Table 3.

Enrichment of MS susceptibility genes among T_H-specific transcripts.

DE transcript group	Cell type	EAE TH cell list size	Overlapping genes	p-value	Adjusted p-value
CDT	TH1	150	10	6.5 × 10−4	5.2 × 10−3
	TH17	30	3	2.1 × 10−2	1.1 × 10−1
OSE4sp	TH1	215	10	9.7 × 10−3	5.8 × 10−2
	TH17	41	3	4.7 × 10−2	1.6 × 10−1
MOG4sp	TH1	37	1	5.1 × 10−1	5.1 × 10−1
	TH17	7	1	1.3 × 10−1	2.6 × 10−1
OSE1ex	TH1	60	6	1.1 × 10−3	7.7 × 10−3
	TH17	16	2	3.9 × 10−2	1.6 × 10−1

The p-values were computed using 100,000 permutations. Enrichments significant after Holm-Bonferroni correction for multiple testing (eight tests) are highlighted in bold font (adjusted p-value < 0.05). DE, differentially expressed; WT, wildtype; CDT, common disease transcripts (differentially expressed for both contrasts OSE₄-OSE₀ and MOG₄-CFA but not in the two control contrasts OSE₀-WT or CFA-WT); OSE₄sp, OSE₄-specific transcripts (differentially expressed for the contrast OSE₄-OSE₀ but not in MOG₄-CFA, OSE₀-WT, or CFA-WT); MOG₄sp, MOG₄ -specific transcripts (differentially expressed for the contrast MOG₄-CFA but not in OSE₄-OSE₀, OSE₀-WT, or CFA-WT); OSE₁ex, OSE₁-specific transcripts (differentially expressed in OSE₁-OSE₀ but not in OSE₀-WT or CFA-WT).