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 (Mar 2008)

Issues

Volume 10 (2011)

Volume 9 (2010)

Volume 6 (2007)

Volume 5 (2006)

Volume 4 (2005)

Volume 2 (2003)

Volume 1 (2002)

Structure Learning in Nested Effects Models

Achim Tresch / Florian Markowetz
Published Online: 2008-03-01 | DOI: https://doi.org/10.2202/1544-6115.1332

Nested Effects Models (NEMs) are a class of graphical models introduced to analyze the results of gene perturbation screens. NEMs explore noisy subset relations between the high-dimensional outputs of phenotyping studies, e.g., the effects showing in gene expression profiles or as morphological features of the perturbed cell.In this paper we expand the statistical basis of NEMs in four directions. First, we derive a new formula for the likelihood function of a NEM, which generalizes previous results for binary data. Second, we prove model identifiability under mild assumptions. Third, we show that the new formulation of the likelihood allows efficiency in traversing model space. Fourth, we incorporate prior knowledge and an automated variable selection criterion to decrease the influence of noise in the data.

Keywords: gene perturbation; pathway reconstruction; model identifiability; feature selection

About the article

Published Online: 2008-03-01


Citation Information: Statistical Applications in Genetics and Molecular Biology, ISSN (Online) 1544-6115, DOI: https://doi.org/10.2202/1544-6115.1332.

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]
Mohammad J. Sadeh, Giusi Moffa, and Rainer Spang
Journal of Computational Biology, 2013, Volume 20, Number 11, Page 920
[2]
Sebastian Dümcke, Johannes Bräuer, Benedict Anchang, Rainer Spang, Niko Beerenwinkel, and Achim Tresch
Bioinformatics, 2014, Volume 30, Number 3, Page 414
[3]
Holger Fröhlich, Paurush Praveen, and Achim Tresch
Bioinformatics, 2011, Volume 27, Number 2, Page 238
[4]
Ana Rodriguez, Isaac Crespo, Ganna Androsova, Antonio del Sol, and Julio Vera
PLOS ONE, 2015, Volume 10, Number 6, Page e0127216
[5]
Florian Markowetz and Fran Lewitter
PLoS Computational Biology, 2010, Volume 6, Number 2, Page e1000655
[6]
Juliane Siebourg-Polster, Daria Mudrak, Mario Emmenlauer, Pauli Rämö, Christoph Dehio, Urs Greber, Holger Fröhlich, Niko Beerenwinkel, and Satoru Miyano
PLOS Computational Biology, 2015, Volume 11, Number 4, Page e1004078
[7]
Bettina Knapp, Lars Kaderali, and Hans A. Kestler
PLoS ONE, 2013, Volume 8, Number 7, Page e69220
[8]
Theresa Niederberger, Stefanie Etzold, Michael Lidschreiber, Kerstin C. Maier, Dietmar E. Martin, Holger Fröhlich, Patrick Cramer, Achim Tresch, and Adam Siepel
PLoS Computational Biology, 2012, Volume 8, Number 6, Page e1002568
[9]
Martin Pirkl, Madeline Diekmann, Marlies van der Wees, Niko Beerenwinkel, Holger Fröhlich, Florian Markowetz, and Quaid Morris
PLOS Computational Biology, 2017, Volume 13, Number 4, Page e1005496
[10]
Ali Shojaie, Alexandra Jauhiainen, Michael Kallitsis, George Michailidis, and Alberto de la Fuente
PLoS ONE, 2014, Volume 9, Number 2, Page e82393
[11]
Paurush Praveen, Helen Hülsmann, Holger Sültmann, Ruprecht Kuner, and Holger Fröhlich
Scientific Reports, 2016, Volume 6, Number 1
[12]
George Michailidis and Florence d’Alché-Buc
Mathematical Biosciences, 2013, Volume 246, Number 2, Page 326
[13]
Sandra Andorf, Tanja Gärtner, Matthias Steinfath, Hanna Witucka-Wall, Thomas Altmann, and Dirk Repsilber
EURASIP Journal on Bioinformatics and Systems Biology, 2009, Volume 2009, Page 1
[14]
Holger Fröhlich, Achim Tresch, and Tim Beißbarth
Biometrical Journal, 2009, Volume 51, Number 2, Page 304

Comments (0)

Please log in or register to comment.
Log in