The bioinformatics and experimental analysis of AlkB family for prognosis and immune cell infiltration in hepatocellular carcinoma

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Introduction

Materials & Methods

RNA extraction and quantitative PCR (qPCR)

The protein levels of AlkB family in clinical samples

Functional and pathway enrichment analysis

The profiles of AlkB family analyzed with several databases

Statistical analyses

Results

Abnormal expression of AlkB family in HCC

The prognostic value of AlkB family in HCC patients

Genetic alteration and enriched functional analysis of AlkB family in HCC patients

Immune cell infiltration under the influence of AlkB family in HCC

The different methylation levels of AlkB family in HCC

Discussion

Conclusion

Supplemental Information

Several reliable and multifunctional databases were used to comprehensively analyze the AlkB family in HCC

DOI: 10.7717/peerj.12123/supp-1

Screened co-expressed genes of the AlkB family in HCC

DOI: 10.7717/peerj.12123/supp-2

The cox proportional hazard model of the AlkB family and six immune cells involved in tumor infiltration in HCC

DOI: 10.7717/peerj.12123/supp-3

The DNA methylation levels of AlkB family in HCC patients

DOI: 10.7717/peerj.12123/supp-4

The Raw Data for mRNA expression values

DOI: 10.7717/peerj.12123/supp-5

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Bi Peng performed the experiments, prepared figures and/or tables, and approved the final draft.

Yuanliang Yan analyzed the data, prepared figures and/or tables, and approved the final draft.

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

Human Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

The ethics of our study has been approved by the Ethical Committee of Xiangya Hospital of Central South University and the ethical approval number is 202109083.

Data Availability

The following information was supplied regarding data availability:

The raw measurements for the qPCR are available in the Supplemental Files.

Funding

This study is supported by grants from the China Postdoctoral Science Foundation (2021T140754, 2020M672521), the National Natural Science Foundation of China (81803035), the Natural Science Foundation of Hunan Province (2020JJ5934, 2019JJ50932), and the Postdoctoral Science Foundation of Central South University (248485). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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