NoRCE

NoRCE performs cis enrichment analysis for a given set of non-coding RNAs (ncRNAs) using the functional annotations of coding genes located proximal to the input ncRNAs, incorporating topologically associating domain boundaries, co-expression patterns, and miRNA target prediction information.

Key Features:

• Cis Enrichment Analysis: Enrichment is carried out using functional annotations of coding genes located proximal to input ncRNAs.
• Topologically Associating Domain Integration: Cell-line specific TAD boundaries can be incorporated to conduct richer enrichment analysis.
• Co-expression Pattern Integration: Co-expression patterns can be incorporated into the enrichment analysis.
• miRNA Target Prediction Integration: miRNA target prediction information can be incorporated into the enrichment analysis.
• Built-in Datasets: Includes cell-line specific TAD boundaries, functional gene sets, and expression data for coding and ncRNAs specific to cancer.
• Custom Data Support: Users can utilize custom data files in their investigation.
• Multiple Output Formats: Enrichment results can be retrieved in tabular format or visualized in several different ways.
• Multi-species Support: Available for human, mouse, rat, zebrafish, fruit fly, worm, and yeast.

Scientific Applications:

• Functional Characterization of ncRNAs: Analyzes functionally uncharacterized ncRNAs in a functional context by leveraging genomic proximity to coding genes.
• Cancer Research: Utilizes cancer-specific expression data for coding and ncRNAs to investigate disease-relevant regulatory relationships.

Methodology:

NoRCE performs cis enrichment analysis by using functional annotations of coding genes located proximal to input ncRNAs, with optional incorporation of topologically associating domain boundaries, co-expression patterns, and miRNA target prediction information.