Protocols

PGnet specifications

Information


Unique identifier OMICS_27450
Name PGnet
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Maintained No

Versioning


No version available

Maintainers


This tool is not available anymore.

Publication for PGnet

PGnet citation

call_split

Identification of epigenetic modifications that contribute to pathogenesis in therapy related AML: Effective integration of genome wide histone modification with transcriptional profiles

2015
BMC Med Genomics
PMCID: 4460748
PMID: 26043758
DOI: 10.1186/1755-8794-8-S2-S6
call_split See protocol

[…] Step 1 to build biomodules: transcriptional association. To identify the potential upstream regulators or down-stream targets of the genes that drive the tumorigenesis in t-AML, we applied the PGNet method []. PGNet evaluates the similarity of the gene orders between two independently ordered lists. Specifically, we used PGNet to compare genome-wide correlated expressions with a seed gene a […]

PGnet institution(s)
Center for Biomedical Informatics and Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA; State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China; The University of Chicago Cancer Research Center, The University of Chicago, Chicago, IL, USA; The Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL, USA; The Institute for Genomics and Systems Biology, and the Computational Institute, The University of Chicago, Chicago, IL, USA
PGnet funding source(s)
Supported in part by The Cancer Research Foundation, the NIH National Center for Multiscale Analyses of Genomic and Cellular Networks (MAGNET) 1U54CA121852, and the Natural Science Foundation of China 60771024, 60121101.

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