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Key Issues in Conducting a Meta-Analysis of Gene Expression Microarray Datasets

Author

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  • Adaikalavan Ramasamy
  • Adrian Mondry
  • Chris C Holmes
  • Douglas G Altman

Abstract

Adaikalavan Ramasamy and colleagues outline seven key issues and suggest a stepwise approach in conducting a meta-analysis of microarray datasets.

Suggested Citation

  • Adaikalavan Ramasamy & Adrian Mondry & Chris C Holmes & Douglas G Altman, 2008. "Key Issues in Conducting a Meta-Analysis of Gene Expression Microarray Datasets," PLOS Medicine, Public Library of Science, vol. 5(9), pages 1-13, September.
    • Handle: RePEc:plo:pmed00:0050184
    DOI: 10.1371/journal.pmed.0050184
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    1. Ram Bhupal Reddy & Anupama Rajan Bhat & Bonney Lee James & Sindhu Valiyaveedan Govindan & Rohit Mathew & Ravindra DR & Naveen Hedne & Jeyaram Illiayaraja & Vikram Kekatpure & Samanta S Khora & Wesley , 2016. "Meta-Analyses of Microarray Datasets Identifies ANO1 and FADD as Prognostic Markers of Head and Neck Cancer," PLOS ONE, Public Library of Science, vol. 11(1), pages 1-21, January.
    2. Miranda van Uitert & Perry D Moerland & Daniel A Enquobahrie & Hannele Laivuori & Joris A M van der Post & Carrie Ris-Stalpers & Gijs B Afink, 2015. "Meta-Analysis of Placental Transcriptome Data Identifies a Novel Molecular Pathway Related to Preeclampsia," PLOS ONE, Public Library of Science, vol. 10(7), pages 1-15, July.
    3. Wei-Chung Cheng & Cheng-Wei Chang & Chaang-Ray Chen & Min-Lung Tsai & Wun-Yi Shu & Chia-Yang Li & Ian C Hsu, 2011. "Identification of Reference Genes across Physiological States for qRT-PCR through Microarray Meta-Analysis," PLOS ONE, Public Library of Science, vol. 6(2), pages 1-8, February.
    4. Claire Grills & Puthen V Jithesh & Jaine Blayney & Shu-Dong Zhang & Dean A Fennell, 2011. "Gene Expression Meta-Analysis Identifies VDAC1 as a Predictor of Poor Outcome in Early Stage Non-Small Cell Lung Cancer," PLOS ONE, Public Library of Science, vol. 6(1), pages 1-8, January.
    5. Atle van Beelen Granlund & Arnar Flatberg & Ann E Østvik & Ignat Drozdov & Bjørn I Gustafsson & Mark Kidd & Vidar Beisvag & Sverre H Torp & Helge L Waldum & Tom Christian Martinsen & Jan Kristian Damå, 2013. "Whole Genome Gene Expression Meta-Analysis of Inflammatory Bowel Disease Colon Mucosa Demonstrates Lack of Major Differences between Crohn's Disease and Ulcerative Colitis," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-14, February.
    6. Diego A Forero & Sandra Lopez-Leon & Yeimy González-Giraldo & Pantelis G Bagos, 2019. "Ten simple rules for carrying out and writing meta-analyses," PLOS Computational Biology, Public Library of Science, vol. 15(5), pages 1-7, May.
    7. Julie E. Goodman & Catherine Petito Boyce & Sonja N. Sax & Leslie A. Beyer & Robyn L. Prueitt, 2015. "Rethinking Meta‐Analysis: Applications for Air Pollution Data and Beyond," Risk Analysis, John Wiley & Sons, vol. 35(6), pages 1017-1039, June.
    8. Won Jun Lee & Sang Cheol Kim & Jung-Ho Yoon & Sang Jun Yoon & Johan Lim & You-Sun Kim & Sung Won Kwon & Jeong Hill Park, 2016. "Meta-Analysis of Tumor Stem-Like Breast Cancer Cells Using Gene Set and Network Analysis," PLOS ONE, Public Library of Science, vol. 11(2), pages 1-20, February.
    9. Cheng-Wei Chang & Wei-Chung Cheng & Chaang-Ray Chen & Wun-Yi Shu & Min-Lung Tsai & Ching-Lung Huang & Ian C Hsu, 2011. "Identification of Human Housekeeping Genes and Tissue-Selective Genes by Microarray Meta-Analysis," PLOS ONE, Public Library of Science, vol. 6(7), pages 1-10, July.
    10. Bidossessi Wilfried Hounkpe & Rafaela de Oliveira Benatti & Benilton de Sá Carvalho & Erich Vinicius De Paula, 2020. "Identification of common and divergent gene expression signatures in patients with venous and arterial thrombosis using data from public repositories," PLOS ONE, Public Library of Science, vol. 15(8), pages 1-19, August.
    11. Hao He & Shaolong Cao & Tianhua Niu & Yu Zhou & Lan Zhang & Yong Zeng & Wei Zhu & Yu-ping Wang & Hong-wen Deng, 2016. "Network-Based Meta-Analyses of Associations of Multiple Gene Expression Profiles with Bone Mineral Density Variations in Women," PLOS ONE, Public Library of Science, vol. 11(1), pages 1-16, January.
    12. Cherif Ben Hamda & Raphael Sangeda & Liberata Mwita & Ayton Meintjes & Siana Nkya & Sumir Panji & Nicola Mulder & Lamia Guizani-Tabbane & Alia Benkahla & Julie Makani & Kais Ghedira & H3ABioNet Consor, 2018. "A common molecular signature of patients with sickle cell disease revealed by microarray meta-analysis and a genome-wide association study," PLOS ONE, Public Library of Science, vol. 13(7), pages 1-21, July.
    13. Daniel Baron & Armelle Magot & Gérard Ramstein & Marja Steenman & Guillemette Fayet & Catherine Chevalier & Philippe Jourdon & Rémi Houlgatte & Frédérique Savagner & Yann Pereon, 2011. "Immune Response and Mitochondrial Metabolism Are Commonly Deregulated in DMD and Aging Skeletal Muscle," PLOS ONE, Public Library of Science, vol. 6(11), pages 1-11, November.
    14. Raihan K Uddin & Shiva M Singh, 2013. "Hippocampal Gene Expression Meta-Analysis Identifies Aging and Age-Associated Spatial Learning Impairment (ASLI) Genes and Pathways," PLOS ONE, Public Library of Science, vol. 8(7), pages 1-16, July.
    15. Peter Langfelder & Paul S Mischel & Steve Horvath, 2013. "When Is Hub Gene Selection Better than Standard Meta-Analysis?," PLOS ONE, Public Library of Science, vol. 8(4), pages 1-16, April.
    16. Hans-Juergen Schulten & Deema Hussein, 2019. "Array expression meta-analysis of cancer stem cell genes identifies upregulation of PODXL especially in DCC low expression meningiomas," PLOS ONE, Public Library of Science, vol. 14(5), pages 1-20, May.
    17. Zhiguang Huo & Li Zhu & Tianzhou Ma & Hongcheng Liu & Song Han & Daiqing Liao & Jinying Zhao & George Tseng, 2020. "Two-Way Horizontal and Vertical Omics Integration for Disease Subtype Discovery," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 12(1), pages 1-22, April.

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