IDEAS home Printed from https://ideas.repec.org/a/abf/journl/v55y2024i3p47045-47054.html

Cluster Analysis of RNA m6A Methylation Regulators Based on TCGA and GEO Database in Hepatocellular Carcinoma

Author

Listed:
  • Xiaoshi Zhang
  • Jianqiang Cai

    (National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, China)

  • Zhuo Yu

    (Beijing Hospital, China)

  • Xiaoyi Zhang

    (Exchange, Development & Service Center for Science & Technology Talents, China)

Abstract

As potential targets and candidate molecules for the treatment of cancer, m6 A RNA and its regulator genes have important application prospects in individualized therapy of Hepatocellular Carcinoma(HCC). Through TCGA and GEO data screening, we demonstrated the expression of different m6 A regulators within HCC related to genetic variation, biological pathways and patients’ prognosis. We use machine learning methods to cluster m6 A regulators and differential expressed genes, which may provide a theoretical basis for the establishment of a risk assessment model.

Suggested Citation

  • Xiaoshi Zhang & Jianqiang Cai & Zhuo Yu & Xiaoyi Zhang, 2024. "Cluster Analysis of RNA m6A Methylation Regulators Based on TCGA and GEO Database in Hepatocellular Carcinoma," Biomedical Journal of Scientific & Technical Research, Biomedical Research Network+, LLC, vol. 55(3), pages 47045-47054, March.
    • Handle: RePEc:abf:journl:v:55:y:2024:i:3:p:47045-47054
    DOI: 10.26717/BJSTR.2024.55.008713
    as

    Download full text from publisher

    File URL: https://biomedres.us/pdfs/BJSTR.MS.ID.008713.pdf
    Download Restriction: no
    File URL: https://biomedres.us/fulltexts/BJSTR.MS.ID.008713.php
    Download Restriction: no
    File URL: https://libkey.io/10.26717/BJSTR.2024.55.008713?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Dan Dominissini & Sharon Moshitch-Moshkovitz & Schraga Schwartz & Mali Salmon-Divon & Lior Ungar & Sivan Osenberg & Karen Cesarkas & Jasmine Jacob-Hirsch & Ninette Amariglio & Martin Kupiec & Rotem So, 2012. "Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq," Nature, Nature, vol. 485(7397), pages 201-206, May.
    2. Dali Han & Jun Liu & Chuanyuan Chen & Lihui Dong & Yi Liu & Renbao Chang & Xiaona Huang & Yuanyuan Liu & Jianying Wang & Urszula Dougherty & Marc B. Bissonnette & Bin Shen & Ralph R. Weichselbaum & Me, 2019. "Anti-tumour immunity controlled through mRNA m6A methylation and YTHDF1 in dendritic cells," Nature, Nature, vol. 566(7743), pages 270-274, February.
    3. Xinyao Lin & Guoshi Chai & Yingmin Wu & Jiexin Li & Feng Chen & Jianzhao Liu & Guanzheng Luo & Jordi Tauler & Jun Du & Shuibin Lin & Chuan He & Hongsheng Wang, 2019. "RETRACTED ARTICLE: RNA m6A methylation regulates the epithelial mesenchymal transition of cancer cells and translation of Snail," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Paulo A. Gameiro & Iosifina P. Foskolou & Yumna A. Butt & Aniek A. M. Martens & Klara Kuret Hodnik & Igor Ruiz de los Mozos & Nordin D. Zandhuis & Žan Hozjan & Veronica M. Kot & Rupert Faraway & Michi, 2026. "Meta-unstable mRNAs in activated CD8+ T cells are defined by interlinked AU-rich elements and m6A mRNA methylation," Nature Communications, Nature, vol. 17(1), pages 1-19, December.
    2. Yuanpei Li & Xiaoniu He & Xiao Lu & Zhicheng Gong & Qing Li & Lei Zhang & Ronghui Yang & Chengyi Wu & Jialiang Huang & Jiancheng Ding & Yaohui He & Wen Liu & Ceshi Chen & Bin Cao & Dawang Zhou & Yufen, 2022. "METTL3 acetylation impedes cancer metastasis via fine-tuning its nuclear and cytosolic functions," Nature Communications, Nature, vol. 13(1), pages 1-23, December.
    3. Hyun Jung Hwang & Tae Lim Park & Hyeong-In Kim & Yeonkyoung Park & Geunhee Kim & Chiyeol Song & Won-Ki Cho & Yoon Ki Kim, 2023. "YTHDF2 facilitates aggresome formation via UPF1 in an m6A-independent manner," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    4. Moshe Shay Ben-Haim & Yishay Pinto & Sharon Moshitch-Moshkovitz & Vera Hershkovitz & Nitzan Kol & Tammy Diamant-Levi & Michal Schnaider Beeri & Ninette Amariglio & Haim Y. Cohen & Gideon Rechavi, 2021. "Dynamic regulation of N6,2′-O-dimethyladenosine (m6Am) in obesity," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    5. Zhen-Dong Zhong & Ying-Yuan Xie & Hong-Xuan Chen & Ye-Lin Lan & Xue-Hong Liu & Jing-Yun Ji & Fu Wu & Lingmei Jin & Jiekai Chen & Daniel W. Mak & Zhang Zhang & Guan-Zheng Luo, 2023. "Systematic comparison of tools used for m6A mapping from nanopore direct RNA sequencing," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    6. Debjit Khan & Iyappan Ramachandiran & Kommireddy Vasu & Arnab China & Krishnendu Khan & Fabio Cumbo & Dalia Halawani & Fulvia Terenzi & Isaac Zin & Briana Long & Gregory Costain & Susan Blaser & Amand, 2024. "Homozygous EPRS1 missense variant causing hypomyelinating leukodystrophy-15 alters variant-distal mRNA m6A site accessibility," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
    7. P Acera Mateos & A J Sethi & A Ravindran & A Srivastava & K Woodward & S Mahmud & M Kanchi & M Guarnacci & J Xu & Z W S Yuen & Y Zhou & A Sneddon & W Hamilton & J Gao & L M Starrs & R Hayashi & V Wick, 2024. "Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    8. Zhiyuan Luo & Jiacheng Zhang & Jingyi Fei & Shengdong Ke, 2022. "Deep learning modeling m6A deposition reveals the importance of downstream cis-element sequences," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    9. Fernando Rodriguez & Irina A. Yushenova & Daniel DiCorpo & Irina R. Arkhipova, 2022. "Bacterial N4-methylcytosine as an epigenetic mark in eukaryotic DNA," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    10. Xiang Zhang & Huilong Yin & Xiaofang Zhang & Xunliang Jiang & Yongkang Liu & Haolin Zhang & Yingran Peng & Da Li & Yanping Yu & Jinbao Zhang & Shuli Cheng & Angang Yang & Rui Zhang, 2022. "N6-methyladenosine modification governs liver glycogenesis by stabilizing the glycogen synthase 2 mRNA," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    11. Harini Ramalingam & Jesus Alvarez & Andrea Flaten & Patricia Cobo-Stark & Nicholas Foster & Elyse Grilli & Ronak Lakhia & Karam Aboudehen & Thomas Carroll & Vishal Patel, 2025. "An RNA transmethylation pathway governs kidney nephrogenic potential," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    12. Dongsheng Mao & Xiaochen Tang & Runchi Zhang & Song Hu & Hongquan Gou & Penghui Zhang & Wenxing Li & Qiuhui Pan & Bing Shen & Xiaoli Zhu, 2025. "Multichrome encoding-based multiplexed, spatially resolved imaging reveals single-cell RNA epigenetic modifications heterogeneity," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    13. Zhiyuan Luo & Qilian Ma & Shan Sun & Ningning Li & Hongfeng Wang & Zheng Ying & Shengdong Ke, 2023. "Exon-intron boundary inhibits m6A deposition, enabling m6A distribution hallmark, longer mRNA half-life and flexible protein coding," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    14. Ruth Verstraten & Pierina Cetraro & Amy H. Fitzpatrick & Yasmine Alwie & Yannick N. Frommeyer & Elene Loliashvili & Saskia C. Stein & Susanne Häussler & Werner J. D. Ouwendijk & Daniel P. Depledge, 2026. "Defining expansions and perturbations to the RNA polymerase III transcriptome and epitranscriptome by modified direct RNA nanopore sequencing," Nature Communications, Nature, vol. 17(1), pages 1-14, December.
    15. Wanzun Lin & Li Chen & Haojiong Zhang & Xianxin Qiu & Qingting Huang & Fangzhu Wan & Ziyu Le & Shikai Geng & Anlan Zhang & Sufang Qiu & Long Chen & Lin Kong & Jiade J. Lu, 2023. "Tumor-intrinsic YTHDF1 drives immune evasion and resistance to immune checkpoint inhibitors via promoting MHC-I degradation," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
    16. Na Shao & Lei Xi & Yangfan Lv & Muhammad Idris & Lin Zhang & Ya Cao & Jingyi Xiang & Xi Xu & Belinda X. Ong & Qiongyi Zhang & Xu Peng & Xiaoyan Yue & Feng Xu & Chungang Liu, 2025. "USP5 stabilizes YTHDF1 to control cancer immune surveillance through mTORC1-mediated phosphorylation," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
    17. Shreya Rajachandran & Qianlan Xu & Qiqi Cao & Xin Zhang & Fei Chen & Sarah M. Mangiameli & Haiqi Chen, 2025. "Subcellular level spatial transcriptomics with PHOTON," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
    18. Zhijun Ren & Jialiang He & Xiang Huang & Yan Gao & Chuanchuan Wei & Zehong Wu & Wenbing Guo & Feng Wang & Qingquan Zhao & Xiang Sun & Jie Zhang & Nan Cao & Lan Lin & Jinkai Wang & Yixian Cun, 2025. "Isoform characterization of m6A in single cells identifies its role in RNA surveillance," Nature Communications, Nature, vol. 16(1), pages 1-19, December.
    19. Zhenxing Guo & Daoyu Duan & Wen Tang & Julia Zhu & William S Bush & Liangliang Zhang & Xiaofeng Zhu & Fulai Jin & Hao Feng, 2024. "magpie: A power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing," PLOS Computational Biology, Public Library of Science, vol. 20(2), pages 1-13, February.
    20. Xiangyu Wang & Yan Ding & Ran Li & Rujun Zhang & Xuejun Ge & Ruifang Gao & Miao Wang & Yubing Huang & Fang Zhang & Bin Zhao & Wang Liao & Jie Du, 2023. "N6-methyladenosine of Spi2a attenuates inflammation and sepsis-associated myocardial dysfunction in mice," Nature Communications, Nature, vol. 14(1), pages 1-17, December.

    More about this item

    Keywords

    ;
    ;
    ;
    ;
    ;
    ;
    ;
    ;
    ;
    ;
    ;

    JEL classification:

    • R00 - Urban, Rural, Regional, Real Estate, and Transportation Economics - - General - - - General
    • Z0 - Other Special Topics - - General

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:abf:journl:v:55:y:2024:i:3:p:47045-47054. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Angela Roy (email available below). General contact details of provider: .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.