Abstract
ChIA-PET Tool can be used to process long-range chromatin interaction data. Results are visualized on a user-friendly genome browser.
Highlights
Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) is a new technology to study genome-wide long-range chromatin interactions bound by protein factors
We demonstrate the effectiveness of ChIA-PET Tool by analyzing a ChIA-PET library IHH015A with statistical results, and show that ChIA-PET Tool is a convenient, user-friendly, accurate bioinformatics solution, and an integral component of the ChIA-PET process for chromatin interaction analysis
We have only reported the use of ChIA-PET Tool in estrogen receptor α (ERα) ChIA-PET analysis, it is obvious that this tool can be applied to different ChIA-PET libraries bound by different transcription factors in different genomes for chromatin interaction analysis
Summary
The architecture design of ChIA-PET Tool The architecture of ChIA-PET Tool includes six modules: Linker filtering, PET mapping, PET classification, Binding site calling, Chromatin interaction calling, and ChIA-PET visualization (Figure 2). Abundant non-chimeric inter-ligation PETs in the IHH015M dataset identified the ERα-bound chromatin interaction event at the KRT8/18 locus in the human genome (Figure 7.), but no chimeric PETs in the IHH015C dataset were found at the KRT8/18 locus. This interaction at the KRT8/18 locus has been validated by 4C experiments [9]. The tabular browser provides an organization of all ChIA-PET experimental datasets (libraries) from a variety of projects It reports the unique PETs with unique mapping, the binding sites and the interaction clusters in tabular forms, and the users can download the data for further analysis. It takes 1 hour for ChIA-PET Tool to process a single lane ChIA-PET dataset and 1 hour to upload the GFF file to the G-browser database (the upload time is subject to existing database size and server load)
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