Comparative analysis of oncogenes identified by microarray and RNA-sequencing as biomarkers for clinical prognosis

被引：13
|
作者：
Liu, Yuan [1 ]
Jing, Runyu [1 ]
Xu, Junmei [1 ]
Liu, Keqin [1 ]
Xue, Jiwei [1 ]
Wen, Zhining [1 ]
Li, Menglong [1 ]
机构：
[1] Sichuan Univ, Coll Chem, Chengdu 610064, Peoples R China
来源：
BIOMARKERS IN MEDICINE | 2015年 / 9卷 / 11期
关键词：
cancer prognosis; comparative analysis; DNA microarray; enrichment analysis; molecular function; oncogene; RNA-sequencing; ENRICHMENT ANALYSIS; SEQ; REPRODUCIBILITY; REVEALS; GENOME; CONCORDANCE; LANDSCAPES; CARCINOMA;
D O I：
10.2217/bmm.15.97
中图分类号：
R-3 [医学研究方法]; R3 [基础医学];
学科分类号：
1001 ;
摘要：
Although RNA-sequencing has been widely used to identify the differentially expressed genes (DEGs) as biomarkers to guide the therapeutic treatment, it is necessary to investigate the concordance of DEGs identified by microarray and RNA-sequencing for the clinical prognosis. Material & methods: By using The Cancer Genome Atlas data sets, we thoroughly investigated the concordance of DEGs identified from microarray and RNA-sequencing data and their molecular functions. Results: The DEGs identified by both technologies averaged similar to 98.6% overlap. The cancer-related gene sets were significantly enriched with the DEGs and consistent between two technologies. Conclusions: The highly consistency of DEGs in their regulation directionality and molecular functions indicated the good reproducibility between microarray and RNA-sequencing in identifying potential oncogenes for clinical prognosis.
引用
收藏
页码：1067 / 1078
页数：12
相关论文
共 50 条
  • [1] RNA-Sequencing Analysis Identification of Potential Biomarkers for Diagnosis of Sarcopenia
    Furutani, Motoki
    Suganuma, Mutsumi
    Akiyama, Shintaro
    Mitsumori, Risa
    Takemura, Marie
    Matsui, Yasumoto
    Satake, Shosuke
    Nakano, Yukiko
    Niida, Shumpei
    Ozaki, Kouichi
    Hosoyama, Tohru
    Shigemizu, Daichi
    JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES, 2023, 78 (11): : 1991 - 1998
  • [2] Novel biomarkers identified in triple-negative breast cancer through RNA-sequencing
    Chen, Yan-li
    Wang, Ke
    Xie, Fei
    Zhuo, Zhong-ling
    Liu, Chang
    Yang, Yu
    Wang, Shu
    Zhao, Xiao-tao
    CLINICA CHIMICA ACTA, 2022, 531 : 302 - 308
  • [3] Comparative RNA-sequencing analysis of myocardial and circulating small RNAs in human heart failure and their utility as biomarkers
    Akat, Kemal Marc
    Moore-McGriff, D'Vesharronne
    Morozova, Pavel
    Browna, Miguel
    Gogakos, Tasos
    Da Rosa, Joel Correa
    Mihailovic, Aleksandra
    Sauer, Markus
    Ji, Ruiping
    Ramarathnam, Aarthi
    Totary-Jain, Hana
    Williams, Zev
    Tuschl, Thomas
    Schulze, P. Christian
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2014, 111 (30) : 11151 - 11156
  • [4] Comprehensive comparative analysis of 5'-end RNA-sequencing methods
    Adiconis, Xian
    Haber, Adam L.
    Simmons, Sean K.
    Moonshine, Ami Levy
    Ji, Zhe
    Busby, Michele A.
    Shi, Xi
    Jacques, Justin
    Lancaster, Madeline A.
    Pan, Jen Q.
    Regev, Aviv
    Levin, Joshua Z.
    NATURE METHODS, 2018, 15 (07) : 505 - +
  • [5] Comprehensive comparative analysis of 5′-end RNA-sequencing methods
    Xian Adiconis
    Adam L. Haber
    Sean K. Simmons
    Ami Levy Moonshine
    Zhe Ji
    Michele A. Busby
    Xi Shi
    Justin Jacques
    Madeline A. Lancaster
    Jen Q. Pan
    Aviv Regev
    Joshua Z. Levin
    Nature Methods, 2018, 15 : 505 - 511
  • [6] Identification of miRNA biomarkers of pneumonia using RNA-sequencing and bioinformatics analysis
    Huang, Sai
    Feng, Cong
    Zhai, Yong-Zhi
    Zhou, Xuan
    Li, Bei
    Wang, Li-Li
    Chen, Wei
    Lv, Fa-Qin
    Li, Tan-Shi
    EXPERIMENTAL AND THERAPEUTIC MEDICINE, 2017, 13 (04) : 1235 - 1244
  • [7] Clinical impact of RNA-sequencing in diagnostics
    De Cock, Laurenz
    D'haenens, Erika
    Vergult, Sarah
    Vantomme, Lies
    Dheedene, Annelies
    de Putter, Robin
    Van Damme, Tim
    Sourbron, Jo
    Callewaert, Bert
    Vanakker, Olivier
    Menten, Bjorn
    EUROPEAN JOURNAL OF HUMAN GENETICS, 2024, 32 : 648 - 648
  • [8] Comparative RNA-Sequencing Analysis Benefits a Pediatric Patient With Relapsed Cancer
    Newton, Yulia
    Rod Rassekh, S.
    Deyell, Rebecca J.
    Shen, Yaoqing
    Jones, Martin R.
    Dunham, Chris
    Yip, Stephen
    Leelakumari, Sreeja
    Zhu, Jingchun
    McColl, Duncan
    Swatloski, Teresa
    Salama, Sofie R.
    Ng, Tony
    Hendson, Glenda
    Lee, Anna E.
    Ma, Yussanne
    Moore, Richard
    Mungall, Andrew J.
    Haussler, David
    Stuart, Joshua M.
    Jantzen, Colleen
    Laskin, Janessa
    Jones, Steven J. M.
    Marra, Marco A.
    Morozova, Olena
    JCO PRECISION ONCOLOGY, 2018, 2 : 1 - 16
  • [9] Key genes affecting the progression of nasopharyngeal carcinoma identified by RNA-sequencing and bioinformatic analysis
    Wang, Yihong
    Li, Manyi
    Guo, Yan
    Huang, Haiping
    Dong, Xuelin
    Sun, Yangguang
    Liu, Jisheng
    AGING-US, 2021, 13 (18): : 22176 - 22187
  • [10] Integrative analysis of RNA-sequencing and microarray for the identification of adverse effects of UVB exposure on human skin
    Jang, Yujin
    Na, Hye-Won
    Shin, Dong Yeop
    Lee, Jun
    Han, Jun Pyo
    Kim, Hyun Soo
    Kim, Su Ji
    Choi, Eun-Jeong
    Lee, Charles
    Hong, Yong Deog
    Kim, Hyoung-June
    Seo, Young Rok
    FRONTIERS IN PUBLIC HEALTH, 2024, 12
12345