    0       |   0.24     |  ...
______|____________|____________|___________
 ...  |    ...     |   ...      |  ....

(all target genes)

This could be a summary of one single microRNA prediction database (e.g. Miranda) or a combination of different databases (e.g. Miranda predictions + Pictar + Diana-T + etc etc).

Thanks!

Answer 1

[Larry_Parnell]

Please see the replies to this question on BioStar. There are different ways that the people behind Pictar, Miranda and others have gone about predicting the mRNA-microRNA interaction. That may complicate the building of such a matrix as you consider above because some of these tools are complementary and not redundant. And that gets into how you score or weight those different measures - and that is not easy at this relatively early stage of microRNA bioinformatics.

Answer 2

[Casey Bergman]

Given a list of all genes & mirnas for your species of interest, you should be able to parse the data from MicroCosm easily into a table and fill the unobserved entries with null values.

MicroCosm is a web resource developed by the Enright Lab at the EMBL-EBI containing computationally predicted targets for microRNAs across many species. The miRNA sequences are obtained from the miRNA Registry and most genomic sequence from EnsEMBL. We aim to provide the most up-to-date and accurate predictions of miRNA targets and hence this resource will be updated regularly.