PT  - JOURNAL ARTICLE
AU  - Ivan Juric
AU  - Miao Yu
AU  - Armen Abnousi
AU  - Ramya Raviram
AU  - Rongxin Fang
AU  - Yuan Zhao
AU  - Yanxiao Zhang
AU  - Yuchen Yang
AU  - Yun Li
AU  - Bing Ren
AU  - Ming Hu
TI  - MAPS: model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments
AID  - 10.1101/411835
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 411835
4099  - http://biorxiv.org/content/early/2018/09/08/411835.short
4100  - http://biorxiv.org/content/early/2018/09/08/411835.full
AB  - Hi-C and chromatin immunoprecipitation (ChIP) have been combined to identify long-range chromatin interactions genome-wide at reduced cost and enhanced resolution, but extracting the information from the resulting datasets has been challenging. Here we describe a computational method, MAPS, Model-based Analysis of PLAC-seq and HiChIP, to process the data from such experiments and identify long-range chromatin interactions. MAPS adopts a zero-truncated Poisson regression framework to explicitly remove systematic biases in the PLAC-seq and HiChIP datasets, and then uses the normalized chromatin contact frequencies to identify significant chromatin interactions anchored at genomic regions bound by the protein of interest. MAPS shows superior performance over existing software tools in analysis of chromatin interactions centered on cohesin, CTCF and H3K4me3 associated regions in multiple cell types. MAPS is freely available at https://github.com/ijuric/MAPS.