A Primer on a Hepatocellular Carcinoma Bioresource Bank Using the Cancer Genome Atlas Guidelines: Practical Issues and Pitfalls

World Journal of Surgery ◽

10.1007/s00268-010-0953-y ◽

2011 ◽

Vol 35 (8) ◽

pp. 1732-1737 ◽

Author(s):

N. Thao T. Nguyen ◽

Ron T. Cotton ◽

Theresa R. Harring ◽

Jacfranz J. Guiteau ◽

Marie-Claude Gingras ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Cancer Genome ◽

The Cancer Genome Atlas ◽

Cancer Genome Atlas ◽

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Analysis of the cancer genome atlas data to determine the correlation between PROX1 and TERT in hepatocellular carcinoma

International Journal of Cancer ◽

10.1002/ijc.31888 ◽

2018 ◽

Vol 144 (7) ◽

pp. 1752-1753 ◽

Author(s):

Jae‐Ho Lee

Keyword(s):

Hepatocellular Carcinoma ◽

Cancer Genome ◽

The Cancer Genome Atlas ◽

Cancer Genome Atlas ◽

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Diagnostic and prognostic roles of IRAK1 in hepatocellular carcinoma tissues: an analysis of immunohistochemistry and RNA-sequencing data from the cancer genome atlas

OncoTargets and Therapy ◽

10.2147/ott.s132120 ◽

2017 ◽

Vol Volume 10 ◽

pp. 1711-1723 ◽

Author(s):

Zhi-hua Ye ◽

Li Gao ◽

Dong-yue Wen ◽

Yun He ◽

Yu-yan Pang ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Rna Sequencing ◽

Cancer Genome ◽

The Cancer Genome Atlas ◽

Sequencing Data ◽

Cancer Genome Atlas ◽

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Prognostic implications of aberrantly expressed methylation‑driven genes in hepatocellular carcinoma: A study based on The Cancer Genome Atlas

Molecular Medicine Reports ◽

10.3892/mmr.2019.10771 ◽

2019 ◽

Author(s):

Jinzhong Li ◽

Ning Chen ◽

Xiaobing Gong

Keyword(s):

Hepatocellular Carcinoma ◽

Cancer Genome ◽

The Cancer Genome Atlas ◽

Cancer Genome Atlas ◽

Prognostic Implications ◽

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Peer Review #1 of "Systematic analysis and prediction model construction of alternative splicing events in hepatocellular carcinoma: a study on the basis of large-scale spliceseq data from The Cancer Genome Atlas (v0.1)"

10.7287/peerj.8245v0.1/reviews/1 ◽

2019 ◽

Keyword(s):

Hepatocellular Carcinoma ◽

Alternative Splicing ◽

Prediction Model ◽

Peer Review ◽

Large Scale ◽

Cancer Genome ◽

The Cancer Genome Atlas ◽

Systematic Analysis ◽

Cancer Genome Atlas ◽

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Uncovering the potential differentially expressed miRNAs as diagnostic biomarkers for hepatocellular carcinoma based on machine learning in The Cancer Genome Atlas database

Oncology Reports ◽

10.3892/or.2020.7551 ◽

2020 ◽

Author(s):

Xin Zhao ◽

Jian Dou ◽

Jinglin Cao ◽

Yang Wang ◽

Qingjun Gao ◽

...

Keyword(s):

Machine Learning ◽

Hepatocellular Carcinoma ◽

Cancer Genome ◽

The Cancer Genome Atlas ◽

Differentially Expressed ◽

Diagnostic Biomarkers ◽

Differentially Expressed Mirnas ◽

Cancer Genome Atlas ◽

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The Cancer Genome Atlas (TCGA) based m6A methylation-related genes predict prognosis in hepatocellular carcinoma

Bioengineered ◽

10.1080/21655979.2020.1787764 ◽

2020 ◽

Vol 11 (1) ◽

pp. 759-768

Author(s):

Jun Liu ◽

Guili Sun ◽

Shangling Pan ◽

Mengbin Qin ◽

Rong Ouyang ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Cancer Genome ◽

The Cancer Genome Atlas ◽

Cancer Genome Atlas ◽

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Integrated analysis of hypoxia-induced miR-210 signature as a potential prognostic biomarker of hepatocellular carcinoma: a study based on The Cancer Genome Atlas

Journal of Zhejiang University SCIENCE B ◽

10.1631/jzus.b1900343 ◽

2019 ◽

Vol 20 (11) ◽

pp. 928-932

Author(s):

Yi Dai ◽

Ji-liang Shen ◽

Xue-yong Zheng ◽

Tian-yu Lin ◽

Hai-tao Yu

Keyword(s):

Hepatocellular Carcinoma ◽

Prognostic Biomarker ◽

Cancer Genome ◽

The Cancer Genome Atlas ◽

Integrated Analysis ◽

Cancer Genome Atlas ◽

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Peer Review #3 of "Systematic analysis and prediction model construction of alternative splicing events in hepatocellular carcinoma: a study on the basis of large-scale spliceseq data from The Cancer Genome Atlas (v0.1)"

10.7287/peerj.8245v0.1/reviews/3 ◽

2019 ◽

Keyword(s):

Hepatocellular Carcinoma ◽

Alternative Splicing ◽

Prediction Model ◽

Peer Review ◽

Large Scale ◽

Cancer Genome ◽

The Cancer Genome Atlas ◽

Systematic Analysis ◽

Cancer Genome Atlas ◽

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Peer Review #3 of "Systematic analysis and prediction model construction of alternative splicing events in hepatocellular carcinoma: a study on the basis of large-scale spliceseq data from The Cancer Genome Atlas (v0.2)"

10.7287/peerj.8245v0.2/reviews/3 ◽

2019 ◽

Keyword(s):

Hepatocellular Carcinoma ◽

Alternative Splicing ◽

Prediction Model ◽

Peer Review ◽

Large Scale ◽

Cancer Genome ◽

The Cancer Genome Atlas ◽

Systematic Analysis ◽

Cancer Genome Atlas ◽

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Identification of prognostic and immune-related lncRNAs in hepatocellular carcinoma based on the cancer genome atlas data mining

Materials Express ◽

10.1166/mex.2020.1736 ◽

2020 ◽

Vol 10 (8) ◽

pp. 1189-1196

Author(s):

Kaikai Ren ◽

Jiakang Ma ◽

Bo Zhou ◽

Xiaoyan Lin ◽

Mingyu Hou ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Expression Profiles ◽

Enrichment Analysis ◽

Cancer Genome ◽

Gene Set Enrichment Analysis ◽

The Cancer Genome Atlas ◽

High Rate ◽

Prognostic Indicators ◽

Cancer Genome Atlas ◽

Hepatocellular carcinoma (HCC) is a malignancy originating from hepatocytes with a high rate of distant metastasis and recurrence. HCC prognosis remains poorly understood, although its diagnosis and treatment have improved globally. Therefore, it is necessary to identify reliable predictive and prognostic indicators of HCC. HCC gene expression profiles and corresponding clinical data were downloaded from The Cancer Genome Atlas. Seven lncRNAs (C10orf91, AC011352.3, AC015722.2, AC006372.1, PICSAR, AC110285.3, and AP001972.4) associated with immune and clinicopathological features were identified as biomarker candidates for HCC prognosis based on single-sample gene set enrichment analysis, the ESTIMATE algorithm, and Cox PHR analyses. Altogether, the findings revealed that the seven immune-related lncRNAs may provide a reference for improving HCC prognosis.

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