title: HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements.
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.
  
  
  METHODS
  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.
  
  
  BACKGROUND
  lswang@mail.med.upenn.edu or bdgregor@sas.upenn.edu
  
  
  BACKGROUND
  Supplementary Material is available at Bioinformatics online.
authors.affiliation: 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.
authors.forename: Yih-Chii
authors.initials: YC
authors.lastname: Hwang
authors.affiliation: 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.
authors.forename: Chiao-Feng
authors.initials: CF
authors.lastname: Lin
authors.affiliation: 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.
authors.forename: Otto
authors.initials: O
authors.lastname: Valladares
authors.affiliation: 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.
authors.forename: John
authors.initials: J
authors.lastname: Malamon
authors.affiliation: 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.
authors.forename: Pavel P
authors.initials: PP
authors.lastname: Kuksa
authors.affiliation: 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.
authors.forename: Qi
authors.initials: Q
authors.lastname: Zheng
authors.affiliation: 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.
authors.forename: Brian D
authors.initials: BD
authors.lastname: Gregory
authors.affiliation: 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.
authors.forename: Li-San
authors.initials: LS
authors.lastname: Wang
mesh_terms: D004247:DNA / Q000235:genetics* / Q000378:metabolism*; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D006801:Humans; D011381:Programming Languages; D011401:Promoter Regions, Genetic / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA