Noncoder

Noncoder re-annotates Affymetrix GeneChip Exon 1.0 ST Array probes to enable genome-wide profiling of long non-coding RNA (lncRNA) expression and isoforms.

Key Features:

• Re-annotation of Exon Array Probes: Re-annotates probes from GeneChip Exon 1.0 ST Arrays (Affymetrix, Inc.) to enable comprehensive profiling of lncRNA expression and isoforms across the genome.
• CEL file processing and differential expression: Processes CEL files from exon arrays including normalization and differential expression analysis to identify differentially expressed lncRNAs.
• Detailed lncRNA annotation: Provides extensive annotation details for lncRNAs to support interpretation of potential roles, regulatory mechanisms, tissue specificity, and disease associations.

Scientific Applications:

• Expression Profiling: Enables profiling of tens of thousands of lncRNAs to assess expression patterns across biological conditions.
• Alternative Splicing Analysis: Supports investigation of alternative splicing events and isoform diversity of lncRNAs using exon-level probe annotations.
• Disease Association Studies: Facilitates exploration of lncRNA regulation differences among tissues and disease states to identify candidate disease-associated lncRNAs.

Methodology:

Re-annotation of exon array probes from Affymetrix GeneChip Exon 1.0 ST Arrays to map lncRNAs and isoforms; normalization and differential expression analysis of CEL files.