Transcriptome analysis revealed key prognostic genes and microRNAs in hepatocellular carcinoma

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Bioinformatics and Genomics

Main article text

 

Introduction

Material and Methods

Profile selection and Data Collection

Data processing and identification of DEGs

Functional and signaling pathway enrichment analysis

PPI network construction and cluster identification

Key gene selection and further analyses

Prognostic signature of miRNAs and target key genes

Results

DEG identification in HCC

GO enrichment analysis of DEGs

Signaling pathway enrichment analysis of DEGs

PPI and cluster analysis

Key gene selection and further analyses

Prognostic miRNA identification and survival analysis

Discussion

Conclusions

Supplemental Information

DEGs identified in HCC samples from GSE36376, GSE39791, GSE57957, and GSE87630

DOI: 10.7717/peerj.8930/supp-1

DEGs identified in HCC samples in TCGA

DOI: 10.7717/peerj.8930/supp-2

The top 20 (a ranking by P-value from Metascape) enriched GO and pathways of genes in cluster 1

DOI: 10.7717/peerj.8930/supp-3

The top 20 (a ranking by P-value from Metascape) enriched GO and pathways of genes in cluster 2

DOI: 10.7717/peerj.8930/supp-4

The top 20 (a ranking by P-value from Metascape) enriched GO and pathways of genes in cluster 3

DOI: 10.7717/peerj.8930/supp-5

Differentially expressed microRNAs in HCC samples in TCGA

DOI: 10.7717/peerj.8930/supp-6

Univariate analysis of microRNAs in HCC (P-value < 0.1)

DOI: 10.7717/peerj.8930/supp-7

Risk scores of HCC samples based on the microRNA prognostic system

DOI: 10.7717/peerj.8930/supp-8

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Xi Ma conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Lin Zhou performed the experiments, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

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

Data Availability

The following information was supplied regarding data availability:

All the raw data are available at GEO: GSE36376, GSE39791, GSE57957, and GSE87630 and at TCGA (search term: LIHC). The code files are available in a Supplemental File.

Funding

This study was supported by grants from the National Science and Technology Major Project (2017ZX10203205). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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