Table 1.

Signal transduction pathway activity in CD4+ T cells. (A,B) GSE71566, CD4+ T cells derived from cord blood, resting or activated using anti CD3/CD28; replicates indicate three cord blood samples (A) or stimulated with IL-12 and IL-4 for differentiation towards T-helper 1 (Th1) and T-helper 2 (Th2) T cells, respectively; replicates indicate three cell culture experiments (B) [23]. (C) GSE11292, CD4+ Treg cells, resting or activated with anti-CD3/-CD28 and IL-2, results from one Treg-activation experiment. For complete data analysis results, see Figure S3 [24]. The first column contains the sample annotation as available from the GEO; the top of columns contains the names of signaling pathways; note that the FOXO transcription factor activity is presented, which is the inverse of the PI3K pathway activity. Signaling pathway activity scores are presented on a log2 odds scale with color coding ranging from blue (most inactive) to red (most active).

A.	Sample Category	Annotation Per Sample	FOXO	NFκB	JAK-STAT1/2	JAK-STAT3	TGFβ	Notch
	CD4+ naive	replicate 1	10.3	−9.6	−7.7	−7.3	−10.9	−5.0
		replicate 2	12.4	−8.2	−8.2	−8.1	−10.9	−3.4
		replicate 3	7.5	−11.7	−9.2	−6.3	−11.0	−4.0
	CD4+ activated	replicate 1	−3.8	−1.8	−2.8	−3.4	−18.8	−4.2
		replicate 2	−3.5	−1.7	−4.4	−2.5	−18.9	−3.9
		replicate 3	−4.9	−0.8	−2.5	−1.6	−18.2	−4.1
B.	Sample Category	Annotation Per Sample	FOXO	NFκB	JAK-STAT1/2	JAK-STAT3	TGFβ	Notch
	CD4+ activated + interleukin 12 (IL-12)	replicate 1	−4.9	5.3	−1.1	−0.1	−15.6	−4.5
		replicate 2	−4.4	6.1	−0.9	−1.1	−14.2	−4.6
		replicate 3	−4.8	5.2	−1.3	−0.3	−14.6	−3.9
	CD4+ activated + IL-4	replicate 1	0.6	−6.2	−7.5	−0.2	−19.0	−4.2
		replicate 2	−0.4	−5.1	−7.0	0.0	−18.3	−3.6
		replicate 3	0.2	−5.1	−5.9	0.6	−18.5	−4.0
C.	Sample Category	Annotation Per Sample	FOXO	NFκB	JAK-STAT1/2	JAK-STAT3	TGFβ	Notch
	Treg, in a resting state		−0.7	−6.7	−2.8	−2.5	−16.3	−0.6
	Treg, in a suppressive state	180 min	8.9	13.3	−5.1	17.0	−9.8	3.6
		200 min	10.6	12.4	−4.7	17.1	−8.9	3.3
		220 min	10.0	12.7	−5.2	16.6	−7.9	1.6