Literature DB >> 31903446

CoralP: Flexible visualization of the human phosphatome.

Amit Min1, Erika Deoudes1, Marielle L Bond1, Eric S Davis2, Douglas H Phanstiel1,2,3,4.   

Abstract

Protein phosphatases and kinases play critical roles in a host of biological processes and diseases via the removal and addition of phosphoryl groups. While kinases have been extensively studied for decades, recent findings regarding the specificity and activities of phosphatases have generated an increased interest in targeting phosphatases for pharmaceutical development. This increased focus has created a need for methods to visualize this important class of proteins within the context of the entire phosphatase protein family. Here, we present CoralP, an interactive web application for the generation of customizable, publication-quality representations of human phosphatome data. Phosphatase attributes can be encoded through edge colors, node colors, and node sizes. CoralP is the first and currently the only tool designed for phosphatome visualization and should be of great use to the signaling community. Source Code: https://github.com/PhanstielLab/coralp Web Application: http://phanstiel-lab.med.unc.edu/coralp.

Entities:  

Year:  2019        PMID: 31903446      PMCID: PMC6941781          DOI: 10.21105/joss.01837

Source DB:  PubMed          Journal:  J Open Source Softw        ISSN: 2475-9066


  7 in total

Review 1.  Protein kinases--the major drug targets of the twenty-first century?

Authors:  Philip Cohen
Journal:  Nat Rev Drug Discov       Date:  2002-04       Impact factor: 84.694

2.  D³: Data-Driven Documents.

Authors:  Michael Bostock; Vadim Ogievetsky; Jeffrey Heer
Journal:  IEEE Trans Vis Comput Graph       Date:  2011-12       Impact factor: 4.579

Review 3.  Protein tyrosine phosphatases: from genes, to function, to disease.

Authors:  Nicholas K Tonks
Journal:  Nat Rev Mol Cell Biol       Date:  2006-11       Impact factor: 94.444

4.  Genomics and evolution of protein phosphatases.

Authors:  Mark J Chen; Jack E Dixon; Gerard Manning
Journal:  Sci Signal       Date:  2017-04-11       Impact factor: 8.192

5.  Coral: Clear and Customizable Visualization of Human Kinome Data.

Authors:  Kathleen S Metz; Erika M Deoudes; Matthew E Berginski; Ivan Jimenez-Ruiz; Bulent Arman Aksoy; Jeff Hammerbacher; Shawn M Gomez; Douglas H Phanstiel
Journal:  Cell Syst       Date:  2018-08-29       Impact factor: 10.304

6.  KinMap: a web-based tool for interactive navigation through human kinome data.

Authors:  Sameh Eid; Samo Turk; Andrea Volkamer; Friedrich Rippmann; Simone Fulle
Journal:  BMC Bioinformatics       Date:  2017-01-05       Impact factor: 3.169

7.  Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree.

Authors:  Matthieu Chartier; Thierry Chénard; Jonathan Barker; Rafael Najmanovich
Journal:  PeerJ       Date:  2013-08-08       Impact factor: 2.984

  7 in total
  1 in total

1.  A spatial vascular transcriptomic, proteomic, and phosphoproteomic atlas unveils an angiocrine Tie-Wnt signaling axis in the liver.

Authors:  Donato Inverso; Jingjing Shi; Ki Hong Lee; Moritz Jakab; Shani Ben-Moshe; Shubhada R Kulkarni; Martin Schneider; Guanxiong Wang; Marziyeh Komeili; Paula Argos Vélez; Maria Riedel; Carleen Spegg; Thomas Ruppert; Christine Schaeffer-Reiss; Dominic Helm; Indrabahadur Singh; Michael Boutros; Sudhakar Chintharlapalli; Mathias Heikenwalder; Shalev Itzkovitz; Hellmut G Augustin
Journal:  Dev Cell       Date:  2021-05-25       Impact factor: 12.270

  1 in total

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