Table S13  Full retrospective analysis of retinal disease genes cloned over the last three years This shows an analysis of retinal disease genes identified in the previous three years and how well the newly identified photoreceptor-enriched/specific genes identified by SAGE in this study would have identified them. Gene shows the LocusLink symbol for the gene in question.  Location indicates the last chromosomal interval published prior to the positional cloning of the gene in question.  Disease indicates the OMIM symbol for the disease associated with the gene.  "In our set?" indicates whether the gene in question appeared at >0.01% in the ONL library.  Category indicates the expression pattern of the cloned gene.  Total PR-enriched genes in interval indicates the total number of genes identified in our study or that met 3 out of 4 Venn criteria but had not been identified at the time of the cloning of the gene. Total genes in interval is derived from genes identified by LocusLink. Total predicted genes in interval are identified by GeneScan.
Retinal disease genes identified by postitional cloning
Gene	Location	Disease	In our set?	Category	Total PR-enriched genes in interval	Total genes in interval	Total predicted genes in interval
Meet 3 out of 4 or more Venn criteria
CACNA1F	Xp11.23	CSNB2	Yes	Rod-enriched	2	36	53
NR2E3	15q22-q24	RP	Yes	Rod-specific	1	162	384
CNGB1	16q13-q21	RP	Yes	Rod-specific	4	52	110
PROML1	4p	RP	Yes	Rod-enriched	3	192	707
GCAP1	6p21.1	COD3	Yes	Rod-specific	5	98	220
TULP1	6p21.1-tel	RP14	Yes	Rod-specific	11	528	1266
ELOVL4	6q	STGD3	Yes	Rod-enriched	5	388	1525
RP1	8q11-q21	RP1	Yes	Rod-specific	3	131	577
AIPL1	17p13.1	LCA4	Yes	Rod-specific	6	27	81
RETGC1	17p13.1	LCA1	Yes	Rod-specific	6	27	81
Shown to be PR-enriched by in situ
BBS2	16q	BBS2	Yes	Rod-enriched	6	357	1055
Meet 1 out of 4 Venn criteria/not tested by in situ
PRPC8	17p13	RP13	Yes/not tested	Widespread?	4	195	387
MKKS	20p12	BBS6	Yes/not tested	Rod-enriched?	1	26	119
Not identified by SAGE/other candidate genes in interval
PCD15	10	USH1F	No	Widespread in brain/retina expression unknown	11	652	2446
CDH23	10q21-22	USH1D	No/no mouse ortholog	Retina-enriched	3	129	411
CRB1	1q31-q32.1	RP12	No/no mouse 3' end	Widespread in brain/retina-enriched, but cell type unknown	3	64	192
usherin	1q41	USH2A	No/no mouse ortholog	Rod-specific?	1	28	61
CNGB3	8q21-q22	ACHM3	No/low abundance	Cone-specific	1	92	347
USH3	3p21-25	USH3A	No/no mouse 3' end	Widespread	2	202	642
Not identified by SAGE/no candidate genes in interval
harmonin	11p15	USH1C	No/no mouse ortholog	Widespread	0	NA	NA
BBS4	15q22.3-q23	BBS4	No/low abundance	Widespread	0	NA	NA
CNGA3	2q11	RM	No/no mouse 3' end	Cone-specific	0	NA	NA
NYX	Xp21	CSNB1	No/no mouse ortholog	Retina-enriched/all cell types	0	NA	NA
PRP31	19q13.4	RP11	Yes	Widespread	0	NA	NA
Retinal disease genes identified by association studies
MERTK		RP	Yes	Rod-enriched
LRAT		RP	No	RPE-specific
RPGRIP1		LCA	Yes	Rod-enriched
HGR4		CORD	Yes	Rod-specific
TTPA		RP	No	RPE-specific
RGR		RP	No	RPE-specific
RDH5		RP	No	RPE-specific
NR2E3		enhanced S-cone syndrome	Yes	Rod-specific
Median number of candidate genes/interval:
PR-enriched retinal disease genes		3
NonPR-enriched disease genes		3