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SUPPLEMETARY NOTES Network inference from gene expression profiles: what "physical"
 

Summary: SUPPLEMETARY NOTES
for
Network inference from gene expression profiles: what "physical"
network are we seeing? (Prokaryotes vs Eukaryotes)
M. Zampieri, N. Soranzo, D. Bianchini and C. Altafini
SISSA-ISAS, International School for Advanced Studies
via Beirut 2-4, 34014 Trieste, Italy
November 14, 2007
Contents
1 Methods and data 2
1.1 Data collected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.2 Algorithms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.3 Overrepresented networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.3.1 Statistical analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.4 Clusterization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.5 Semantic similarity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.5.1 Statistical analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.6 Genes physical distance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2 E.coli correlation clusters 6
2.1 Functional annotation of the clusters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

  

Source: Altafini, Claudio - Functional Analysis Sector, Scuola Internazionale Superiore di Studi Avanzati (SISSA)

 

Collections: Engineering; Mathematics