The co-fractionation technique combines extensive biochemical fractionation with quantitative mass spectrometry for mapping protein interactions in different organelles and tissues (link). These interactions are measured by separating proteins across multiple biochemical fractions to create a distinct elution profile for each protein. In the subsequent step, computational scoring is applied to identify protein pairs with similar elution profiles, which is highly associated with physical interaction. Test data is here available. It consist of an matrix where each column represents a biochemical fraction, and each row a protein.
Goals
The goal of this project is the creation of a Cytoscape app that automatically creates networks from co-fractionation data. The co-fractionation method is executed by many research groups around the world, and in order to help them processing their own data, we plan to help create a Cytoscape app, that:
Allows for quick and easy processing of the co-fractionation data
Has a intuitive graphical user interface for reading, and processing co-fractionation data
Automatically build, visualize and layout the created interaction network
Allow the integration of additional annotation data such as functional associations
khanspers
commented
7 years ago
Background
The co-fractionation technique combines extensive biochemical fractionation with quantitative mass spectrometry for mapping protein interactions in different organelles and tissues (link). These interactions are measured by separating proteins across multiple biochemical fractions to create a distinct elution profile for each protein. In the subsequent step, computational scoring is applied to identify protein pairs with similar elution profiles, which is highly associated with physical interaction. Test data is here available. It consist of an matrix where each column represents a biochemical fraction, and each row a protein.
Goals
The goal of this project is the creation of a Cytoscape app that automatically creates networks from co-fractionation data. The co-fractionation method is executed by many research groups around the world, and in order to help them processing their own data, we plan to help create a Cytoscape app, that:
Language Skills
Cytoscape, Java, Python
Potential Mentors
Florian Goebels, Gary Bader
Difficulty
2
Contact
Florian Goebels