Molecular Vision: Demos, Mol Vis 2008; 14:1639-1649. Table 2

Table 2. Characterization of genes identified as candidates for human disease loci.

Affymetrix gene ID	Gene symbol	Mis- regulation	Animal models	Probability	Score	ONL: sage, qRT-PCR*	Injury	Bright LD #	Retina network
160901_at	*Fos*	up	rd1/rd2/LD	0.044	15	x*	+		1
97540_f_at	H2-D1	up	rd1/rd2/LD	0.046	15	x			3
101923_at	*Pla2g7*	down	rd1/rd2/LD	0.046	15	x			2
98549_at	Vtn	down	rd2/LD	0.019	10	x			2
98579_at	*Egr1*	up	rd1/rd2	0.132	6	x*	+		1
92223_at	C1qc	up	rd1/rd2	0.143	6	x	+	+	3
96020_at	*C1qb*	up	rd1/rd2	0.116	6	_*	+		3
103033_at	C4	up	rd2	0.046	5	?	+	+	3
98472_at	H2-T23	up	rd2	0.046	5	?		+	3
94701_at	Pde6b	down	rd1/rd2	0.179	4	x			2
102612_at	Nrl	down	rd2	0.066	4	x			2
160894_at	*Cebpd*	up	rd1/rd2/LD	0.238	3	_	+	+	1
94854_g_at	*Gnb1*	down	rd2/LD	0.135	2	x			2
93120_f_at	H2-K	up	rd2/LD	0.046	2	x		+	3
98562_at	*C1qa*	down	rd2	0.135	1	_		+	3
95974_at	Gbp1	down	rd2	0.0338	1	?		+	na
103202_at	Gbp3	down	rd2	0.0338	1	x			na
103634_at	Isgf3g	up	rd2	0.066	1	x		+	3
104669_at	Irf7	down	rd2	0.0611	1	_		+	3
99608_at	Prdx2	down	rd2	0.4691	1	?			na

Genes are identified by Affymetrix Gene ID (column 1) and gene symbol (column 2) for easy comparison with Table 1. Column 3 identifies the type of misregulation (up- or down-regulated) and column 4 documents in which animal models the misregulation occurs. The probability of each gene to fall within the respective locus is listed in column 5; this probability multiplied by the number of models in which the genes are differentially expressed (3, 2, or 1) produced a gene ranking score (maximum column 6). The remaining columns document whether the respective gene is present in photoreceptors based on the retina SAGE library (column 7: x, present; -, absent; ?, no data available; *confirmed by qRT-PCR [9]), whether the gene is misregulated in retina injury models (column 8; identified by +) or after bright light exposure (column 9; identified by +), or which genes were found to cluster together (eye database at Genenetwork; column 10; 3 clusters, 1-3 were identified, as well as three unclustered genes).