LncRNAEngine

Long Non-Coding RNA Regulatory Analysis Pipeline

A pure-Python pipeline for lncRNA co-expression network analysis, RBP motif enrichment, and ceRNA network construction.

Features

• lncRNA-mRNA co-expression network (Pearson correlation, BH FDR)
• RNA-binding protein (RBP) motif enrichment (50 RBPs)
• ceRNA network via shared miRNA targets (Jaccard similarity)
• Nuclear vs cytoplasmic localization prediction
• lncRNA conservation scoring (PhyloP)

Results

• 100 samples × 2000 lncRNAs + 5000 mRNAs
• Significant co-expression pairs: 3 (FDR<0.05, |r|>0.5)
• Significant RBPs: 50/50
• Max ceRNA Jaccard score: 0.456
• Nuclear: 809 (40.5%), Cytoplasmic: 1191 (59.5%)
• Conservation t-stat: 23.69, p=1.39e-109

Usage

pip install numpy scipy matplotlib
python lncrna_engine.py

Tags

lncrna long-noncoding-rna rna-binding-protein ceRNA nuclear-retention noncoding-rna