PTHGRN – Post-translational Hierarchal Gene Regulatory Network

PTHGRN

:: DESCRIPTION

PTHGRN is able to unravel interrelationships among PTMs, TFs, epigenetic modifications and gene expression and to reconstruct hierarchical gene regulatory networks underlying biological functions.

::DEVELOPER

Systems bioinformatics lab , Hong Kong Baptist University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data.
Guan D, Shao J, Zhao Z, Wang P, Qin J, Deng Y, Boheler KR, Wang J, Yan B.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W130-6. doi: 10.1093/nar/gku471. Epub 2014 May 29

ProteomeScout – Visualization and Analysis Framework for Proteins

ProteomeScout

:: DESCRIPTION

ProteomeScout is a database of proteins and post-translational modifications.

::DEVELOPER

The Naegle Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Web Server
  • MySQL

:: DOWNLOAD

ProteomeScout

:: MORE INFORMATION

Citation:

Naegle KM, Gymrek M, Joughin BA, Wagner JP, Welsch RE, Yaffe MB, Lauffenburger DA, White FM.
ProteomeScout: A web resource for analysis of high-throughput post-translational proteomic studies.
Molecular and Cellular Proteomics, 2010.

Mol Cell Proteomics. 2010 Nov;9(11):2558-70. doi: 10.1074/mcp.M110.001206.
PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies.
Naegle KM, Gymrek M, Joughin BA, Wagner JP, Welsch RE, Yaffe MB, Lauffenburger DA, White FM.

POSTMan 2.0a – POST-translational Modification analysis

POSTMan 2.0a

:: DESCRIPTION

POSTMan is a software application developed at PROBE in cooperation with Stix AS, designed to aid the researcher in identifying post-translationally modified peptides present in a given sample. POSTMan aligns LC-MS runs (MS1 data) and isolates pairs of peptides which differ by a user defined specific mass difference (Post-translationally modified peptides). Candidate peptides can then be targeted for fragmentation in a second round of analysis allowing the identification of low abundant post-translationally modified peptides.

::DEVELOPER

The Proteomics Unit at the University of Bergen (PROBE)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  POSTMan

:: MORE INFORMATION

Citation

POSTMan (POST-translational modification analysis), a software application for PTM discovery.
Arntzen MØ, Osland CL, Raa CR, Kopperud R, Døskeland SO, Lewis AE, D’Santos CS.
Proteomics. 2009 Mar;9(5):1400-6.