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 9, Issue 1 (Aug 2010)

Issues

Volume 10 (2011)

Volume 9 (2010)

Volume 6 (2007)

Volume 5 (2006)

Volume 4 (2005)

Volume 2 (2003)

Volume 1 (2002)

Generalizing Moving Averages for Tiling Arrays Using Combined P-Value Statistics

Katerina J Kechris / Brian Biehs / Thomas B Kornberg
Published Online: 2010-08-06 | DOI: https://doi.org/10.2202/1544-6115.1434

High density tiling arrays are an effective strategy for genome-wide identification of transcription factor binding regions. Sliding window methods that calculate moving averages of log ratios or t-statistics have been useful for the analysis of tiling array data. Here, we present a method that generalizes the moving average approach to evaluate sliding windows of p-values by using combined p-value statistics. In particular, the combined p-value framework can be useful in situations when taking averages of the corresponding test-statistic for the hypothesis may not be appropriate or when it is difficult to assess the significance of these averages. We exhibit the strengths of the combined p-values methods on Drosophila tiling array data and assess their ability to predict genomic regions enriched for transcription factor binding. The predictions are evaluated based on their proximity to target genes and their enrichment of known transcription factor binding sites. We also present an application for the generalization of the moving average based on integrating two different tiling array experiments.

Keywords: transcription factor; binding sequence; tiling array; combined p-value

About the article

Published Online: 2010-08-06


Citation Information: Statistical Applications in Genetics and Molecular Biology, ISSN (Online) 1544-6115, DOI: https://doi.org/10.2202/1544-6115.1434.

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]
P. L. Hoffman, L. M. Saba, S. Flink, N. J. Grahame, K. Kechris, and B. Tabakoff
Genes, Brain and Behavior, 2014, Volume 13, Number 8, Page 743
[2]
Christian Otto, Kristin Reiche, and Jörg Hackermüller
Bioinformatics, 2012, Volume 28, Number 11, Page 1471
[3]
Nichole Reisdorph, Robert Stearman, Katerina Kechris, Tzu Lip Phang, Richard Reisdorph, Jessica Prenni, David J. Erle, Christopher Coldren, Kevin Schey, Alexey Nesvizhskii, and Mark Geraci
Genomics, Proteomics & Bioinformatics, 2013, Volume 11, Number 6, Page 368
[4]
Hilaire C. Lam, Suzanne M. Cloonan, Abhiram R. Bhashyam, Jeffery A. Haspel, Anju Singh, J. Fah Sathirapongsasuti, Morgan Cervo, Hongwei Yao, Anna L. Chung, Kenji Mizumura, Chang Hyeok An, Bin Shan, Jonathan M. Franks, Kathleen J. Haley, Caroline A. Owen, Yohannes Tesfaigzi, George R. Washko, John Quackenbush, Edwin K. Silverman, Irfan Rahman, Hong Pyo Kim, Ashfaq Mahmood, Shyam S. Biswal, Stefan W. Ryter, and Augustine M.K. Choi
Journal of Clinical Investigation, 2013, Volume 123, Number 12, Page 5212
[5]
R Cervera-Juanes, L J Wilhelm, B Park, K A Grant, and B Ferguson
Translational Psychiatry, 2017, Volume 7, Number 1, Page e994
[6]
Ching-Lin Hsiao, Ai-Ru Hsieh, Ie-Bin Lian, Ying-Chao Lin, Hui-Min Wang, Cathy S. J. Fann, and Valerie W. Hu
PLoS ONE, 2014, Volume 9, Number 5, Page e97513
[7]
Ivana V. Yang, Brent S. Pedersen, Andrew Liu, George T. O'Connor, Stephen J. Teach, Meyer Kattan, Rana Tawil Misiak, Rebecca Gruchalla, Suzanne F. Steinbach, Stanley J. Szefler, Michelle A. Gill, Agustin Calatroni, Gloria David, Corinne E. Hennessy, Elizabeth J. Davidson, Weiming Zhang, Peter Gergen, Alkis Togias, William W. Busse, and David A. Schwartz
Journal of Allergy and Clinical Immunology, 2015, Volume 136, Number 1, Page 69
[8]
Raivo Kolde, Kaspar Märtens, Kaie Lokk, Sven Laur, and Jaak Vilo
Bioinformatics, 2016, Volume 32, Number 17, Page 2604
[9]
Lin Wan and Fengzhu Sun
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2012, Volume 9, Number 5, Page 1281
[10]
Kevin S. S. Henning and Peter H. Westfall
Statistics in Biopharmaceutical Research, 2015, Volume 7, Number 2, Page 126
[11]
Mark D. Robinson, Abdullah Kahraman, Charity W. Law, Helen Lindsay, Malgorzata Nowicka, Lukas M. Weber, and Xiaobei Zhou
Frontiers in Genetics, 2014, Volume 5

Comments (0)

Please log in or register to comment.
Log in