ChIA-PET Data Analysis And Website Construction

Long-range chromatin interactions play an important role in transcription regulation. Since 2002, chromatin conformation capture technique(3C) and its derivatives have continued to develop, and been used to reveal the spatial relationships between the DNA and DNA. Among the 3C-derived technologies, the Chromatin Interaction Analysis with Paired-End Tag sequencing(ChIA-PET) which combined 3C and ChIP indicated the genome-wide chromatin interactions associated with a specific protein of interest.ChIA-PET Tool is a software specialized for ChIA-PET data analysis. It is originally developed in 2010. In this study, we updated the package as ChIA-PET Tool-v3.0 and improved its performance: it is easier to use and install, more efficient and more stringent in threshold. In addition, we added new functions to the package:1) a report with statistics information is generated during the data processing procedure in order to help users evaluate the quality of data; 2) the new package can process both single-end and paired-end short-read ChIA-PET sequencing data; 3) the new package can process long-read ChIA-PET data through further modification. The updated version is available from Git Hub(https://github.com/GuoliangLi-HZAU/ChIA-PET_Tool).We used the updated package to process all the published ChIA-PET data. The resultant files, including genome-wide chromatin interactions and protein binding sites, are used to build a database. This database contains all the processed data except GSE42237 that we didn’t get interactions. In total, there are 64 libraries in the database. Our database contains the following features: 1) Store all the processed ChIA-PET data; 2) Make basic statistical analysis of processed data;3) Retrieve data and visualize chromatin interactions and protein binding sites using D3, including intra and inter chromosomal interactions, as well as multiple level interaction networks; Search for chromatin interactions based on one or two interacting regions; 4)Collect the related ChIA-PET articles.The author provided the user more conveniences on the processing and usage of results gotten from ChIA-PET experiment by improving ChIA-PET Tool and constructing a database website.