Cross-platform analysis of global microRNA expression technologies

BMC Genomics

Table 1 Within platform correlations for miRNA arrays.

	Probe Technology	MiRBase version	One or two-color analysis	Number of miRNAs considered	Correlation	Standard Error	95% Confidence intervals
Agilent Mouse miRNA (P/NG4472A)	60 mer probes with hairpin loop structure and 5'G residue complement to the C residue added to the microRNA during labelling	MirBase 12	One	122	0.995	0.0014	0.991-0.997
				54	0.995	0.0035	0.984-0.997
LC Science Mouse miRNA Microarray MRA-1002	μParafloTM Technology uses proprietary in-situ oligo synthesis, microfluidic reaction cells, and novel photochemistry coupled with photolithography; full content flexibility	MirBase 12	One	131	0.978	0.0068	0.961-0.987
				54	0.981	0.0105	0.952-0.992
Exiqon miRCURY LNA™ microRNA Array kit	LNA Locked Nucleic Acids are conformationally locked into a favourable confirmation for miRNA binding	MirBase 11	Two	131	0.914	0.0189	0.870-0.944
				54	0.913	0.0258	0.848-0.948
			One	125	0.874	0.0330	0.798-0.925
				54	0.802	0.0723	0.631-0.910
Invitrogen NCode Multi-Species miRNA Microarray Probe Set V2	34-44 nucleotide probes designed as dimers of sequences complementary to mature miRNAs, trimmed to reduce melt temperature variability between probes.	MirBase 9	Two	118	0.706	0.0544	0.586-0.798
				54	0.816	0.0532	0.686-0.892
			One	124	0.853	0.0338	0.775-0.907
				54	0.850	0.0553	0.716-0.928

Spearman correlations and the 95% confidence intervals are presented for the miRNAs that were present within a platform from the sequence-matched list, as well as the 54 miRNAs that gave detectable signals on all four platforms.

ISSN: 1471-2164