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Proximal And Distal PAD

Identify chromatin immunoprecipitation of 104 DNA binding proteins in embryonic stem cell (ESC) lines co-localization at these respective regions. PAD was applied to characterize protein co-localization at proximal and distal regions using this large compendium of ESC-specific protein binding profiles. The tool has permitted to discover an extensive co-localization of BRG1 and CHD7 at distal but not proximal regions. It reveals the co-dependency of BRG1 and CHD7 at distal regions on regulating expression of their common target genes in ESC.

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PAD forum

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PAD classification

PAD specifications

Interface:
Web user interface
Programming languages:
Javascript, Python
Computer skills:
Basic
Maintained:
Yes
Restrictions to use:
None
License:
GNU General Public License version 3.0
Stability:
Stable

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PAD forum

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PAD classification

PAD specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
Python
Computer skills:
Advanced
Requirements:
MySQL, MySQL-python, Django, django-crispy-forms, Django-multiupload, numpy, plotly, pybedtools, bedtools, scipy
Interface:
Command line interface
Operating system:
Unix/Linux
License:
GNU General Public License version 3.0
Stability:
Stable
Maintained:
Yes

PAD distribution

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PAD support

Maintainer

  • Pengyi Yang <>
  • Pengyi Yang <>

Credits

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Publications

Funding source(s)

Supported in part by funds from University of Sydney, the New South Wales Ministry of Health, the Human Frontier Science Program (RGY0084/2014), National Health and Medical Research Council (1105271), National Heart Foundation, the Amazon Web Service Cloud Credits for Research Program.

Link to literature

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