miRcode

miRcode predicts microRNA target sites across the human transcriptome and supports analysis of competing endogenous RNA (ceRNA) networks involving coding and long non-coding RNAs.

Key Features:

• Whole Transcriptome Prediction: Provides miRNA target predictions across the human transcriptome, including over 10,000 lncRNAs annotated by GENCODE v11.
• Genome Assembly and Annotation: Leverages the UCSC GRCh37/hg19 genome assembly and GENCODE version 11 transcripts for genomic coordinates and transcript annotation.
• Conservation Analysis: Incorporates multiz alignment of 46 species to assess evolutionary conservation of predicted sites.
• Target Prediction Algorithm: Bases miRNA interaction predictions on TargetScan6 families.
• ceRNA Network Integration: Enables construction and analysis of competing endogenous RNA (ceRNA) networks linking lncRNAs, mRNAs, and miRNAs.
• Cross-database References: Integrates or cross-references data from miRTarBase and TargetScan for interaction evidence.
• Differential Expression and Pathway Analysis: Supports identification of differentially expressed RNAs with edgeR and subsequent pathway analysis using KEGG and gene ontology via STRING including protein-protein interaction (PPI) context.
• Prognostic and Survival Analysis: Facilitates Cox regression and Kaplan-Meier survival analyses to associate RNAs with overall survival.
• Data Integration: Used in analyses integrating high-throughput RNA sequencing data from The Cancer Genome Atlas (TCGA) and validation with GEPIA.

Scientific Applications:

• Cancer Research: Enables identification of miRNA–lncRNA–mRNA regulatory interactions and ceRNA networks in cancer studies, including analyses of bladder urothelial carcinoma (BUC).
• Biomarker and Prognostic Discovery: Supports discovery of RNAs associated with patient survival for potential biomarker and therapeutic target investigation.
• Regulatory Network Mapping: Facilitates mapping of miRNA-mediated regulatory networks across coding and non-coding transcripts.

Methodology:

Uses UCSC GRCh37/hg19 and GENCODE v11 transcripts, incorporates multiz 46-species alignments, applies TargetScan6 family-based miRNA target predictions, integrates TCGA RNA-seq data with differential expression analysis via edgeR, constructs ceRNA networks and cross-references miRTarBase and TargetScan, performs pathway analysis via KEGG and gene ontology/PPI context via STRING, and applies Cox regression and Kaplan-Meier survival analyses with validation using GEPIA.