ExiMiR

ExiMiR applies a spike-in control probe–based multi-array normalization to microRNA (miRNA) microarray data to improve between-array comparability for Exiqon dual-channel miRCURY LNA™ common-reference datasets treated as pseudo-single-channel.

Key Features:

• Platform Support: Processes raw data from the Exiqon dual-channel miRCURY LNA™ platform in a common reference design by treating it as pseudo-single-channel.
• Normalization Methodology: Implements a novel multi-array normalization method specifically tailored for miRNA expression data that leverages spike-in control probes and controllable assumptions to adjust measured intensities across arrays.
• Quality Assessment: Computes quality metrics based on the coefficient of variation to assess between-array reliability of normalized miRNA expression values.
• Validation and Reliability: Validation includes comparison against 13 other normalization approaches and confirmation of differential expression values for selected miRNAs by quantitative reverse transcription–polymerase chain reaction (qRT-PCR).
• Research Applications: Produces high-quality normalized miRNA expression datasets suitable for downstream biological and medical studies.

Scientific Applications:

• Differential expression analysis: Enables detection of differentially expressed miRNAs with reliability corroborated by qRT-PCR for selected targets.
• Environmental exposure studies: Facilitates investigation of environmental effects on gene expression, exemplified by studies of cigarette smoke exposure impact on lung tissue.

Methodology:

Treats Exiqon dual-channel miRCURY LNA™ common-reference arrays as pseudo-single-channel, applies a spike-in control probe–based multi-array normalization to adjust intensities across arrays, and computes coefficient of variation–based quality metrics.