FIND: DifFerential Chromatin INteractions Detection Using a Spatial Poisson Process

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dc.contributor.ISNI0000 0001 1707 1372 (Zhang, MQ)
dc.contributor.authorDjekidel, Mohamed Nadhir
dc.contributor.authorChen, Yang
dc.contributor.authorZhang, Michael Q.
dc.contributor.utdAuthorZhang, Michael Q.
dc.date.accessioned2019-05-03T20:16:41Z
dc.date.available2019-05-03T20:16:41Z
dc.date.created2018-02-12
dc.descriptionIncludes supplementary material
dc.description.abstractPolymer-based simulations and experimental studies indicate the existence of a spatial dependency between the adjacent DNA fibers involved in the formation of chromatin loops. However, the existing strategies for detecting differential chromatin interactions assume that the interacting segments are spatially independent from the other segments nearby. To resolve this issue, we developed a new computational method, FIND, which considers the local spatial dependency between interacting loci. FIND uses a spatial Poisson process to detect differential chromatin interactions that show a significant difference in their interaction frequency and the interaction frequency of their neighbors. Simulation and biological data analysis show that FIND outperforms the widely used count-based methods and has a better signal-to-noise ratio.
dc.description.departmentSchool of Natural Sciences and Mathematics
dc.description.sponsorshipNational Basic Research Program of China (2017YFA0505503), the National Natural Science Foundation of China (91729301, 31671384, 31301044, and 81630103).
dc.identifier.bibliographicCitationDjekidel, Mohamed Nadhir, Yang Chen, and Michael Q. Zhang. 2018. "FIND: difFerential chromatin INteractions Detection using a spatial Poisson process." Genome Research 28(3): 412-422, doi:10.1101/gr.212241.116
dc.identifier.issn1088-9051
dc.identifier.issue3
dc.identifier.urihttps://hdl.handle.net/10735.1/6457
dc.identifier.volume28
dc.language.isoen
dc.publisherCold Spring Harbor Lab Press, Publications Dept
dc.relation.urihttp://dx.doi.org/10.1101/gr.212241.116
dc.rightsCC BY-NC 4.0 (Attribution-NonCommercial)
dc.rights©2018 The Authors
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/
dc.source.journalGenome Research
dc.subjectHuman genome
dc.subjectBioconductor (Computer file)
dc.subjectGene expression
dc.subjectChromatin
dc.subjectPoisson processes
dc.titleFIND: DifFerential Chromatin INteractions Detection Using a Spatial Poisson Process
dc.type.genrearticle

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