Co-expression analysis and ceRNA network reveal eight novel potential lncRNA biomarkers in hepatocellular carcinoma

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Bioinformatics and Genomics

Main article text

 

Introduction

Materials and Methods

Data preprocessing and differential gene selection

Determination of ceRNA

WGCNA model related computing

Prediction of interrelationship between lncRNA-related mRNAs

Gene ontology and KEGG enrichment analysis

Results

Analysis of differential miRNAs and differential lncRNAs

Weighted gene co-expression network analysis of lncRNA

ceRNA network of lncRNA reveals potential biomarkers in liver cancer

The interactions between lncRNAs and mRNAs

GO and KEGG pathway enrichment analyses of lncRNA-targeted gene

Discussion

Conclusions

Supplemental Information

Clinical characteristics of patients

DOI: 10.7717/peerj.8101/supp-1

Identification of DEGs

DOI: 10.7717/peerj.8101/supp-2

Expression data of LncRNA

DOI: 10.7717/peerj.8101/supp-3

The basic attributes for ceRNA network

DOI: 10.7717/peerj.8101/supp-4

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Ren-chao Zou performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Zhi-tian Shi performed the experiments, analyzed the data, prepared figures and/or tables, approved the final draft.

Shu-feng Xiao analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, approved the final draft.

Yang Ke analyzed the data, prepared figures and/or tables, approved the final draft.

Hao-ran Tang analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Tian-gen Wu analyzed the data, prepared figures and/or tables, approved the final draft, review and editing.

Zhi-tang Guo prepared figures and/or tables, approved the final draft, validation.

Fan Ni analyzed the data, prepared figures and/or tables, approved the final draft, data curation.

Sanqi An conceived and designed the experiments, authored or reviewed drafts of the paper, approved the final draft.

Lin Wang conceived and designed the experiments, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Data Availability

The following information was supplied regarding data availability:

The raw measurements are available in the Supplementary Files.

Funding

This work was supported by National Natural Science Foundation of China (No. 81660399 and 81860423), Yunnan Provincial Clinical Center of Hepato-biliary-pancreatic Diseases [no specific number], the Doctor Newcomer Award of Yunnan Province in 2017 [no specific number], and Ph.D. Student Innovation Fund of Kunming Medical University (No. 2019D004). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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