Social network of the cell
Protein complex network parts
Background: The fundamental unit of life, the cell, can be perceived as a large network community of interacting protein molecules. Each gene in our DNA codes for a protein and all the cells functions are carried out by interactions between proteins in complex “social networks”. However, any given gene may code information for several variations of a protein, known as isoforms. Each isoform has a unique community of interacting neighbors within the cell, corresponding to different functions depending on the cell type or conditions.
A tool that organizes isoform-isoform networks will contribute to a more precise and complete understanding of the cells social network, and how this network is altered in diseases such as cancer. Currently, networks of isoform-isoform interactions are grossly incomplete and computational tools to construct these networks are lacking.
Objective: The goal of this project is to build a bioinformatics tool to construct maps of isoform-isoform interaction networks. The tool will use as input, “experimental readouts” of the isoforms present in a cell type, then: isoform-isoform interaction networks will be computed. The candidate will apply and gain an in-depth understanding of protein interaction databases, bioinformatics programming, network theory and statistics to achieve this goal.
- Surveying and acquiring an understanding of relevant data (experimental readouts), available online, and programming to organize this information
- Integration and handling of bioinformatics databases related to protein interactions, and mapping these to the experimental data.
- Statistical analysis to predict potential isoform-isoform interactions from an experimental readout of isoforms in a given cell.
- Network analysis: gaining an understanding of the concepts of network theory and the state-of-the-art software tools available to analyze biological networks
It is necessary to have an adequate background in programming and database management, in addition, a desire to apply some statistics and algorithm development.
It is advantageous to have an understanding of cell biology. However, the candidate will gain sufficient biological understanding in the duration of the project to fulfill the goals.