FARNA: knowledgebase of inferred functions of non-coding RNA transcripts

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Non-coding RNA (ncRNA) genes are critical regulators of cellular behavior, but their functions remain largely uncharacterized.
• Existing databases offer limited information on ncRNA functions across diverse human cells and tissues.

Purpose of the Study:

• To present FARNA, a comprehensive knowledgebase for inferred functions of human ncRNA transcripts.
• To provide insights into the roles and regulatory mechanisms of ncRNAs in various human cellular contexts.

Main Methods:

• Inferred ncRNA functions from co-expression with transcription factors (TFs) and TF co-factors (TcoFs) across 119 human tissues and 177 primary cell types.
• Utilized statistically enriched Gene Ontology (GO) terms, pathways, and diseases based on the guilt-by-association principle for annotation.
• Incorporated Cap Analysis of Gene Expression (CAGE) data for expression profiling across cellular and tissue types.

Main Results:

• Annotated 10,289 human ncRNA transcripts (2,734 microRNAs and 7,555 long ncRNAs) with inferred functions.
• Provided comprehensive functional annotations for ncRNAs across a wide spectrum of human cells and tissues.
• Detailed expression profiles derived from CAGE data are available for each transcript.

Conclusions:

• FARNA offers the most extensive functional annotation of human ncRNAs across the broadest range of cells and tissues to date.
• This knowledgebase has significant potential to advance the understanding of ncRNA functions and their regulatory roles in human biology.
• FARNA is accessible online at http://cbrc.kaust.edu.sa/farna, facilitating research in ncRNA biology.