1. dia

1
Gene expression profiling of retinoic acid
treated nur77/ and -/- thymocytes
2
Mouse Affymetrix 430Av2 arrays carring 22690
transcripts Samples in duplicates nur77/ and
-/- control and 4h 9cRA treated thymocytes Total
RNA was sent to Genomics Core Facility in
Heidelberg for hybridization Raw intensity data
was scaled and normalized in Affymetrix
Microarray suite 5.0 Filtering of changed
transcripts was carried out in Microsoft
Acces Increased transcripts present and
increased 2 fold in both duplicates Decreased
transcripts minimum of -1.6 fold change value in
both duplicates 460 (205 upregulated and 255
downregulated) genes matched the criterias for
being regulated by 9cRA 182 out of the 205 proved
to be nur77 dependent Functional enrichment in
GeneOntology categories was determined using
FatiGO webtool Genes were sorted into biological
pathways using Onto-Tools from http//vortex.cs.wa
yne.edu
1
3
Log-log scatter plot of 460 transcripts
originated form 9cRA treated samples that showed
2 fold increase or -1.6 fold decrease compared to
control samples
Signal (Nur77/ 9cRA)
Signal (Nur77/ control)
2
4
Distribution of fold change values between the
460 transcripts
3
5
4
6
5
7
Fold change values of cell death associated genes
6
8
460 retinoid regulated transcripts. One BioCarta
pathway affected il2rb
Bcl2-Mm.257460
Shp1-Ptpn6-Mm.271799
Il2ra-Mm.915
cMyc-Mm.2444
cFos-Mm.246513
Pik3r1-Mm.259333
Socs3-Mm.3468
Il2rb-Mm.35287
Socs1-Mm.130
-2.7
2.4
2.1
-1.9
2.2
-2.7
3.1
-1.9
8.3
5.1
3.4
7
9
8
10
Red upregulated Blue downregulated
9
11
10