UROP Project

Graph Properties of Gene Networks

It has been well-established that networks representing real-world systems exhibit non-trivial graph topologies, and are often characterized as small-world or scale-free. Gene networks also exhibit such topologies which are neither lattice-like nor random. On one hand, significant research has been done on the properties of such graphs including degree sequence, modularity, clustering coefficient, spectral properties among many other. On the other hand, several public databases such as Database of Interacting Proteins (DIP), RegulonDB, etc. are available for continuous analysis of gene networks. The objective of this project is to systematically summarize all publicly available sources of gene network databases and analyze the aforementioned graph properties for these networks. Ideally, in this project, we will achieve a look-up table of graphs, their source and their respective graph properties which will enable a swift analysis of these gene networks in the future.

Task

The everyday task of the candidate will one or more of the following: 1. Literature review: Of papers or reviews to gain a fundamental understanding of the project idea 2. Web search: to identify candidate public network databases 3. Programming: to import graph data and implement functions that can compute graph properties 4. Scientific exchange: within the group in the form of presentations or reports

Requirements

Programming Language: Python Version Control: Git Typesetting: LaTeX Familiarty with Shell Knowledge of program parallelization is a plus.