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/Bild:Lac-operon.jpg

7. Example 2: co-expression Source: http://www.nature.com/ng/journal/v37/n6s/full/ng1561.html

8. Example 3: Signal transduction pathways Source: http://www.sigmaaldrich.com/img/assets/6460/egf_r.gif

9. Example 4: Transcription Source: http://www.medscape.com/pi/editorial/conferences/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 4;307(5710)

13. In this session Source: http://bioinformatics.oxfordjournals.org/cgi/reprint/18/suppl_1/S233