Computational Challenges in miRNA Target Predictions: To Be or Not to Be a True Target?

Table 3

Other computational and experimental approaches capable of performing more reliable analysis by combining miRNA and mRNA expression data.

Reference	Brief description	Computer platform
Kort et al. [32]	Two signatures of differentially expressed mRNAs and microRNAs are used to cluster the data. Qualitative combination of mRNA and microRNA expression data.	Any platform, web browser, R language
Lanza et al. [33]	One signature of differentially expressed mRNAs and microRNAs in combination is used to correctly cluster the data. Qualitative combination of mRNA and microRNA expression data.	Any platform, GeneSpring software
Salter et al. [34]	Qualitative combining of mRNA profiling and microRNA expression, by clustering separately the data and analyzing differentially modulated pathways.	Any platform, GeneSpring software, R Language, GenePattern software
Nicolas et al. [15]	Experimental identification of real microRNA targets by overexpression or silencing of miR-140.	Any platform, web browser
Sood et al. [29]	A computational tool to directly correlate 3'UTR motifs with changes in mRNA levels upon miRNA overexpression or knockdown.	Linux, Cygwin (Windows), Mac OS X, SunOS platform. A web version is also available