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ncFN: a comprehensive non-coding RNA function annotation framework based on a
global and heterogeneous biomolecular network
#MMPMID41143282
Long M
; Liu H
; Yuan M
; Zhou X
; Zhang T
; Wang Q
; Jiang W
Noncoding RNA Res
2026[Feb]; 16
(?): 70-78
PMID41143282
show ga
Increasing evidence indicates that non-coding RNAs (ncRNAs) have emerged as
essential factors in most biological processes through diverse mechanisms.
However, the biological functions of most ncRNAs are still poorly understood.
Here, we developed ncFN, a novel and comprehensive framework for ncRNA function
annotation based on a global and heterogeneous biomolecular network.
Specifically, we constructed a Global Interaction Network (GIN) by integrating
ncRNA-ncRNA, ncRNA-protein coding gene (PCG), and PCG-PCG interactions. The GIN
consists of 565,482 edges connecting 17,060 PCGs and 12,616 ncRNAs, including
1095 microRNAs (miRNAs), 3563 long non-coding RNAs (lncRNAs), and 7958 circular
RNAs (circRNAs). For each ncRNA, we quantified Association Strengths (ASs)
between the ncRNA and PCGs through Random Walk with Restart in GIN. Then, Gene
Set Enrichment Analysis was performed with ASs as input to annotate the function
of the ncRNA. Compared to most conventional methods that only focus on a single
ncRNA type, ncFN offers significant advantages in covering diverse ncRNA types
and a larger number of ncRNA molecules. Moreover, we demonstrated the superiority
of ncFN by comparing it with other methods in the annotation of well-acknowledged
disease-relevant ncRNAs and differentially expressed ncRNAs in diseases. Finally,
ncFN also facilitated enrichment analysis with multiple ncRNAs or pathways as
input. In conclusion, ncFN is a comprehensive and reliable tool for functional
annotation of miRNAs, lncRNAs, and circRNAs, making it highly suitable for
widespread use in ncRNA research. ncFN is freely accessible at
http://www.jianglab.cn/ncFN/, and all codes are deposited on GitHub
(https://github.com/LongMin0705/ncFN).
free
free
free
