Table 2.

Gene expression differences comparing treated vs. control, treated vs. normal, and control vs. normal eyes.

	26 Normal	37 Normal	37N vs. 26N	LIM-2			LIM-11			REC-2
	RE vs. LE	RE vs. LE		T vs. C	T vs. N	C vs. N	T vs. C	T vs. N	C vs. N	T vs. C	T vs. N	C vs. N
Signaling – Cell surface
ADORA2A	1.06	−1.10	1.46	−1.24	−1.88	−1.52	1.03	1.39	1.36	−1.03	−2.00	−1.94
AQP4	1.50	−1.08	1.00	1.46	1.65	1.12	−1.48	−4.20	−2.84	1.93	−1.11	−2.14
CHRNA7	−1.03	1.09	2.15	1.15	1.42	1.23	1.19	1.26	1.06	1.28	−1.57	−2.02
DRD2	1.21	−1.11	−1.09	1.68	1.70	1.01	1.19	−1.03	−1.22	1.95	2.17	1.11
EPHA1	1.01	1.02	−1.20	−1.55	−1.75	−1.13	−1.37 x	1.07	1.46	1.77	2.08	1.18
FGFR1	−1.05	1.07	−1.41	−1.68	−1.87	−1.11	−1.00	1.42	1.42	1.22	1.33	1.10
GFRA1	1.22	1.18	−2.34	−1.12	−1.18	−1.05	1.15	−1.03	−1.18	1.48	2.39	1.62
GRM5	1.57	−1.32	2.51	1.34	1.50	1.12	1.29	−2.13	−2.74	2.67	1.02	−2.61
IGF2R	1.01	−1.02	1.33	−1.16	1.01	1.17	1.05	1.02	−1.03	−1.06	−1.63	−1.53
INSR	1.07	1.05	1.23	−1.49	−1.76	−1.18	1.04	1.16	1.11	1.01	−1.93	−1.96
OPN1LW	1.12	−1.50	1.77	1.13	1.07	−1.06	1.04	−3.74	−3.90	1.75	1.17	−1.49
P2RY1	1.12	−1.02	−1.08	1.29	−1.24	−1.60	1.22	1.70	1.39	−1.16	−1.53	−1.32
SCUBE3	−1.00	−1.09	1.49	−1.62	−1.28	1.27	−1.31 x	1.29	1.69	1.61	1.25	−1.29
TNMD	1.06	1.07	−1.72	−1.27	−2.23	−1.76	−1.42	−1.06	1.34	1.37	1.13	−1.21
VIPR1	1.24	1.19	−1.57	1.11	1.03	−1.07	−1.01	−1.75	−1.74	1.48	1.48	1.00
VIPR2	1.22	−1.08	−1.18	−1.55	−1.63	−1.05	−1.08	1.17	1.25	1.13	1.22	1.08
Signaling – Intracellular
BCO2	1.06	1.06	1.21	−1.48	−1.33	1.11	−1.26	−1.05	1.20	1.53	1.70	1.11
CABP5	1.74	−1.10	1.28	2.14	2.14	1.00	−1.01	−1.71	−1.70	3.05	2.62	−1.16
CAMP	−1.19	−1.36	1.13	2.25	4.00	1.78	1.05	−1.73	−1.81	−1.30	1.09	1.42
CDC42	1.02	1.03	1.21	−1.25	−1.46	−1.16	1.05	1.02	−1.02	−1.05	−1.60	−1.52
CHAT	1.49	−1.17	1.77	1.22	1.70	1.39	−1.31	−1.61	−1.23	3.37	1.78	−1.89
CYP26B1	1.31	−1.04	−1.06	−4.05	−3.28	1.24	−1.60	−1.06	1.51	1.43	1.11	−1.29
NOS1	−1.27	1.37	−4.07	1.53	−1.62	−2.46	1.03	−1.89	−1.96	3.34	4.35	1.30
RASGRF1	1.26	−1.17	1.69	1.06	1.43	1.34	−1.03	1.08	1.12	2.20	1.28	−1.72
RLBP1	1.14	1.31	−13.98	2.76 x	−1.22	−3.37	3.79	1.83	−2.07	3.58	23.43	6.55
RPE65	1.20	1.26	1.26	2.28	1.59	−1.43	6.36 x	1.02	−6.23	3.64	1.84	−1.98
S100A12	−1.04	1.13	−1.50	1.62	2.34	1.45	1.20	2.04	1.71	−1.83	1.21	2.22
ZNF185	1.01	1.09	1.13	−1.35	−1.62	−1.20	−1.12	−1.03	1.08	1.37	−1.07	−1.47
Signaling – Transcription
EGR1	1.05	−1.07	1.52	−1.33	−1.42	−1.07	−1.14	−4.28	−3.76	−1.05	−1.17	−1.12
HIF1A	1.07	1.15	−1.17	1.20	1.07	−1.12	1.05	1.54	1.47	1.15	−1.00	−1.15
PER2	1.02	1.01	−1.10	−1.35	−1.36	−1.01	1.06	1.14	1.07	1.04	−1.06	−1.10
RXRB	1.05	1.06	−1.85	−1.22	−1.28	−1.05	1.00	1.11	1.11	−1.08	1.56	1.68
VDR	−1.12	−1.06	−1.06	−1.69	−1.86	−1.10	−1.09	1.19	1.30	−1.12	−1.33	−1.18
Signaling – Secreted
ANGPTL7	1.11	1.10	−1.58	1.27	1.17	−1.09	1.40	2.44	1.74	1.15	1.19	1.04
APOE	1.04	1.32	−2.23	1.49	2.83	1.90	1.14	1.07	−1.06	1.13	2.22	1.98
BMP2	1.09	1.11	1.00	1.54	1.18	−1.30	1.93 x	1.10	−1.75	2.16 x	1.12	−1.92
BMP4	−1.08	1.14	1.11	1.48	1.48	1.00	1.58	1.90	1.20	1.18	−1.21	−1.43
CILP	1.31	1.07	1.14	−3.00	−2.52	1.19	−1.57	1.19	1.86	1.17	−1.10	−1.29
EGF	1.16	1.13	−1.23	2.09	1.38	−1.51	6.83 x	1.19	−5.73	4.06	1.98	−2.06
FAM180A	1.03	−1.03	1.09	−1.60	−1.58	1.01	−1.22	1.17	1.43	1.96	1.27	−1.54
IGF2	1.01	−1.09	−1.20	1.24	1.44	1.16	1.21	1.45	1.20	−1.38	−1.14	1.20
IL1B	1.10	−1.06	2.33	1.05	1.16	1.11	−1.03	1.12	1.16	−1.28	−3.26	−2.54
LTBP1	−1.05	1.14	−1.21	1.03	−1.15	−1.19	1.08	1.28	1.19	1.23	−1.02	−1.25
LTF	−1.19	−1.15	−1.29	1.36	2.20	1.62	1.26	1.07	−1.18	−1.24	1.12	1.39
MEST	−1.02	1.00	−1.30	−1.64	−1.55	1.06	−1.45	1.26	1.83	1.88	3.03	1.62
NRG1	1.09	1.06	1.03	1.47	1.55	1.06	1.54	2.34	1.52	−1.87	−1.36	1.37
NTS	1.15	1.16	−1.30	1.41	1.03	−1.36	1.30	1.66	1.27	2.36	2.35	−1.00
PENK	1.06	−1.14	−1.02	−1.73	−1.90	−1.09	−1.57	1.13	1.77	−1.28	1.05	1.35
PI15	1.22	1.32	−2.35	3.41	2.87	−1.19	4.18	10.83	2.59	−5.73	−6.52	−1.14
PTX3	1.10	−1.06	1.45	−3.48	−2.25	1.55	−2.21	−1.65	1.34	1.53	1.39	−1.10
SOSTDC1	1.04	1.07	1.15	−1.70	−2.22	−1.31	−1.39	−1.07	1.30	2.06	1.62	−1.27
SST	−1.02	−1.33	−1.79	−1.45	−1.17	1.25	−1.16	−1.67	−1.44	2.92	3.67	1.26
TAC1	1.35	−1.36	−2.20	1.22	1.28	1.05	−1.25	1.48	1.85	1.59	2.76	1.73
TGFB2	−1.12	1.19	−1.87	−1.03	−1.72	−1.67	−1.02	−1.17	−1.15	1.51	1.60	1.05
TGFB3	−1.10	1.16	−1.89	−1.07	1.03	1.10	−1.11	1.39	1.54	1.61	2.60	1.61
TGFBI	1.06	1.06	−1.03	1.46	1.48	1.02	1.32	−1.11	−1.46	−1.21	−1.44	−1.19
VIP	1.62	−1.24	−1.05	1.03	−1.10	−1.13	−1.02	1.00	1.02	1.27	−1.14	−1.45
Signaling – Matricellular
CYR61	1.15	−1.06	2.14	−1.63	−1.20	1.35	−1.09	−2.06	−1.89	1.43	1.29	−1.10
NOV	1.11	1.07	1.03	−2.14	−2.75	−1.28	−1.55	1.18	1.84	1.37	−1.06	−1.45
THBS1	1.11	−1.06	1.01	−2.97	−3.08	−1.04	−1.59	−1.10	1.45	1.11	−1.05	−1.17
THBS2	1.04	−1.03	−1.24	−1.98	−2.25	−1.14	−1.03	1.08	1.11	1.00	1.03	1.03
TNC	−1.12	−1.04	−1.52	−1.24	1.21	1.49	1.17	1.46	1.24	1.44	1.78	1.24
MP/TIMP
ADAMTS4	−1.03	1.02	1.04	−1.33	1.08	1.44	1.04	1.30	1.25	−1.07	1.06	1.13
ADAMTS5	−1.03	1.16	−1.56	−1.06	−1.20	−1.13	1.26	1.29	1.02	1.15	−1.01	−1.16
ADAMTSL3	1.02	1.00	1.73	−1.99	−1.20	1.65	−1.35	1.17	1.57	1.60	1.44	−1.11
MMP14	1.07	1.01	−1.68	1.14	1.05	−1.09	1.07	1.73	1.62	−1.06	1.27	1.35
TIMP2	−1.01	1.03	−1.17	−1.42	−1.29	1.09	1.07	1.50	1.40	−1.04	−1.03	1.01
TIMP3	−1.05	−1.00	1.06	−1.28	−1.53	−1.20	−1.09	1.11	1.21	1.04	−1.18	−1.23
Extracellular matrix
COL12A1	1.08	−1.06	−1.38	−1.90	−1.97	−1.04	−1.25	1.63	2.03	1.22	1.18	−1.03
COL6A6	1.04	−1.00	1.68	−1.83	−1.35	1.35	−1.25	1.61	2.01	2.75	2.01	−1.37
DCN	1.09	−1.00	1.04	1.07	1.08	1.00	1.11	1.80	1.62	−1.13	−1.20	−1.07
FMOD	1.01	−1.05	−1.89	−1.19	−1.82	−1.52	−1.03	−1.00	1.03	1.04	1.57	1.52
MXRA5	−1.03	−1.12	1.21	−1.18	−1.04	1.13	1.10	2.05	1.87	1.62	1.26	−1.29
NYX	1.09	1.04	1.01	−1.09	−1.26	−1.16	−1.02	1.38	1.41	−1.28	−1.58	−1.24
OGN	1.00	1.05	−1.33	−1.32	−1.70	−1.29	−1.13	1.30	1.47	1.14	1.15	1.00
PRELP	−1.02	1.01	−1.13	−1.08	−1.29	−1.20	1.08	1.31	1.22	−1.13	−1.04	1.09
SERPINH1	1.00	−1.06	1.29	−1.12	−1.09	1.03	−1.01	1.19	1.20	−1.01	−1.52	−1.51

Red text = significant down-regulation, blue = significant up-regulation, grey = expression difference not statistically significant, “X” = differential expression likely due to control eye effect.