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opplncRNA: A MATLAB Package for Comprehensive Pathway Analysis of lncRNA-miRNA-mRNA in Humans

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Abstract

The discovery of new lncRNAs (long noncoding RNAs) and their regulatory pathways has always been a hotspot in the field of ceRNA (competing endogenous RNA). Herein, we report opplncRNA (Omics Pilot Platform of lncRNA), a novel and rapid tool for investigating lncRNA-miRNA-mRNA interactions based on the architecture of MATLAB AppDesigner. opplncRNA is useful to analyze the regulatory interaction networks of lncRNA with a friendly GUI (graphical user interface). There are three lncRNA databases (ENCORI, LncBase, and miRcode) about lncRNA-miRNA interactions that have been integrated into opplncRNA, as well as seven miRNA databases (miRcode, ENCORI, TarBase, miRTarBase, miRDB, miRanda, and miRecords) about miRNA-mRNA interactions as also. opplncRNA can read expression data from any profile techniques, such as microarray or RNA-seq. Then, the relationships between lncRNA-miRNA and miRNA-mRNA can be directly calculated through the profile data of lncRNA, miRNA, and mRNA by the threshold of correlation coefficients. Integrated databases can be used to filter calculation outcomes to obtain more reliable pathways. Moreover, opplncRNA has the functionality of directly demonstrating 3 layers network from lncRNA to mRNA in command line form.

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Data Availability

The program of opplncRNA was available at https://github.com/HangZhouSheep/opplncRNA.

Abbreviations

GDC:

Genomic Data Commons

GUI:

Graphical user interface

OPP:

Omics Pilot Platform

TSV:

Tab-separated values

URS:

Unique RNA sequence

ceRNA:

Competing endogenous RNA

lncRNA:

Long noncoding RNA

mRNA:

Messenger RNA

miRNA:

MicroRNA

pre-miRNAs:

Precursor miRNAs

ncRNA:

Noncoding RNA

opplncRNA:

Omics Pilot Platform of lncRNA

RBPs:

RNA‐binding proteins:

pre-miRNA:

Precursor miRNA

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Acknowledgements

We are so grateful for the selfless help from the Shanghai Huisen Science & Technology Company for the daily maintenance of the website.

Funding

This research was supported by the National Key R&D Program of China (2021YFF0703702) and the National Nature Science Foundation of China (32070605).

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Author notes

  1. Sheng-yang Ge and Yi-fan Tan contributed equally.

Authors and Affiliations

  1. Department of Urology, Huashan Hospital, Fudan University, Shanghai, 200040, People’s Republic of China

    Sheng-yang Ge, Yi-fan Tan & Chuan-yu Sun

  2. Institute of Biomedical Sciences, Fudan University, Shanghai, 200032, People’s Republic of China

    Ze-ning Wang & Yang Zhang

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  1. Sheng-yang Ge
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  2. Yi-fan Tan
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  3. Ze-ning Wang
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Contributions

Conception and design: Shengyang Ge and Yang Zhang; administrative support: Chuanyu Sun and Yang Zhang; provision of study materials or patients: Shengyang Ge and Chuan-yu Sun; collection and assembly of data: Yang Zhang; data analysis and interpretation: Yang Zhang and Zening Wang; program writing: Yang Zhang; manuscript writing: all authors; final approval of manuscript: all authors.

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Correspondence to Chuan-yu Sun or Yang Zhang.

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Ge, Sy., Tan, Yf., Wang, Zn. et al. opplncRNA: A MATLAB Package for Comprehensive Pathway Analysis of lncRNA-miRNA-mRNA in Humans. Appl Biochem Biotechnol 194, 5644–5654 (2022). https://doi.org/10.1007/s12010-022-04025-0

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