NoRCE

NoRCE performs cis enrichment analysis of non-coding RNA (ncRNA) sets to identify potential functional associations with nearby coding genes based on genomic proximity.

Key Features:

• Cis Enrichment Analysis: Conducts enrichment analysis using functional annotations of coding genes proximal to input ncRNAs, assuming genomic proximity may indicate regulatory or functional relationships.
• Integration of Biological Information: Incorporates Topologically Associating Domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information.
• Comprehensive Data Repository: Includes cell-line specific TAD boundaries, functional gene sets, and expression data for coding and ncRNAs with emphasis on cancer-related datasets.
• Custom Data Input and Output Formats: Accepts custom data files and provides results in tabular format and as visualization outputs.
• Species Coverage: Supports human, mouse, rat, zebrafish, fruit fly, worm, and yeast.

Scientific Applications:

• Investigating regulatory roles of ncRNAs: Enables exploration of potential cis-regulatory relationships between ncRNAs and nearby coding genes.
• Exploring ncRNA–coding gene associations: Maps functional associations between ncRNA sets and proximal coding gene functions using gene annotations and expression data.
• Cancer-related genomic studies: Facilitates analysis of cancer-focused gene sets and expression profiles in the context of ncRNA cis enrichment.

Methodology:

Maps input ncRNAs to proximal coding genes and performs enrichment analysis using functional annotations while integrating TAD boundaries, co-expression patterns, miRNA target predictions, cell-line–specific TADs, and expression data.