
	Gene expression analysis of mammary gland transdifferentiation

1. Experimental description and design

2. Expression views and clustering

Analysis notes [pdf]
Analysis pipeline [png]
Hierarchical clustering (Average linkage) [png]
k-means clustering (k=2): [png]
1. Cluster 1 - upregulated genes (619 genes) [png]
2. Cluster 2 - downregulated genes (893 genes) [png]
Principal component analysis [png]
List of 2-fold over- and underexpressed genes (ESTs annotated) [xls]
Manual functional classification (adipo and epithelial markers) [xls]
Mapping to secreted protein database (SPD) [xls]

3. Pathway mapping

4. Gene ontology mappings

Cluster GO mapping using Genesis: 3% limit [png] 2% limit [png]
In house gene ontology mapping [htm]
Functional annotation using DAVID web service [htm]
1. Cluster 1 - upregulated [htm]
2. Cluster 2 - downregulated [htm]

5. Report (outdated) [pdf]

6. Verification by means of qPCR [ppt]

7. qPCR of reprogramming candidates [ppt]

(Primer information [Klf4] [cMyc] [Oct3/4] [Sox2] [Nanog] [Hic5] [Fbx15] [Uxt])

20.12.2007

Andreas Prokesch (andreas.prokesch@tugraz.at)