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

Statistical Applications in Genetics and Molecular Biology

Editor-in-Chief: Stumpf, Michael P.H.

6 Issues per year


IMPACT FACTOR 2016: 0.646
5-year IMPACT FACTOR: 1.191

CiteScore 2016: 0.94

SCImago Journal Rank (SJR) 2016: 0.625
Source Normalized Impact per Paper (SNIP) 2016: 0.596

Mathematical Citation Quotient (MCQ) 2016: 0.06

Online
ISSN
1544-6115
See all formats and pricing
More options …
Volume 7, Issue 1 (Nov 2008)

Issues

Volume 10 (2011)

Volume 9 (2010)

Volume 6 (2007)

Volume 5 (2006)

Volume 4 (2005)

Volume 2 (2003)

Volume 1 (2002)

A Sparse PLS for Variable Selection when Integrating Omics Data

Kim-Anh Lê Cao / Debra Rossouw / Christèle Robert-Granié / Philippe Besse
Published Online: 2008-11-18 | DOI: https://doi.org/10.2202/1544-6115.1390

Recent biotechnology advances allow for multiple types of omics data, such as transcriptomic, proteomic or metabolomic data sets to be integrated. The problem of feature selection has been addressed several times in the context of classification, but needs to be handled in a specific manner when integrating data. In this study, we focus on the integration of two-block data that are measured on the same samples. Our goal is to combine integration and simultaneous variable selection of the two data sets in a one-step procedure using a Partial Least Squares regression (PLS) variant to facilitate the biologists' interpretation. A novel computational methodology called ``sparse PLS" is introduced for a predictive analysis to deal with these newly arisen problems. The sparsity of our approach is achieved with a Lasso penalization of the PLS loading vectors when computing the Singular Value Decomposition.Sparse PLS is shown to be effective and biologically meaningful. Comparisons with classical PLS are performed on a simulated data set and on real data sets. On one data set, a thorough biological interpretation of the obtained results is provided. We show that sparse PLS provides a valuable variable selection tool for highly dimensional data sets.

Keywords: joint analysis; two-block data set; multivariate regression; dimension reduction

About the article

Published Online: 2008-11-18


Citation Information: Statistical Applications in Genetics and Molecular Biology, ISSN (Online) 1544-6115, DOI: https://doi.org/10.2202/1544-6115.1390.

Export Citation

©2011 Walter de Gruyter GmbH & Co. KG, Berlin/Boston. Copyright Clearance Center

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.

[1]
Li-Li Wang, You-Wu Lin, Xu-Fei Wang, Nan Xiao, Yuan-Da Xu, Hong-Dong Li, and Qing-Song Xu
Chemometrics and Intelligent Laboratory Systems, 2017
[2]
Boris Zimmermann, Murat Bağcıoğlu, Valeria Tafinstseva, Achim Kohler, Mikael Ohlson, and Siri Fjellheim
Ecology and Evolution, 2017
[3]
Kirsten Tillisch, Emeran A. Mayer, Arpana Gupta, Zafar Gill, Rémi Brazeilles, Boris Le Nevé, Johan E.T. van Hylckama Vlieg, Denis Guyonnet, Muriel Derrien, and Jennifer S. Labus
Psychosomatic Medicine, 2017, Volume 79, Number 8, Page 905
[4]
Claudia P. Sanmiguel, Jonathan Jacobs, Arpana Gupta, Tiffany Ju, Jean Stains, Kristen Coveleskie, Venu Lagishetty, Anna Balioukova, Yijun Chen, Erik Dutson, Emeran A. Mayer, and Jennifer S. Labus
Psychosomatic Medicine, 2017, Volume 79, Number 8, Page 880
[5]
Christopher J. Stewart, Jonathan M. Mansbach, Matthew C. Wong, Nadim J. Ajami, Joseph F. Petrosino, Carlos A. Camargo, and Kohei Hasegawa
American Journal of Respiratory and Critical Care Medicine, 2017, Volume 196, Number 7, Page 882
[6]
Baptiste Féraud, Carine Munaut, Manon Martin, Michel Verleysen, and Bernadette Govaerts
Metabolomics, 2017, Volume 13, Number 11
[7]
Marion Schiavone, Sébastien Déjean, Nathalie Sieczkowski, Mathieu Castex, Etienne Dague, and Jean M. François
Frontiers in Microbiology, 2017, Volume 8
[8]
Anne Rechtien, Laura Richert, Hadrien Lorenzo, Gloria Martrus, Boris Hejblum, Christine Dahlke, Rahel Kasonta, Madeleine Zinser, Hans Stubbe, Urte Matschl, Ansgar Lohse, Verena Krähling, Markus Eickmann, Stephan Becker, Rodolphe Thiébaut, Marcus Altfeld, Marylyn Addo, Selidji Todagbe Agnandji, Sanjeev Krishna, Peter G. Kremsner, Jessica S. Brosnahan, Philip Bejon, Patricia Njuguna, Marylyn M. Addo, Stephan Becker, Verena Krähling, Claire-Anne Siegrist, Angela Huttner, Marie-Paule Kieny, Vasee Moorthy, Patricia Fast, Barbara Savarese, and Olivier Lapujade
Cell Reports, 2017, Volume 20, Number 9, Page 2251
[9]
Carlos Bustos-Segura, Amanda Padovan, David Kainer, William J. Foley, and Carsten Külheim
Plant, Cell & Environment, 2017
[10]
Ying Yao, Valentin Voillet, Maeva Jegou, Magali SanCristobal, Samir Dou, Véronique Romé, Yannick Lippi, Yvon Billon, Marie-Christine Père, Gaëlle Boudry, Laure Gress, Nathalie Iannucelli, Pierre Mormède, Hélène Quesnel, Laurianne Canario, Laurence Liaubet, and Isabelle Le Huërou-Luron
BMC Genomics, 2017, Volume 18, Number 1
[11]
Denis Blache, Emmanuel Bourdon, Pauline Salloignon, Géraldine Lucchi, Patrick Ducoroy, Jean-Michel Petit, Bruno Verges, and Laurent Lagrost
Diabetes, 2015, Volume 64, Number 3, Page 960
[12]
Naifei Zhao, Qingsong Xu, and Hong Wang
IEEE Access, 2017, Volume 5, Page 14047
[13]
Arpana Gupta, Emeran A. Mayer, Claudia P. Sanmiguel, John D. Van Horn, Davis Woodworth, Benjamin M. Ellingson, Connor Fling, Aubrey Love, Kirsten Tillisch, and Jennifer S. Labus
NeuroImage: Clinical, 2015, Volume 7, Page 506
[14]
Rémy Burcelin, Matteo Serino, Chantal Chabo, Lucile Garidou, Celine Pomié, Michael Courtney, Jacques Amar, and Anne Bouloumié
Diabetes, Obesity and Metabolism, 2013, Volume 15, Number s3, Page 61
[15]
C. Colombani, A. Legarra, S. Fritz, F. Guillaume, P. Croiseau, V. Ducrocq, and C. Robert-Granié
Journal of Dairy Science, 2013, Volume 96, Number 1, Page 575
[16]
Édith Le Floch, Vincent Guillemot, Vincent Frouin, Philippe Pinel, Christophe Lalanne, Laura Trinchera, Arthur Tenenhaus, Antonio Moreno, Monica Zilbovicius, Thomas Bourgeron, Stanislas Dehaene, Bertrand Thirion, Jean-Baptiste Poline, and Édouard Duchesnay
NeuroImage, 2012, Volume 63, Number 1, Page 11
[17]
Kim De Paepe, Frederiek-Maarten Kerckhof, Joran Verspreet, Christophe M. Courtin, and Tom Van de Wiele
Environmental Microbiology, 2017, Volume 19, Number 8, Page 3251
[18]
Christopher J. Stewart, Nicholas D. Embleton, Emma C. L. Marrs, Daniel P. Smith, Tatiana Fofanova, Andrew Nelson, Tom Skeath, John D. Perry, Joseph F. Petrosino, Janet E. Berrington, and Stephen P. Cummings
Microbiome, 2017, Volume 5, Number 1
[19]
Zi Wang, Edward Curry, and Giovanni Montana
Bioinformatics, 2014, Volume 30, Number 19, Page 2693
[20]
Kim-Anh Lê Cao, Ignacio González, and Sébastien Déjean
Bioinformatics, 2009, Volume 25, Number 21, Page 2855
[21]
Yang Ai-Jun and Song Xin-Yuan
Bioinformatics, 2010, Volume 26, Number 2, Page 215
[22]
Miaomiao Jiang, Chunhua Wang, Yu Zhang, Yifan Feng, Yuefei Wang, and Yan Zhu
Phytochemical Analysis, 2014, Volume 25, Number 1, Page 50
[23]
Erik Andries and Shawn Martin
Applied Spectroscopy, 2013, Volume 67, Number 6, Page 579
[24]
Dongdong Lin, Vince D. Calhoun, and Yu-Ping Wang
Medical Image Analysis, 2014, Volume 18, Number 6, Page 891
[25]
Jakob Theorell, Indre Bileviciute-Ljungar, Bianca Tesi, Heinrich Schlums, Mette Sophie Johnsgaard, Babak Asadi-Azarbaijani, Elin Bolle Strand, and Yenan T. Bryceson
Frontiers in Immunology, 2017, Volume 8
[26]
Domenico Ciavardelli, Fabrizio Piras, Ada Consalvo, Claudia Rossi, Mirco Zucchelli, Carmine Di Ilio, Valerio Frazzini, Carlo Caltagirone, Gianfranco Spalletta, and Stefano L. Sensi
Neurobiology of Aging, 2016, Volume 43, Page 1
[27]
Patrick Trainor, Andrew DeFilippis, and Shesh Rai
Metabolites, 2017, Volume 7, Number 2, Page 30
[28]
Dongdong Lin, Hongbao Cao, Vince D. Calhoun, and Yu-Ping Wang
Journal of Neuroscience Methods, 2014, Volume 237, Page 69
[29]
E. Betoret, C. Mannozzi, N. Dellarosa, L. Laghi, P. Rocculi, and M. Dalla Rosa
Journal of Food Engineering, 2017, Volume 200, Page 22
[30]
Susie S.Y. Huang, Jonathan P. Benskin, Nik Veldhoen, Bharat Chandramouli, Heather Butler, Caren C. Helbing, and John R. Cosgrove
Aquatic Toxicology, 2017, Volume 182, Page 102
[31]
Hidetake Fujinaka, Toru Takeshita, Hirayuki Sato, Tetsuji Yamamoto, Junji Nakamura, Tadashi Hase, and Yoshihisa Yamashita
Archives of Microbiology, 2013, Volume 195, Number 6, Page 371
[32]
Marta Peciña, Hamdan Azhar, Tiffany M Love, Tingting Lu, Barbara L Fredrickson, Christian S Stohler, and Jon-Kar Zubieta
Neuropsychopharmacology, 2013, Volume 38, Number 4, Page 639
[33]
January Weiner, Stefan H.E. Kaufmann, and Jeroen Maertzdorf
Vaccine, 2015, Volume 33, Number 40, Page 5249
[34]
Bobbie-Jo Webb-Robertson, Courtney Corley, Lee Ann McCue, Karen Wahl, and Helen Kreuzer
Forensic Science International, 2013, Volume 226, Number 1-3, Page 118
[35]
Nicholas D. Embleton, Janet E. Berrington, Jon Dorling, Andrew K. Ewer, Edmund Juszczak, John A. Kirby, Christopher A. Lamb, Clare V. Lanyon, William McGuire, Christopher S. Probert, Stephen P. Rushton, Mark D. Shirley, Christopher J. Stewart, and Stephen P. Cummings
Frontiers in Nutrition, 2017, Volume 4
[36]
Dhivyaa Rajasundaram, Jean-Luc Runavot, Xiaoyuan Guo, William G. T. Willats, Frank Meulewaeter, Joachim Selbig, and David D. Fang
PLoS ONE, 2014, Volume 9, Number 11, Page e112168
[37]
Claire Saulou-Bérion, Ignacio Gonzalez, Brice Enjalbert, Jean-Nicolas Audinot, Isabelle Fourquaux, Frédéric Jamme, Muriel Cocaign-Bousquet, Muriel Mercier-Bonin, Laurence Girbal, and Ying-Jan Wang
PLOS ONE, 2015, Volume 10, Number 12, Page e0145748
[38]
Mahbaneh Eshaghzadeh Torbati, Makedonka Mitreva, and Vanathi Gopalakrishnan
Data, 2016, Volume 1, Number 3, Page 19
[39]
Douglas Mahana, Chad M. Trent, Zachary D. Kurtz, Nicholas A. Bokulich, Thomas Battaglia, Jennifer Chung, Christian L. Müller, Huilin Li, Richard A. Bonneau, and Martin J. Blaser
Genome Medicine, 2016, Volume 8, Number 1
[40]
B. Zimmerman, V. Tafintseva, M. Bağcıoğlu, M. Høegh Berdahl, and A. Kohler
Analytical Chemistry, 2016, Volume 88, Number 1, Page 803
[41]
Tomasz Waller, Tomasz Gubała, Krzysztof Sarapata, Monika Piwowar, and Wiktor Jurkowski
BioData Mining, 2015, Volume 8, Number 1
[42]
Mingon Kang, Dong-Chul Kim, Chunyu Liu, and Jean Gao
BioMed Research International, 2015, Volume 2015, Page 1
[43]
Ewa Szymańska, Emma Brodrick, Mark Williams, Antony N. Davies, Henk-Jan van Manen, and Lutgarde M. C. Buydens
Analytical Chemistry, 2015, Volume 87, Number 2, Page 869
[44]
Mingkun Chen and Evelyne Vigneau
Advances in Data Analysis and Classification, 2016, Volume 10, Number 1, Page 85
[45]
İbrahim Karaman, Natalja P. Nørskov, Christian Clement Yde, Mette Skou Hedemann, Knud Erik Bach Knudsen, and Achim Kohler
Metabolomics, 2015, Volume 11, Number 2, Page 367
[46]
Julieta Fuentes, Pilar Poncela, and Julio Rodríguez
Journal of Applied Econometrics, 2015, Volume 30, Number 4, Page 576
[47]
C. Corbane, S. Alleaume, and M. Deshayes
International Journal of Remote Sensing, 2013, Volume 34, Number 21, Page 7625
[48]
Kristian Hovde Liland, Martin Høy, Harald Martens, and Solve Sæbø
Chemometrics and Intelligent Laboratory Systems, 2013, Volume 122, Page 103
[49]
İbrahim Karaman, El Mostafa Qannari, Harald Martens, Mette Skou Hedemann, Knud Erik Bach Knudsen, and Achim Kohler
Chemometrics and Intelligent Laboratory Systems, 2013, Volume 122, Page 65
[50]
Tahir Mehmood, Kristian Hovde Liland, Lars Snipen, and Solve Sæbø
Chemometrics and Intelligent Laboratory Systems, 2012, Volume 118, Page 62
[51]
Athanassios Kondylis and Joe Whittaker
Chemometrics and Intelligent Laboratory Systems, 2010, Volume 104, Number 2, Page 205
[52]
Cinnamon S. Bloss, Kelly M. Schiabor, and Nicholas J. Schork
Brain Research Bulletin, 2010, Volume 83, Number 3-4, Page 177
[53]
Maria Vounou, Thomas E. Nichols, and Giovanni Montana
NeuroImage, 2010, Volume 53, Number 3, Page 1147
[54]
P. Roy, C. Truntzer, D. Maucort-Boulch, T. Jouve, and N. Molinari
Briefings in Bioinformatics, 2011, Volume 12, Number 2, Page 176

Comments (0)

Please log in or register to comment.
Log in