NONCODE

NONCODE catalogs and integrates long noncoding RNA (lncRNA) and other noncoding RNA data excluding tRNAs and rRNAs, providing a comprehensive repository of expression profiles, molecular features, and functional annotations.

Key Features:

• Integrated Data Collection: Integrates expression profiles, molecular features, and biological function annotations of lncRNAs derived from re-annotated microarray studies.
• Genome Browser: Provides a local Genome Browser for visualization of genomic contexts and alignments of lncRNAs.
• Sequence-Alignment Search (BLAST): Includes a BLAST server for sequence-alignment searches used in comparative genomics and functional annotation.
• Literature Integration: Collates ncRNA information and annotations reported in the scientific literature to update database content.
• Versioned Content: Contains consolidated entries from NONCODE v3.0 reflecting re-annotated microarray-derived lncRNA data.

Scientific Applications:

• Functional characterization: Investigating lncRNA roles in imprinting control, pluripotency regulation, immune responses, and chromosome dynamics.
• Disease association studies: Identifying and interpreting lncRNA associations with disease etiology and pathogenesis.
• Expression profiling: Analyzing expression patterns of lncRNAs across experiments re-annotated from microarrays.
• Comparative genomics and annotation: Performing sequence-alignment and comparative analyses with BLAST to support functional annotation.
• Genomic context analysis: Examining genomic context and alignments of lncRNAs using the local Genome Browser.

Methodology:

Re-annotation of microarray studies, literature curation of ncRNA reports, sequence-alignment searches via BLAST, and visualization of genomic contexts using a local Genome Browser.