Please use this identifier to cite or link to this item:
Title: A signal-noise model for significance analysis of ChIP-seq with negative control
Authors: Xu, H.
Handoko, L.
Wei, X.
Ye, C.
Sheng, J.
Wei, C.-L.
Lin, F.
Sung, W.-K. 
Issue Date: 2010
Citation: Xu, H., Handoko, L., Wei, X., Ye, C., Sheng, J., Wei, C.-L., Lin, F., Sung, W.-K. (2010). A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics 26 (9) : 1199-1204. ScholarBank@NUS Repository.
Abstract: Motivation: ChIP-seq is becoming the main approach to the genome-wide study of protein-DNA interactions and histone modifications. Existing informatics tools perform well to extract strong ChIP-enriched sites. However, two questions remain to be answered: (i) to which extent is a ChIP-seq experiment able to reveal the weak ChIP-enriched sites? (ii) are the weak sites biologically meaningful? To answer these questions, it is necessary to identify the weak ChIP signals from background noise. Results: We propose a linear signal-noise model, in which a noise rate was introduced to represent the fraction of noise in a ChIP library. We developed an iterative algorithm to estimate the noise rate using a control library, and derived a library-swapping strategy for the false discovery rate estimation. These approaches were integrated in a general-purpose framework, named CCAT (Control-based ChIP-seq Analysis Tool), for the significance analysis of ChIP-seq. Applications to H3K4me3 and H3K36me3 datasets showed that CCAT predicted significantly more ChIP-enriched sites that the previous methods did. With the high sensitivity of CCAT prediction, we revealed distinct chromatin features associated to the strong and weak H3K4me3 sites. Availability: Contact:; Supplementary Information:Supplementary data are available at Bioinformatics online. © The Author 2010. Published by Oxford University Press. All rights reserved. For Permissions, please email:
Source Title: Bioinformatics
ISSN: 13674803
DOI: 10.1093/bioinformatics/btq128
Appears in Collections:Staff Publications

Show full item record
Files in This Item:
There are no files associated with this item.


checked on Jun 18, 2021


checked on Jun 18, 2021

Page view(s)

checked on Jun 11, 2021

Google ScholarTM



Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.