Please use this identifier to cite or link to this item: https://doi.org/10.1093/bioinformatics/btq128
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dc.titleA signal-noise model for significance analysis of ChIP-seq with negative control
dc.contributor.authorXu, H.
dc.contributor.authorHandoko, L.
dc.contributor.authorWei, X.
dc.contributor.authorYe, C.
dc.contributor.authorSheng, J.
dc.contributor.authorWei, C.-L.
dc.contributor.authorLin, F.
dc.contributor.authorSung, W.-K.
dc.date.accessioned2013-07-04T07:42:30Z
dc.date.available2013-07-04T07:42:30Z
dc.date.issued2010
dc.identifier.citationXu, 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. https://doi.org/10.1093/bioinformatics/btq128
dc.identifier.issn13674803
dc.identifier.urihttp://scholarbank.nus.edu.sg/handle/10635/39478
dc.description.abstractMotivation: 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: http://cmb.gis.a-star.edu.sg/ChIPSeq/tools.htm. Contact: sungk@gis.a-star.edu.sg; asflin@ntu.edu.sg. Supplementary Information:Supplementary data are available at Bioinformatics online. © The Author 2010. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org.
dc.description.urihttp://libproxy1.nus.edu.sg/login?url=http://dx.doi.org/10.1093/bioinformatics/btq128
dc.sourceScopus
dc.typeArticle
dc.contributor.departmentCOMPUTER SCIENCE
dc.description.doi10.1093/bioinformatics/btq128
dc.description.sourcetitleBioinformatics
dc.description.volume26
dc.description.issue9
dc.description.page1199-1204
dc.description.codenBOINF
dc.identifier.isiut000277225400010
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