We support your research through our insight into microRNA (miRNA) function. The primary goal of these collaborative efforts is to produce research papers presenting readily testable hypotheses. Significant results will allow pursuit of grant applications and patents. Our efforts will be compensated following a fee-based schedule until mutual grants or subcontracts are in place. You can consult without hiring. We ask for co-authorship if our analyses significantly contribute to your research.
Our unique methods in analyzing miRNA
This miRNA target prediction method is based on the miRNA target class we have found, in which the 5’ and 3’ UTR of a target gene simultaneously interact with a miRNA (Genome Research 19, 2009: 1175-1183). Our target prediction method achieves increased specificity of miRNA targets by including 5’ UTR interactions as well as the current conventional 3’ UTR interactions which have till now led to a high number of false positives, constituting the bottleneck of current miRNA research. It turns out that most known miRNAs have potential miBridge targets and most known genes have potential miBridge regulating miRNAs, essentially covering the whole genome. A paper describing miBridge target characteristics for human miRNAs, based on the latest genome annotations, is in progress. All targets of mouse and rat miRNAs will also be available on this site.
This method identifies important miRNAs in a system of interest based on expression patterns alone without factoring previous knowledge into the analysis. As an example, we identified miR-200a, miR-223,and miR-335 in a comparison of metastatic and non-metastatic cancer cell line data using our high stringent cutoff criteria (paper in preparation). Confirming the validity of this method, previously only miR-200a (as we had known) and miR-335 (which we had not known) had already been found to be anti-metastatic miRNAs. The specificity of the result makes the case for testing the hypothesis that miR-223 is another anti-metastatic miRNA. Note that miRNAs are identified together with potential targets in the process. In this specific example, all predicted targets were validated in a collaborator’s laboratory.
Two sets of upregulated and downregulated mRNA and miRNA profiling data (e.g., disease and normal, pre- and post-treatment, two drug effects, positive and negative outcomes).
– Predicted crucial miRNA-mRNA target networks, including novel miRNA—candidate target genes.
– Hypotheses generated within a biological context.
– Normally, fewer than 10 miRNA—target gene pairs are identified through this process, enabling which validation in your lab.