[talks] J Song preFPO

Melissa Lawson mml at CS.Princeton.EDU
Thu Apr 14 12:02:03 EDT 2011

Jimin Song will present her preFPO on Thursday April 21 at 10AM in 

Carl Icahn Lab 280 (note room!).  The members of her committee are:  Mona Singh, 

advisor; Olga Troyanskaya and Tom Funkhouser, readers; Bernard Chazelle and 

Andrea LaPaugh, nonreaders.  Everyone is invited to attend her talk. Her abstract follows 



Protein functioning and the role of cellular network topology

Virtually all biological processes are accomplished via numerous specific interactions
amongst various types of molecules. In the past decade, experimental and computational
technologies have determined large numbers of interactions of various types, including
those corresponding to direct physical binding, to regulatory relationships, and to more
abstract linkages such as genetic interactions which indicate that two proteins
participate in related biological processes. Analysis of the resulting interaction
networks are a promising approach for expanding our understanding of cellular functioning,
pathways and organization. In this work, I use high-throughput protein physical
interactions to uncover hints about the overall functional organization of the cell, and
to understand the role of network topology in this functioning.

In the first part of my thesis, I study the problem of uncovering, from large-scale
protein physical interaction data, protein complexes and "functional modules", so-called
groups of proteins that work together to perform some larger biological process.  I
develop a framework to assess how well network clustering approaches perform in uncovering
protein complexes and biological processes, and in predicting protein functions.  From an
application of this framework, I find that topological characteristics of networks are a
significant factor in the accuracy trade-offs between local and global (i.e. clustering)
approaches for uncovering cellular functioning.

In the second part of my thesis, I analyze protein physical interaction networks in order
to better characterize a protein's essentiality (i.e., the property of whether a protein
is necessary for a cell to
survive) and to understand the interplay between different protein complexes and
biological processes. First, in agreement with previous studies, I find that proteins that
are central in cellular networks tend to be essential more frequently. Second, I find
essential proteins within complexes and processes are topologically more central within
these subnetworks. Third, I infer significant cross-talk relationships between complexes
and processes. This "module network," comprised of complexes or processes as nodes and
cross-talk between them as edges, shows how complexes and processes are organized in a
cell. Finally, I uncover that essential complexes and processes are topologically more
central in the module network.

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