Lantern

Lantern provides integrative functional annotations for human long non-coding RNAs (lncRNAs) to support analysis of their molecular interactions and regulatory roles.

Key Features:

• Ontology Annotation Extraction: Semi-automatic extraction of ontology annotations from the lncRNA literature using PubMed's abstract retrieval engine and NCBO's recommender annotation system.
• Benchmarking Performance: Performance evaluated against manually curated resources such as lncRNAdb, reporting recall 0.62 and precision 0.8 for annotating 182 lncRNAs.
• Multi-Omics Annotations: Provides annotations including predicted cis-regulatory transcription factors (TFs), interactions with RNA-binding proteins (RBPs), tissue-specific expression profiles, protein co-expression networks, coding potential assessments, sub-cellular localization data, and single nucleotide polymorphisms (SNPs).
• Comprehensive Coverage: Covers approximately 11,000 human lncRNAs with integrated functional annotations.

Scientific Applications:

• Functional exploration: Enables detailed investigation of lncRNA functions and their regulatory roles.
• Interaction discovery: Supports identification of lncRNA interactions with proteins, transcription factors, and other genomic elements.
• Tissue-specific expression analysis: Assists in discovering tissue-specific expression patterns relevant to disease research and therapeutic development.

Methodology:

Uses a semi-automatic ontology annotation engine that combines automated extraction from PubMed abstracts with NCBO recommender annotations, integrates multi-omics data sources, and was benchmarked against lncRNAdb (recall 0.62, precision 0.8 on 182 lncRNAs).