Table 1.

Significantly over-represented regulators in clusters D, E, and F

Cluster name	Pathway regulator	Gene count in pathway	Gene count in cluster	P0a	P1b	FDRc
Cluster D	Egf	459	8	0.084	0.364	0.000
Cluster D	Mapk1	528	6	0.096	0.273	0.013
Cluster D	Ppara	255	5	0.046	0.227	0.003
Cluster D	Mapk3	283	5	0.052	0.227	0.004
Cluster D	Lep	295	5	0.054	0.227	0.005
Cluster D	Mapk14	386	5	0.070	0.227	0.014
Cluster D	Trp53	405	5	0.074	0.227	0.016
Cluster D	Il4	446	5	0.081	0.227	0.025
Cluster D	Il6	478	5	0.087	0.227	0.031
Cluster E	Tnf	1061	17	0.193	0.370	0.003
Cluster E	Tgfb1	966	15	0.176	0.326	0.007
Cluster E	Fgf2	397	8	0.072	0.174	0.015
Cluster E	Il4	446	8	0.081	0.174	0.024
Cluster E	Creb1	247	7	0.045	0.152	0.005
Cluster E	Bdnf	123	6	0.022	0.130	0.001
Cluster E	Ifnb1	168	6	0.031	0.130	0.003
Cluster E	Cd8a	159	6	0.029	0.130	0.003
Cluster E	Hgf	237	6	0.043	0.130	0.013
Cluster E	Il2	245	6	0.045	0.130	0.015
Cluster E	Notch1	255	6	0.046	0.130	0.016
Cluster E	Csf2	249	6	0.045	0.130	0.019
Cluster E	Sirt1	89	5	0.016	0.109	0.001
Cluster E	Pten	102	5	0.019	0.109	0.002
Cluster E	Csf3	127	5	0.023	0.109	0.005
Cluster E	Src	188	5	0.034	0.109	0.017
Cluster E	Edn1	188	5	0.034	0.109	0.021
Cluster E	Egfr	218	5	0.040	0.109	0.034
Cluster E	Bmp4	197	5	0.036	0.109	0.035
Cluster E	Vegfa	250	5	0.046	0.109	0.043
Cluster F	Trp53	405	14	0.074	0.128	0.017
Cluster F	Mapk14	386	13	0.070	0.119	0.027
Cluster F	Cd8a	159	7	0.029	0.064	0.047
Cluster F	Gata1	88	5	0.016	0.046	0.031

^aAn expected ratio in the background.

^bAn observed ratio in the list of differentially expressed gene.

^cStatistical analysis was performed based on cumulative hypergeometric distribution and corrected by Benjamini and Hochberg method.