Introduction

BACKGROUND: A typical affinity purification coupled to mass spectrometry (AP-MS) experiment includes the purification of a target protein (bait) using an antibody and subsequent mass spectrometry analysis of all proteins co-purifying with the bait (aka prey proteins). Like any other systems biology approach, AP-MS experiments generate a lot of data and visualization has been challenging, especially when integrating AP-MS experiments with orthogonal datasets. RESULTS: We present Circular Interaction Graph for Proteomics (CIG-P), which generates circular diagrams for visually appealing final representation of AP-MS data. Through a Java based GUI, the user inputs experimental and reference data as file in csv format. The resulting circular representation can be manipulated live within the GUI before exporting the diagram as vector graphic in pdf format. The strength of CIG-P is the ability to integrate orthogonal datasets with each other, e.g. affinity purification data of kinase PRPF4B in relation to the functional components of the spliceosome. Further, various AP-MS experiments can be compared to each other. CONCLUSIONS: CIG-P aids to present AP-MS data to a wider audience and we envision that the tool finds other applications too, e.g. kinase - substrate relationships as a function of perturbation. CIG-P is available under: http://sourceforge.net/projects/cig-p/

Publications

  1. CIG-P: Circular Interaction Graph for Proteomics.
    Cite this
    Hobbs CK, Leung M, Tsang HH, Ebhardt HA, 2014-01-01 - BMC Bioinformatics

Credits

  1. Christopher K Hobbs
    Developer

  2. Michelle Leung
    Developer

  3. Herbert H Tsang
    Developer

    Applied Research Lab, Faculty of Natural and Applied Sciences

  4. H Alexander Ebhardt
    Investigator

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Summary
AccessionBT004141
Tool TypeApplication
Category
PlatformsWindows
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByH Alexander Ebhardt