Overview

1
Overview

• Introduction
• Biological network data
• Text mining
• Gene Ontology
• Expression data basics
• Expression, text mining, and GO
• Modules and complexes
• Domains and conclusion

2
In this section

• Network topology primer
• Finding complexes using topology data
• Finding complexes using coexpression
• Finding active modules

3
Modules

• A self-contained component of a system
• With well-defined interfaces to other components

4
Network modules
5
Why study modularity in networks?

• To reduce complexity

6
Example 1 operons
Source http//de.wikipedia.org/wiki/BildLac-oper
on.jpg
7
Example 2 co-expression
Source http//www.nature.com/ng/journal/v37/n6s/f
ull/ng1561.html
8
Example 3 Signal transduction pathways
Source http//www.sigmaaldrich.com/img/assets/646
0/egf_r.gif
9
Example 4 Transcription
Source http//www.medscape.com/pi/editorial/confe
rences/2001/873/art-amc.fig2.jpg
10
Example 5 Topological modules (a.k.a. complexes)
Source http//www.esrf.fr/info/science/highlights
/2001/life-sciences/LS1.html
11
Complex

• A structure consisting of several
  weakly-connected macromolecules
• Ribosome
• Spliceosome
• Transcription factor complex

12
Characteristics of complexes
Source Science. 2005 Feb 4307(5710)
13
In this session
Source http//bioinformatics.oxfordjournals.org/c
gi/reprint/18/suppl_1/S233