HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements

Yih-Chii Hwang¹, Chiao-Feng Lin², Otto Valladares², John Malamon², Pavel P Kuksa², Qi Zheng¹, Brian D Gregory², Li-San Wang³

Affiliations

¹ Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104.
² Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104.
³ Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104.

PMID: 25480377
PMCID: PMC4393516
DOI: 10.1093/bioinformatics/btu801

HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements

Yih-Chii Hwang et al. Bioinformatics. 2015.

. 2015 Apr 15;31(8):1290-2.

doi: 10.1093/bioinformatics/btu801. Epub 2014 Dec 4.

Authors

Yih-Chii Hwang¹, Chiao-Feng Lin², Otto Valladares², John Malamon², Pavel P Kuksa², Qi Zheng¹, Brian D Gregory², Li-San Wang³

Affiliations

¹ Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104.
² Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104.
³ Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104.

PMID: 25480377
PMCID: PMC4393516
DOI: 10.1093/bioinformatics/btu801

Abstract

We implemented a high-throughput identification pipeline for promoter interacting enhancer element to streamline the workflow from mapping raw Hi-C reads, identifying DNA-DNA interacting fragments with high confidence and quality control, detecting histone modifications and DNase hypersensitive enrichments in putative enhancer elements, to ultimately extracting possible intra- and inter-chromosomal enhancer-target gene relationships.

Availability and implementation: This software package is designed to run on high-performance computing clusters with Oracle Grid Engine. The source code is freely available under the MIT license for academic and nonprofit use. The source code and instructions are available at the Wang lab website (http://wanglab.pcbi.upenn.edu/hippie/). It is also provided as an Amazon Machine Image to be used directly on Amazon Cloud with minimal installation.

Contact: lswang@mail.med.upenn.edu or bdgregor@sas.upenn.edu

Supplementary information: Supplementary Material is available at Bioinformatics online.

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References

1. Dixon J.R., et al. . (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485, 1–5. - PMC - PubMed
1. Hoffman M.M., et al. . (2013) Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res., 41, 827–841. - PMC - PubMed
1. Hwang Y.-C., et al. . (2013) High-throughput identification of long-range regulatory elements and their target promoters in the human genome. Nucleic Acids Res., 41, 4835–4846. - PMC - PubMed
1. Jin F., et al. . (2013) A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature, 503, 290–294. - PMC - PubMed
1. Karolchik D., et al. . (2014) The UCSC Genome Browser database: 2014 update. Nucleic Acids Res., 42, D764–D770. - PMC - PubMed

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HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements

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HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements

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