Non-Coding RNA Analysis

Pipeline for identifying, annotating, and interpreting non-coding RNAs and their biological roles. Covers microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and other ncRNA classes.

Key principles:

1. Class determines function — miRNAs repress mRNA translation; lncRNAs have diverse mechanisms (scaffolds, guides, decoys, enhancers); rRNAs/tRNAs are structural
2. Targets matter more than the ncRNA itself — for miRNAs, the regulated mRNA targets determine the phenotype
3. Expression context is critical — ncRNAs are highly tissue/cell-type specific
4. Conservation indicates function — deeply conserved ncRNAs (miR-let-7, MALAT1) have well-established roles
5. Evidence grading — T1: validated targets (reporter assay, CLIP-seq), T2: high-confidence computational prediction, T3: expression correlation, T4: sequence-based prediction only

Type-based reasoning — look up, don't guess: Non-coding RNA function depends on type: miRNA silences target mRNAs (look up targets in miRTarBase/TargetScan), lncRNA has diverse functions (scaffolding, guiding, decoying — check literature for the specific lncRNA), circRNA may sponge miRNAs.

For any ncRNA query: first identify the class from the name/sequence, then select the appropriate evidence source. Do not assume function based on name alone — a gene named "LINC" may have a characterized mechanism, or none at all. Always search PubMed for the specific ncRNA before interpreting. For miRNAs, validated targets (T1) from miRTarBase outweigh any computational prediction — a predicted target with no experimental support is a hypothesis, not a finding. For lncRNAs, mechanism is almost always determined by experimental studies; use PubMed_search_articles with the lncRNA name + "mechanism" or "function" to find relevant evidence. For circRNAs, miRNA sponging is the most common proposed mechanism but is frequently over-claimed — look for CLIP-seq or reporter assay evidence before asserting it.

When to Use