Jump to ContentJump to Main Navigation
Show Summary Details
More options …

Statistical Applications in Genetics and Molecular Biology

Editor-in-Chief: Sanguinetti, Guido

IMPACT FACTOR 2018: 0.536
5-year IMPACT FACTOR: 0.764

CiteScore 2018: 0.49

SCImago Journal Rank (SJR) 2018: 0.316
Source Normalized Impact per Paper (SNIP) 2018: 0.342

Mathematical Citation Quotient (MCQ) 2018: 0.02

See all formats and pricing
More options …
Volume 6, Issue 1


Volume 10 (2011)

Volume 9 (2010)

Volume 6 (2007)

Volume 5 (2006)

Volume 4 (2005)

Volume 2 (2003)

Volume 1 (2002)

Accurate Ranking of Differentially Expressed Genes by a Distribution-Free Shrinkage Approach

Rainer Opgen-Rhein / Korbinian Strimmer
Published Online: 2007-02-23 | DOI: https://doi.org/10.2202/1544-6115.1252

High-dimensional case-control analysis is encountered in many different settings in genomics. In order to rank genes accordingly, many different scores have been proposed, ranging from ad hoc modifications of the ordinary t statistic to complicated hierarchical Bayesian models.Here, we introduce the “shrinkage t” statistic that is based on a novel and model-free shrinkage estimate of the variance vector across genes. This is derived in a quasi-empirical Bayes setting. The new rank score is fully automatic and requires no specification of parameters or distributions. It is computationally inexpensive and can be written analytically in closed form.Using a series of synthetic and three real expression data we studied the quality of gene rankings produced by the “shrinkage t” statistic. The new score consistently leads to highly accurate rankings for the complete range of investigated data sets and all considered scenarios for across-gene variance structures.

Keywords: high-dimensional case-control data; James-Stein shrinkage; limited-translation; quasi-empirical Bayes; regularized t statistic; variance shrinkage

About the article

Published Online: 2007-02-23

Citation Information: Statistical Applications in Genetics and Molecular Biology, Volume 6, Issue 1, ISSN (Online) 1544-6115, ISSN (Print) 2194-6302, DOI: https://doi.org/10.2202/1544-6115.1252.

Export Citation

©2011 Walter de Gruyter GmbH & Co. KG, Berlin/Boston.Get Permission

Citing Articles

Here you can find all Crossref-listed publications in which this article is cited. If you would like to receive automatic email messages as soon as this article is cited in other publications, simply activate the “Citation Alert” on the top of this page.

Daniel Stöckel, Tim Kehl, Patrick Trampert, Lara Schneider, Christina Backes, Nicole Ludwig, Andreas Gerasch, Michael Kaufmann, Manfred Gessler, Norbert Graf, Eckart Meese, Andreas Keller, and Hans-Peter Lenhof
Bioinformatics, 2016, Volume 32, Number 10, Page 1502
Insha Ullah and Beatrix Jones
Australian & New Zealand Journal of Statistics, 2015, Volume 57, Number 3, Page 377
Oghenemise Abirhire, Rebecca L. North, Kristine Hunter, David M. Vandergucht, Jeff Sereda, and Jeff J. Hudson
Journal of Great Lakes Research, 2015, Volume 41, Page 118
Johannes Eichner, Clemens Wrzodek, Michael Römer, Heidrun Ellinger-Ziegelbauer, Andreas Zell, and Holger Fröhlich
PLoS ONE, 2014, Volume 9, Number 5, Page e97678
Piotr Iwo Wójcik, Thérèse Ouellet, Margaret Balcerzak, and Witold Dzwinel
Journal of Bioinformatics and Computational Biology, 2015, Volume 13, Number 04, Page 1550013
Manman Guo, Anetta Härtlova, Marek Gierliński, Alan Prescott, Josep Castellvi, Javier Hernandez Losa, Sine K Petersen, Ulf A Wenzel, Brian D Dill, Christoph H Emmerich, Santiago Ramon Y Cajal, David G Russell, and Matthias Trost
The EMBO Journal, 2019, Volume 38, Number 11
Jane E. Joseph, Brandon K. Vaughan, Christopher C. Camp, Nathaniel L. Baker, Brian J. Sherman, Megan Moran-Santa Maria, Aimee McRae-Clark, and Kathleen T. Brady
Frontiers in Psychiatry, 2019, Volume 10
Rafael Romero-Garcia, Mercedes Atienza, Line H. Clemmensen, and Jose L. Cantero
NeuroImage, 2012, Volume 59, Number 4, Page 3522
Katarina Radulovic, Calin Manta, Valerio Rossini, Karlheinz Holzmann, Hans A. Kestler, Ursula Maria Wegenka, Toshinori Nakayama, and Jan Hendrik Niess
The Journal of Immunology, 2012, Volume 188, Number 4, Page 2001
Lüder Hinrich Meyer, Sarah Mirjam Eckhoff, Manon Queudeville, Johann Michael Kraus, Marco Giordan, Jana Stursberg, Andrea Zangrando, Elena Vendramini, Anja Möricke, Martin Zimmermann, Andre Schrauder, Georgia Lahr, Karlheinz Holzmann, Martin Schrappe, Giuseppe Basso, Karsten Stahnke, Hans Armin Kestler, Geertruy te Kronnie, and Klaus-Michael Debatin
Cancer Cell, 2011, Volume 19, Number 2, Page 206
Michael Pierre, Benoît DeHertogh, Anthoula Gaigneaux, Bertrand DeMeulder, Fabrice Berger, Eric Bareke, Carine Michiels, and Eric Depiereux
BMC Cancer, 2010, Volume 10, Number 1
Simon Schwörer, Friedrich Becker, Christian Feller, Ali H. Baig, Ute Köber, Henriette Henze, Johann M. Kraus, Beibei Xin, André Lechel, Daniel B. Lipka, Christy S. Varghese, Manuel Schmidt, Remo Rohs, Ruedi Aebersold, Kay L. Medina, Hans A. Kestler, Francesco Neri, Julia von Maltzahn, Stefan Tümpel, and K. Lenhard Rudolph
Nature, 2016, Volume 540, Number 7633, Page 428
S Bresolin, L Trentin, M Zecca, M Giordan, L Sainati, F Locatelli, G Basso, and G te Kronnie
Leukemia, 2012, Volume 26, Number 7, Page 1717
Franka Voigt, Lisa Wiedemann, Cecilia Zuliani, Irma Querques, Attila Sebe, Lajos Mátés, Zsuzsanna Izsvák, Zoltán Ivics, and Orsolya Barabas
Nature Communications, 2016, Volume 7, Number 1
M Pinazza, C Borga, V Agnusdei, S Minuzzo, G Fossati, M Paganin, B Michielotto, A De Paoli, G Basso, A Amadori, G te Kronnie, and S Indraccolo
Cell Death & Disease, 2016, Volume 7, Number 1, Page e2047
Marit Ackermann and Korbinian Strimmer
BMC Bioinformatics, 2009, Volume 10, Number 1
Jing Cao, Xian-Jin Xie, Song Zhang, Angelique Whitehurst, and Michael A White
BMC Bioinformatics, 2009, Volume 10, Number 1
Magnus Åstrand, Petter Mostad, and Mats Rudemo
BMC Bioinformatics, 2008, Volume 9, Number 1
Peter Humburg, David Bulger, and Glenn Stone
BMC Bioinformatics, 2008, Volume 9, Number 1
Koji Kadota, Yuji Nakai, and Kentaro Shimizu
Algorithms for Molecular Biology, 2008, Volume 3, Number 1
Henry Wirth, Martin von Bergen, and Hans Binder
BioData Mining, 2012, Volume 5, Number 1
Koji Kadota, Yuji Nakai, and Kentaro Shimizu
Algorithms for Molecular Biology, 2009, Volume 4, Number 1
Vadim Farztdinov and Fionnuala McDyer
Algorithms for Molecular Biology, 2012, Volume 7, Number 1
Tim Kehl, Lara Schneider, Kathrin Kattler, Daniel Stöckel, Jenny Wegert, Nico Gerstner, Nicole Ludwig, Ute Distler, Stefan Tenzer, Manfred Gessler, Jörn Walter, Andreas Keller, Norbert Graf, Eckart Meese, and Hans-Peter Lenhof
International Journal of Cancer, 2018
Tim Kehl, Lara Schneider, Kathrin Kattler, Daniel Stöckel, Jenny Wegert, Nico Gerstner, Nicole Ludwig, Ute Distler, Markus Schick, Ulrich Keller, Stefan Tenzer, Manfred Gessler, Jörn Walter, Andreas Keller, Norbert Graf, Eckart Meese, and Hans-Peter Lenhof
Bioinformatics, 2018
Insha Ullah, Matthew D.M. Pawley, Adam N.H. Smith, and Beatrix Jones
Australian & New Zealand Journal of Statistics, 2017
Jorge Chan-Lau
IMF Working Papers, 2017, Volume 17, Number 107, Page 1
Syuan-Ming Guo, Jun He, Nilah Monnier, Guangyu Sun, Thorsten Wohland, and Mark Bathe
Analytical Chemistry, 2012, Volume 84, Number 9, Page 3880
Paolo Martini, Gabriele Sales, M. Sofia Massa, Monica Chiogna, and Chiara Romualdi
Nucleic Acids Research, 2013, Volume 41, Number 1, Page e19
A.-L. Boulesteix, C. Strobl, T. Augustin, and M. Daumer
Cancer Informatics, 2008, Volume 6, Page CIN.S408
Xian-Jin Xie
Frontiers in Biology, 2010, Volume 5, Number 4, Page 354
Noriko Sato, Katsuko Sudo, Masayo Mori, Chihiro Imai, Masaaki Muramatsu, and Masahiro Sugimoto
Scientific Reports, 2017, Volume 7, Number 1
Jennifer J. Hill, Tammy-Lynn Tremblay, François Fauteux, Jie Li, Edwin Wang, Adriana Aguilar-Mahecha, Mark Basik, and Maureen O’Connor-McCourt
Journal of Proteome Research, 2015, Volume 14, Number 3, Page 1376
Peter Hall, D. M. Titterington, and Jing-Hao Xue
Journal of the Royal Statistical Society: Series B (Statistical Methodology), 2009, Volume 71, Number 4, Page 783
Katja Sygnecka, Claudia Heine, Nico Scherf, Mario Fasold, Hans Binder, Christian Scheller, and Heike Franke
International Journal of Developmental Neuroscience, 2015, Volume 40, Page 1
Vera Münch, Luca Trentin, Julia Herzig, Salih Demir, Felix Seyfried, Johann M. Kraus, Hans A. Kestler, Rolf Köhler, Thomas F. E. Barth, Geertruy te Kronnie, Klaus-Michael Debatin, and Lüder H. Meyer
Blood, 2017, Volume 130, Number 5, Page 643
Fabrice Berger, Benoît Hertogh, Michaël Pierre, Anthoula Gaigneaux, and Eric Depiereux
Open Life Sciences, 2008, Volume 3, Number 3
Xiang Li, Chathura Gunasekara, Yufeng Guo, Hang Zhang, Liang Lei, Sermsawat Tunlaya-Anukit, Victor Busov, Vincent Chiang, and Hairong Wei
Tree Genetics & Genomes, 2014, Volume 10, Number 4, Page 1093
Maurice Berk, Timothy Ebbels, and Giovanni Montana
Bioinformatics, 2011, Volume 27, Number 14, Page 1979
Jan Kalina
Biocybernetics and Biomedical Engineering, 2014, Volume 34, Number 1, Page 10
Eugene Demidenko
BioData Mining, 2015, Volume 8, Number 1
Sophie Depiereux, Bertrand De Meulder, Eric Bareke, Fabrice Berger, Florence Le Gac, Eric Depiereux, Patrick Kestemont, and Gen Hua Yue
PLOS ONE, 2015, Volume 10, Number 7, Page e0128598
Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg, and Mark Isalan
PLoS ONE, 2009, Volume 4, Number 1, Page e4203
Hyuna Yang, Christina A. Harrington, Kristina Vartanian, Christopher D. Coldren, Rob Hall, Gary A. Churchill, and Thomas Preiss
PLoS ONE, 2008, Volume 3, Number 11, Page e3724
Rafael Romero-Garcia, Mercedes Atienza, and Jose L. Cantero
Human Brain Mapping, 2014, Volume 35, Number 6, Page 2724
Bertrand De Meulder, Fabrice Berger, Eric Bareke, Sophie Depiereux, Carine Michiels, Eric Depiereux, and Aedín C. Culhane
PLoS ONE, 2014, Volume 9, Number 1, Page e86699
Ekaterina Kotelnikova, Maria A. Shkrob, Mikhail A. Pyatnitskiy, Alessandra Ferlini, Nikolai Daraselia, and Russ B. Altman
PLoS Computational Biology, 2012, Volume 8, Number 2, Page e1002365
Yu-Shuen Tsai, Kripamoy Aguan, Nikhil R. Pal, I-Fang Chung, and Sumitra Deb
PLoS ONE, 2011, Volume 6, Number 9, Page e24259
Sophie Depiereux, Florence Le Gac, Bertrand De Meulder, Michael Pierre, Raphaël Helaers, Yann Guiguen, Patrick Kestemont, Eric Depiereux, and Josep V. Planas
PLOS ONE, 2015, Volume 10, Number 9, Page e0135799
Martin Bod’a
Central European Journal of Operations Research, 2017, Volume 25, Number 2, Page 441
Jana Trenner, Yvonne Poeschl, Jan Grau, Andreas Gogol-Döring, Marcel Quint, and Carolin Delker
Journal of Experimental Botany, 2016, Page erw457
Qiongling Li, Xinwei Li, Xuetong Wang, Yuxia Li, Kuncheng Li, Yang Yu, Changhao Yin, Shuyu Li, and Ying Han
Neural Plasticity, 2016, Volume 2016, Page 1
Tiejun Tong, Homin Jang, and Yuedong Wang
Journal of Multivariate Analysis, 2012, Volume 107, Page 232
Xinyu Zhang, Ti Chen, Alan T.K. Wan, and Guohua Zou
Journal of Multivariate Analysis, 2009, Volume 100, Number 10, Page 2376
Guillemette Marot, Jean-Louis Foulley, and Florence Jaffrézic
Computational Statistics & Data Analysis, 2009, Volume 53, Number 5, Page 1630
Gareth P. Campbell and James M. Curran
Science & Justice, 2009, Volume 49, Number 1, Page 2
Anne-Laure Boulesteix, Vincent Guillemot, and Willi Sauerbrei
Biometrical Journal, 2011, Volume 53, Number 4, Page 673

Comments (0)

Please log in or register to comment.
Log in