IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0076746.html
   My bibliography  Save this article

Meta-Analysis Identifies NF-κB as a Therapeutic Target in Renal Cancer

Author

Listed:
  • Suraj Peri
  • Karthik Devarajan
  • Dong-Hua Yang
  • Alfred G Knudson
  • Siddharth Balachandran

Abstract

Objective: To determine the expression patterns of NF-κB regulators and target genes in clear cell renal cell carcinoma (ccRCC), their correlation with von Hippel Lindau (VHL) mutational status, and their association with survival outcomes. Methods: Meta-analyses were carried out on published ccRCC gene expression datasets by RankProd, a non-parametric statistical method. DEGs with a False Discovery Rate of

Suggested Citation

  • Suraj Peri & Karthik Devarajan & Dong-Hua Yang & Alfred G Knudson & Siddharth Balachandran, 2013. "Meta-Analysis Identifies NF-κB as a Therapeutic Target in Renal Cancer," PLOS ONE, Public Library of Science, vol. 8(10), pages 1-1, October.
    • Handle: RePEc:plo:pone00:0076746
    DOI: 10.1371/journal.pone.0076746
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0076746
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0076746&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0076746?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. Devarajan, Karthik & Ebrahimi, Nader, 2011. "A semi-parametric generalization of the Cox proportional hazards regression model: Inference and applications," Computational Statistics & Data Analysis, Elsevier, vol. 55(1), pages 667-676, January.
    2. Kenya Honda & Hideyuki Yanai & Hideo Negishi & Masataka Asagiri & Mitsuharu Sato & Tatsuaki Mizutani & Naoya Shimada & Yusuke Ohba & Akinori Takaoka & Nobuaki Yoshida & Tadatsugu Taniguchi, 2005. "IRF-7 is the master regulator of type-I interferon-dependent immune responses," Nature, Nature, vol. 434(7034), pages 772-777, April.
    3. Zhezhen Jin & D. Y. Lin & Zhiliang Ying, 2006. "On least-squares regression with censored data," Biometrika, Biometrika Trust, vol. 93(1), pages 147-161, March.
    4. Smyth Gordon K, 2004. "Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 3(1), pages 1-28, February.
    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. Aaron C Ericsson & J Wade Davis & William Spollen & Nathan Bivens & Scott Givan & Catherine E Hagan & Mark McIntosh & Craig L Franklin, 2015. "Effects of Vendor and Genetic Background on the Composition of the Fecal Microbiota of Inbred Mice," PLOS ONE, Public Library of Science, vol. 10(2), pages 1-19, February.
    2. Changrong Yan & Dixin Zhang, 2013. "Sparse dimension reduction for survival data," Computational Statistics, Springer, vol. 28(4), pages 1835-1852, August.
    3. Hossain, Ahmed & Beyene, Joseph & Willan, Andrew R. & Hu, Pingzhao, 2009. "A flexible approximate likelihood ratio test for detecting differential expression in microarray data," Computational Statistics & Data Analysis, Elsevier, vol. 53(10), pages 3685-3695, August.
    4. Yongli Qin & Lina Jia & Huijiao Liu & Wenqiang Ma & Xinmin Ren & Haifeng Li & Yuanwu Liu & Haiwen Li & Shuoqian Ma & Mei Liu & Pingping Li & Jinghua Yan & Jiyan Zhang & Yangdong Guo & Hua You & Yan Gu, 2021. "Macrophage deletion of Noc4l triggers endosomal TLR4/TRIF signal and leads to insulin resistance," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
    5. Xu, Linzhi & Zhang, Jiajia, 2010. "An EM-like algorithm for the semiparametric accelerated failure time gamma frailty model," Computational Statistics & Data Analysis, Elsevier, vol. 54(6), pages 1467-1474, June.
    6. Xiaohong Li & Guy N Brock & Eric C Rouchka & Nigel G F Cooper & Dongfeng Wu & Timothy E O’Toole & Ryan S Gill & Abdallah M Eteleeb & Liz O’Brien & Shesh N Rai, 2017. "A comparison of per sample global scaling and per gene normalization methods for differential expression analysis of RNA-seq data," PLOS ONE, Public Library of Science, vol. 12(5), pages 1-22, May.
    7. Kerr Kathleen F., 2012. "Optimality Criteria for the Design of 2-Color Microarray Studies," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(1), pages 1-9, January.
    8. Marschner, Ian C. & Gillett, Alexandra C. & O’Connell, Rachel L., 2012. "Stratified additive Poisson models: Computational methods and applications in clinical epidemiology," Computational Statistics & Data Analysis, Elsevier, vol. 56(5), pages 1115-1130.
    9. Ambroise Jérôme & Bearzatto Bertrand & Robert Annie & Macq Benoit & Gala Jean-Luc, 2012. "Combining Multiple Laser Scans of Spotted Microarrays by Means of a Two-Way ANOVA Model," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(3), pages 1-20, February.
    10. J. McClatchy & R. Strogantsev & E. Wolfe & H. Y. Lin & M. Mohammadhosseini & B. A. Davis & C. Eden & D. Goldman & W. H. Fleming & P. Conley & G. Wu & L. Cimmino & H. Mohammed & A. Agarwal, 2023. "Clonal hematopoiesis related TET2 loss-of-function impedes IL1β-mediated epigenetic reprogramming in hematopoietic stem and progenitor cells," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    11. Alexandra Gyurdieva & Stefan Zajic & Ya-Fang Chang & E. Andres Houseman & Shan Zhong & Jaegil Kim & Michael Nathenson & Thomas Faitg & Mary Woessner & David C. Turner & Aisha N. Hasan & John Glod & Ro, 2022. "Biomarker correlates with response to NY-ESO-1 TCR T cells in patients with synovial sarcoma," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    12. Lu, Xuewen, 2010. "Asymptotic distributions of two "synthetic data" estimators for censored single-index models," Journal of Multivariate Analysis, Elsevier, vol. 101(4), pages 999-1015, April.
    13. Sora Yoon & Seon-Young Kim & Dougu Nam, 2016. "Improving Gene-Set Enrichment Analysis of RNA-Seq Data with Small Replicates," PLOS ONE, Public Library of Science, vol. 11(11), pages 1-16, November.
    14. Yu Lianbo & Gulati Parul & Fernandez Soledad & Pennell Michael & Kirschner Lawrence & Jarjoura David, 2011. "Fully Moderated T-statistic for Small Sample Size Gene Expression Arrays," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-22, September.
    15. Zhou, Mai & Li, Gang, 2008. "Empirical likelihood analysis of the Buckley-James estimator," Journal of Multivariate Analysis, Elsevier, vol. 99(4), pages 649-664, April.
    16. Sinan Xiong & Jianbiao Zhou & Tze King Tan & Tae-Hoon Chung & Tuan Zea Tan & Sabrina Hui-Min Toh & Nicole Xin Ning Tang & Yunlu Jia & Yi Xiang See & Melissa Jane Fullwood & Takaomi Sanda & Wee-Joo Chn, 2024. "Super enhancer acquisition drives expression of oncogenic PPP1R15B that regulates protein homeostasis in multiple myeloma," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    17. Chaofeng Yuan & Wensheng Zhu & Xuming He & Jianhua Guo, 2019. "A mixture factor model with applications to microarray data," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 28(1), pages 60-76, March.
    18. Nan Li & Matthew N. McCall & Zhijin Wu, 2017. "Establishing Informative Prior for Gene Expression Variance from Public Databases," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 9(1), pages 160-177, June.
    19. Brian Caffo & Liu Dongmei & Giovanni Parmigiani, 2004. "Power Conjugate Multilevel Models with Applications to Genomics," Johns Hopkins University Dept. of Biostatistics Working Paper Series 1062, Berkeley Electronic Press.
    20. Nott, David J. & Yu, Zeming & Chan, Eva & Cotsapas, Chris & Cowley, Mark J. & Pulvers, Jeremy & Williams, Rohan & Little, Peter, 2007. "Hierarchical Bayes variable selection and microarray experiments," Journal of Multivariate Analysis, Elsevier, vol. 98(4), pages 852-872, April.

    More about this item

    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:plo:pone00:0076746. 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: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    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.