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Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments

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  1. Arsheed H. Sheikh & Iosif Zacharia & Alonso J. Pardal & Ana Dominguez-Ferreras & Daniela J. Sueldo & Jung-Gun Kim & Alexi Balmuth & Jose R. Gutierrez & Brendon F. Conlan & Najeeb Ullah & Olivia M. Nip, 2023. "Dynamic changes of the Prf/Pto tomato resistance complex following effector recognition," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
  2. Nicola J. Armstrong, 2008. "The changing focus of microarray analysis," Statistica Neerlandica, Netherlands Society for Statistics and Operations Research, vol. 62(3), pages 364-373, August.
  3. Xu, Ping & Brock, Guy N. & Parrish, Rudolph S., 2009. "Modified linear discriminant analysis approaches for classification of high-dimensional microarray data," Computational Statistics & Data Analysis, Elsevier, vol. 53(5), pages 1674-1687, March.
  4. Bilgrau, Anders Ellern & Eriksen, Poul Svante & Rasmussen, Jakob Gulddahl & Johnsen, Hans Erik & Dybkaer, Karen & Boegsted, Martin, 2016. "GMCM: Unsupervised Clustering and Meta-Analysis Using Gaussian Mixture Copula Models," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 70(i02).
  5. Xiao Min & Chen Ting & Ming Ruixing & Huang Kunpeng, 2020. "Optimal Estimation for Power of Variance with Application to Gene-Set Testing," Journal of Systems Science and Information, De Gruyter, vol. 8(6), pages 549-564, December.
  6. Ila Pant & Neeraj Kumar & Imran Khan & Somanahalli Girish Rao & Paturu Kondaiah, 2015. "Role of Areca Nut Induced TGF-β and Epithelial-Mesenchymal Interaction in the Pathogenesis of Oral Submucous Fibrosis," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-19, June.
  7. Dazard, Jean-Eudes & Sunil Rao, J., 2012. "Joint adaptive mean–variance regularization and variance stabilization of high dimensional data," Computational Statistics & Data Analysis, Elsevier, vol. 56(7), pages 2317-2333.
  8. Montazeri Zahra & Yanofsky Corey M. & Bickel David R., 2010. "Shrinkage Estimation of Effect Sizes as an Alternative to Hypothesis Testing Followed by Estimation in High-Dimensional Biology: Applications to Differential Gene Expression," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-33, June.
  9. 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.
  10. Dominic Coey & Kenneth Hung, 2022. "Empirical Bayes Selection for Value Maximization," Papers 2210.03905, arXiv.org, revised Jan 2023.
  11. 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.
  12. 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.
  13. Ricardo C Gehrau & Kellie J Archer & Valeria R Mas & Daniel G Maluf, 2012. "Molecular Profiles of HCV Cirrhotic Tissues Derived in a Panel of Markers with Clinical Utility for Hepatocellular Carcinoma Surveillance," PLOS ONE, Public Library of Science, vol. 7(7), pages 1-12, July.
  14. 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.
  15. Yeil Kwon & Zhigen Zhao, 2023. "On F-modelling-based empirical Bayes estimation of variances," Biometrika, Biometrika Trust, vol. 110(1), pages 69-81.
  16. Ming Yuan & Christina Kendziorski, 2006. "A Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification," Biometrics, The International Biometric Society, vol. 62(4), pages 1089-1098, December.
  17. Bernie J Daigle Jr & Alicia Deng & Tracey McLaughlin & Samuel W Cushman & Margaret C Cam & Gerald Reaven & Philip S Tsao & Russ B Altman, 2010. "Using Pre-existing Microarray Datasets to Increase Experimental Power: Application to Insulin Resistance," PLOS Computational Biology, Public Library of Science, vol. 6(3), pages 1-15, March.
  18. Debajyoti Ghosh & Lili Ding & Umasundari Sivaprasad & Esmond Geh & Jocelyn Biagini Myers & Jonathan A Bernstein & Gurjit K Khurana Hershey & Tesfaye B Mersha, 2015. "Multiple Transcriptome Data Analysis Reveals Biologically Relevant Atopic Dermatitis Signature Genes and Pathways," PLOS ONE, Public Library of Science, vol. 10(12), pages 1-23, December.
  19. Olivia Prazeres da Costa & Arthur Hoffman & Johannes W Rey & Ulrich Mansmann & Thorsten Buch & Achim Tresch, 2014. "Selection of Higher Order Regression Models in the Analysis of Multi-Factorial Transcription Data," PLOS ONE, Public Library of Science, vol. 9(3), pages 1-8, March.
  20. Tony Marion & Husni Elbahesh & Paul G Thomas & John P DeVincenzo & Richard Webby & Klaus Schughart, 2016. "Respiratory Mucosal Proteome Quantification in Human Influenza Infections," PLOS ONE, Public Library of Science, vol. 11(4), pages 1-16, April.
  21. Ju Han & Hang Chang & Orsi Giricz & Genee Y Lee & Frederick L Baehner & Joe W Gray & Mina J Bissell & Paraic A Kenny & Bahram Parvin, 2010. "Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture," PLOS Computational Biology, Public Library of Science, vol. 6(2), pages 1-12, February.
  22. Andres Tapia del Fierro & Bianca den Hamer & Natalia Benetti & Natasha Jansz & Kelan Chen & Tamara Beck & Hannah Vanyai & Alexandra D. Gurzau & Lucia Daxinger & Shifeng Xue & Thanh Thao Nguyen Ly & Ir, 2023. "SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
  23. Jianhua Hu & Fred A. Wright, 2007. "Assessing Differential Gene Expression with Small Sample Sizes in Oligonucleotide Arrays Using a Mean-Variance Model," Biometrics, The International Biometric Society, vol. 63(1), pages 41-49, March.
  24. 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.
  25. Yan Geng & Lin Li & Jie Yan & Kevin Liu & Aizhen Yang & Lin Zhang & Yingzhi Shen & Han Gao & Xuefeng Wu & Imre Noth & Yong Huang & Junling Liu & Xuemei Fan, 2022. "PEAR1 regulates expansion of activated fibroblasts and deposition of extracellular matrix in pulmonary fibrosis," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  26. Theresa Niederberger & Stefanie Etzold & Michael Lidschreiber & Kerstin C Maier & Dietmar E Martin & Holger Fröhlich & Patrick Cramer & Achim Tresch, 2012. "MC EMiNEM Maps the Interaction Landscape of the Mediator," PLOS Computational Biology, Public Library of Science, vol. 8(6), pages 1-10, June.
  27. Francesca Cordero & Marco Beccuti & Maddalena Arigoni & Susanna Donatelli & Raffaele A Calogero, 2012. "Optimizing a Massive Parallel Sequencing Workflow for Quantitative miRNA Expression Analysis," PLOS ONE, Public Library of Science, vol. 7(2), pages 1-10, February.
  28. 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.
  29. Daniel J. Fazakerley & Julian van Gerwen & Kristen C. Cooke & Xiaowen Duan & Elise J. Needham & Alexis Díaz-Vegas & Søren Madsen & Dougall M. Norris & Amber S. Shun-Shion & James R. Krycer & James G. , 2023. "Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
  30. Soneson, Charlotte & Fontes, Magnus, 2014. "Incorporation of gene exchangeabilities improves the reproducibility of gene set rankings," Computational Statistics & Data Analysis, Elsevier, vol. 71(C), pages 588-598.
  31. Santu Ghosh & Alan M. Polansky, 2022. "Large-Scale Simultaneous Testing Using Kernel Density Estimation," Sankhya A: The Indian Journal of Statistics, Springer;Indian Statistical Institute, vol. 84(2), pages 808-843, August.
  32. Alastair G. Kerr & Zuoneng Wang & Na Wang & Kelvin H. M. Kwok & Jutta Jalkanen & Alison Ludzki & Simon Lecoutre & Dominique Langin & Martin O. Bergo & Ingrid Dahlman & Carsten Mim & Peter Arner & Hui , 2022. "The long noncoding RNA ADIPINT regulates human adipocyte metabolism via pyruvate carboxylase," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  33. Simina M. Boca & Héctor Céorrada Bravo & Brian Caffo & Jeffrey T. Leek & Giovanni Parmigiani, 2013. "A Decision-Theory Approach to Interpretable Set Analysis for High-Dimensional Data," Biometrics, The International Biometric Society, vol. 69(3), pages 614-623, September.
  34. Morten Tulstrup & Mette Soerensen & Jakob Werner Hansen & Linn Gillberg & Maria Needhamsen & Katja Kaastrup & Kristian Helin & Kaare Christensen & Joachim Weischenfeldt & Kirsten Grønbæk, 2021. "TET2 mutations are associated with hypermethylation at key regulatory enhancers in normal and malignant hematopoiesis," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
  35. Asta Laiho & Laura L Elo, 2014. "A Note on an Exon-Based Strategy to Identify Differentially Expressed Genes in RNA-Seq Experiments," PLOS ONE, Public Library of Science, vol. 9(12), pages 1-12, December.
  36. 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.
  37. Madsen Tobias & Świtnicki Michał & Juul Malene & Pedersen Jakob Skou, 2019. "EBADIMEX: an empirical Bayes approach to detect joint differential expression and methylation and to classify samples," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 18(6), pages 1-23, December.
  38. Xin Victoria Wang & Roel G W Verhaak & Elizabeth Purdom & Paul T Spellman & Terence P Speed, 2011. "Unifying Gene Expression Measures from Multiple Platforms Using Factor Analysis," PLOS ONE, Public Library of Science, vol. 6(3), pages 1-14, March.
  39. Mark Pinese & Christopher J Scarlett & James G Kench & Emily K Colvin & Davendra Segara & Susan M Henshall & Robert L Sutherland & Andrew V Biankin, 2009. "Messina: A Novel Analysis Tool to Identify Biologically Relevant Molecules in Disease," PLOS ONE, Public Library of Science, vol. 4(4), pages 1-7, April.
  40. Sayantee Jana & Narayanaswamy Balakrishnan & Dietrich Rosen & Jemila Seid Hamid, 2017. "High dimensional extension of the growth curve model and its application in genetics," Statistical Methods & Applications, Springer;Società Italiana di Statistica, vol. 26(2), pages 273-292, June.
  41. Nicholas C. Henderson & Michael A. Newton, 2016. "Making the cut: improved ranking and selection for large-scale inference," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 78(4), pages 781-804, September.
  42. 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.
  43. Alin Tomoiaga & Peter Westfall & Michele Donato & Sorin Draghici & Sonia Hassan & Roberto Romero & Paola Tellaroli, 2016. "Pathway crosstalk effects: shrinkage and disentanglement using a Bayesian hierarchical model," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 8(2), pages 374-394, October.
  44. Chee Ho H’ng & Shanika L. Amarasinghe & Boya Zhang & Hojin Chang & Xinli Qu & David R. Powell & Alberto Rosello-Diez, 2024. "Compensatory growth and recovery of cartilage cytoarchitecture after transient cell death in fetal mouse limbs," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  45. Qianxing Mo & Faming Liang, 2010. "Bayesian Modeling of ChIP-chip Data Through a High-Order Ising Model," Biometrics, The International Biometric Society, vol. 66(4), pages 1284-1294, December.
  46. 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.
  47. Way-Champ Mah & Thomas Thurnherr & Pierce K H Chow & Alexander Y F Chung & London L P J Ooi & Han Chong Toh & Bin Tean Teh & Yogen Saunthararajah & Caroline G L Lee, 2014. "Methylation Profiles Reveal Distinct Subgroup of Hepatocellular Carcinoma Patients with Poor Prognosis," PLOS ONE, Public Library of Science, vol. 9(8), pages 1-10, August.
  48. 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.
  49. Cecilia Patitucci & Juan Diego Hernández-Camacho & Elodie Vimont & Sonny Yde & Thomas Cokelaer & Thibault Chaze & Quentin Giai Gianetto & Mariette Matondo & Anastasia Gazi & Ivan Nemazanyy & David A. , 2023. "Mtfp1 ablation enhances mitochondrial respiration and protects against hepatic steatosis," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
  50. N. Bochkina & S. Richardson, 2007. "Tail Posterior Probability for Inference in Pairwise and Multiclass Gene Expression Data," Biometrics, The International Biometric Society, vol. 63(4), pages 1117-1125, December.
  51. 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.
  52. Marko Sysi-Aho & Andrey Ermolov & Peddinti V Gopalacharyulu & Abhishek Tripathi & Tuulikki Seppänen-Laakso & Johanna Maukonen & Ismo Mattila & Suvi T Ruohonen & Laura Vähätalo & Laxman Yetukuri & Tain, 2011. "Metabolic Regulation in Progression to Autoimmune Diabetes," PLOS Computational Biology, Public Library of Science, vol. 7(10), pages 1-16, October.
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