Table S5 Tags up in P10.5 crx-/- This is a full list of genes that are more highly expressed in the P10.5 crx-/- retina at P<0.005 as determined by Monte Carlo simulation analysis.  Tag abundance levels are not normalized in this case. These charts list the SAGE tag, followed by the putative Unigene number and identity of the transcript.  The P-value of each comparison is listed, along with the cellular expression pattern of the gene in the retina where this is known either from this study or from previous work.  Finally, the known or putative functional category of each gene is listed.  Abbreviations:  AC=amacrine cells, BP=bipolar neurons, GC=ganglion cells, , HZ=horizontal cells INL=inner nuclear layer, , MG=Muller glia, ONL=outer nuclear layer.
Tag	Gene	Crx+/+	Crx-/-	P-value	Expression in retina	Function
TGACTAGCGT	1339 chromogranin B	19	70	0.0000	AC/HZ	SIGNAL TRANSDUCTION
TATAATACCA	3951 thymus cell antigen 1, theta	5	20	0.0036	GC	CELL ADHESION
AGACTATGCA	17484 synuclein, alpha	3	17	0.0019	GC	OTHER
GGATTTTGAT	132269 ESTs 3644 fatty acid binding protein 7, brain	2	25	0.0000	MG	LIPID METABOLISM/TRANSPORT
TATAGTATGT	2338 glutamine synthetase	1	19	0.0000	MG	METABOLIC
AATTTCCCCT	30245 ESTs, Highly  similar to PHOSPHATIDYLSERINE DECARBOXYLASE PROENZYME [Cricetulus griseus]	7	35	0.0000	MG	METABOLIC
TGGGGATGCG	30245 ESTs, Highly  similar to PHOSPHATIDYLSERINE DECARBOXYLASE PROENZYME [Cricetulus griseus]	0	9	0.0028	MG	METABOLIC
GAAATGATGA	22491 prefoldin 5	7	26	0.0014	MG	OTHER
CAGAAAGGCA	29227 ESTs	15	40	0.0012	MG	OTHER
AATAGGGGTG	9114 crystallin, mu	0	10	0.0014	MG	OTHER
TAGGAGGTAA	7335 cellular nucleic acid binding protein	0	11	0.0008	MG	RNA BINDING PROTEINS
TGTCAAGGTT	138316 ESTs 72646 ESTs	17	41	0.0029	ONL	OTHER
TATTAGTCTT	1843 heat shock protein, 86 kDa 1	13	33	0.0043	ONL	PROTEIN PROCESSING
TATGTGTGTT	43737 casein kinase I-alpha	1	11	0.0042	ONL	SIGNAL TRANSDUCTION
TTCAGGAAGG	27744 unc119 homolog (C. elegans)	13	39	0.0005	ONL	SYNAPTIC
AAAAGATACT	9524 Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	2	23	0.0000	ONL	TRANSCRIPTION
AGAGACAAGG	30837 N-myc downstream regulated-like 4063 N-myc downstream regulated 1	8	28	0.0014	ONL/BP/HZ	OTHER
GGAGTAAGAA	18516 H3 histone, family 3B	32	91	0.0000	ONL/IS+AC	TRANSCRIPTION
ACCAACAGGT	Otx2	9	27	0.0041	ONL+BP	TRANSCRIPTION
AACGGGAGGT	2319 Scgn10 like-protein	7	29	0.0003	retinal precursors	CYTOSKELETAL
AAAACATCTC	16553 neural precursor cell expressed, developmentally down-regulated gene 4	2	26	0.0000	widespread	OTHER
TGGATCCTGA	4284 guanine nucleotide binding protein, alpha inhibiting 2	16	54	0.0000	widespread	SIGNAL TRANSDUCTION
CTAGGTGGTG	34411 glycosylation dependent cell adhesion molecule 1	0	33	0.0000		CELL ADHESION
AAGGATGTGC	21162 Mus musculus novel cell death-regulatory protein GRIM19 (Grim19) mRNA, complete cds	7	33	0.0001		CELL DEATH
GCTGCCCTAG	4591 tubulin alpha 2 88110 tubulin alpha 1	90	197	0.0000		CYTOSKELETAL
TCTGTAATTG	12625 microtubule-associated protein 4	8	25	0.0047		CYTOSKELETAL
TTTCCTTAGG	18562 phosphotidylinositol transfer protein, beta	0	9	0.0028		LIPID METABOLISM/TRANSPORT
GACTGAATCT	298 stearoyl-Coenzyme A desaturase 2 9244 suppressor of variegation 3-9 homologue 1 (Drosophila)	18	42	0.0038		LIPID METABOLISM/TRANSPORT
AGACAAACTG	1186 carbonic anhydrase 2	12	54	0.0000		METABOLIC
AATTAGTTGT	353 ATP synthase, H+ transporting, mitochondrial F0 complex subunit F	12	50	0.0000		METABOLIC
AATTCGCGGA	2108 transthyretin	1	18	0.0001		METABOLIC
TTTGGGGCTG	3479 ESTs, Highly  similar to PROTEOLIPID PROTEIN PPA1 [Saccharomyces cerevisiae] 3264 TXK tyrosine kinase	8	34	0.0001		METABOLIC
TCTTTGGAAC	21743 malate dehydrogenase, mitochondrial	13	40	0.0003		METABOLIC
TGATATGAGC	9745 lactate dehydrogenase 2, B chain	6	27	0.0004		METABOLIC
TATTGGCTCT	14022 cytochrome c oxidase, subunit VIIIa	75	132	0.0004		METABOLIC
TGGTGAAGAG	30112 ATP synthase, H+ transporting, mitochondrial  F0 complex, subunit b, isoform 1	6	26	0.0006		METABOLIC
TCGTGATTGT	683 ornithine decarboxylase antizyme	35	71	0.0012		METABOLIC
CTCTATTTAA	29541 ESTs, Highly  similar to VACUOLAR ATP SYNTHASE 14 KD SUBUNIT [Manduca sexta]	0	9	0.0028		METABOLIC
AACAAAGCAA	29842 NADH dehydrogenase flavoprotein 1	0	9	0.0028		METABOLIC
ACATACAAAT	19039 glutamate oxaloacetate transaminase 1, soluble	2	14	0.0033		METABOLIC
AAGCTGGAAA	10406 ESTs, Moderately similar to DHSD_HUMAN SUCCINATE DEHYDROGENASE [H.sapiens] 143741 neighbor of Punc E11 18888 lumican 4114 antigen identified by monoclonal antibodies 4F2	1	11	0.0042		METABOLIC
CGCTGGTTCC	4280 replication factor C, 140 kDa	86	189	0.0000		OTHER
TCCCCGTACA	108612 ESTs	162	364	0.0000		OTHER
CCCGTGTGCT	13944 amelogenin	27	78	0.0000		OTHER
ACTCCTGTCA	36879 ESTs, Moderately  similar to CLATHRIN LIGHT CHAIN B [Bos taurus] 18834 ESTs, Moderately similar to PWP1_HUMAN PERIODIC TRYPTOPHAN PROTEIN 1 HOMOLOG [H.sapiens]	4	43	0.0000		OTHER
CATTGCGTGG	27955 Williams-Beuren syndrome chromosome region 1 homolog (human)	13	52	0.0000		OTHER
TCCCTATTAA	40945 ESTs	149	732	0.0000		OTHER
ACTTCAGCCA	1948 t-complex testis expressed 1	24	102	0.0000		OTHER
AAGGTGGAAG	16820 hemoglobin alpha, adult chain 1	30	85	0.0000		OTHER
AAGTGATGGC	17697 ESTs, Moderately similar to hypothetical protein [H.sapiens]	0	19	0.0000		OTHER
ATGACAAAGA	40684 ESTs	16	51	0.0000		OTHER
GCCCGCGAGG	22623 Mus musculus gene trap ROSA b-geo 22 (Gtrgeo22) gene, partial cds	0	14	0.0001		OTHER
ATAGACGCAA	21802 ESTs, Highly similar to hypothetical protein [H.sapiens]	11	38	0.0002		OTHER
ACCAAGATCT	22103 thymine DNA glycosylase	5	26	0.0002		OTHER
AAGCCTTTGT	28689 transforming growth factor beta regulated gene 1	0	12	0.0004		OTHER
GTAGGATAGC	10178 ESTs	3	20	0.0004		OTHER
AAAAAAAAAA	41415 Mus musculus PLK interacting protein (Mmip) mRNA, complete cds 143771 WD repeat domain 4 16620 glutamic acid decarboxylase 1 18805 prediabetic NOD sera-reactive autoantigen 26789 casein kinase II, beta subunit 27545 heterogeneous nuclear ribonucleoproteins  methyltransferase-like 2 (S. cerevisiae) 2760 zinc finger protein 38 29652 glutathione transferase zeta 1 (maleylacetoacetate isomerase) 3373 cofilin 2, muscle 44229 hypothetical protein, MNCb-1301 4715 protein tyrosine phosphatase, receptor type, O 4851 endoglin 4873 distal-less homeobox 5 4927 aconitase 1 6904 fibroblast growth factor receptor 3 8015 serine/threonine kinase 22 substrate 1	50	24	0.0006		OTHER
TCACAGAAAA	133692 ESTs 9210 ESTs 94882 ESTs	0	11	0.0008		OTHER
CCTCAAGAGC	26614 ESTs, Weakly similar to AF151083_1 HSPC249 [H.sapiens]	0	11	0.0008		OTHER
CCAGCCAACA	35098 ESTs, Weakly similar to CG18661 gene product [D.melanogaster]	0	11	0.0008		OTHER
TTTATTTCAT	2469 split hand/foot deleted gene 1	1	14	0.0009		OTHER
AAGACCTATG	2785 diazepam binding inhibitor	6	24	0.0014		OTHER
GACTCTATAT	154486 ESTs 4105 casein beta	0	10	0.0014		OTHER
ACCATTAACT	mito Tag matches mitochondrial sequence	1	13	0.0014		OTHER
TCTGTGATGT	30179 ESTs	11	33	0.0014		OTHER
TAACTTTAAG	43278 olfactomedin related ER localized protein	4	20	0.0014		OTHER
CTGCATCGTT	204 ESTs	6	23	0.0021		OTHER
AACTGAATGG	114886 ESTs	0	9	0.0028		OTHER
TGGAATGCAG	23929 DNA segment, Chr 11, ERATO Doi 153, expressed	0	9	0.0028		OTHER
GCAGCATCTG	29600 ESTs, Moderately similar to unnamed protein product [H.sapiens]	0	9	0.0028		OTHER
AACTCGCCGG	30261 ESTs	0	9	0.0028		OTHER
GTTCATTCAG	28869 ESTs	4	18	0.0039		OTHER
TAGCTTCCTC	9846 oxidative stress induced	8	25	0.0047		OTHER
GAGCGTTTTG	5246 peptidylprolyl isomerase A	91	218	0.0000		PROTEIN PROCESSING
GGTCTAATTT	3670 chaperonin subunit 2 (beta)	3	17	0.0019		PROTEIN PROCESSING
GAATAATAAA	2944 heat shock protein cognate 70	25	55	0.0019		PROTEIN PROCESSING
TTTTATGTTT	10331 tumor necrosis factor, alpha-induced protein 1 (endothelial) 103633 ribosomal protein L32, pseudogene	23	131	0.0000		PROTEIN SYNTHESIS
GCCTTTATGA	16775 ribosomal protein S24	23	88	0.0000		PROTEIN SYNTHESIS
AAGAAAATAG	22723 ESTs, Highly  similar to 60S RIBOSOMAL PROTEIN L23A [Homo sapiens]	11	74	0.0000		PROTEIN SYNTHESIS
CCCACAAGGT	28985 ribosomal protein L27	13	49	0.0000		PROTEIN SYNTHESIS
CACAAACGGT	29911 ESTs, Highly  similar to 40S RIBOSOMAL PROTEIN S27 [Homo sapiens]	43	120	0.0000		PROTEIN SYNTHESIS
AATTTCAAAA	42767 ribosomal protein S17	26	107	0.0000		PROTEIN SYNTHESIS
TATGTCAAGC	43452 ribosomal protein S12	14	71	0.0000		PROTEIN SYNTHESIS
AGGCAGACAG	16317 eukaryotic translation elongation factor 1 alpha 1	55	123	0.0000		PROTEIN SYNTHESIS
GATTCCGTGA	10474 ESTs, Highly  similar to 60S RIBOSOMAL PROTEIN L37 [Homo sapiens; Rattus norvegicus]	50	109	0.0000		PROTEIN SYNTHESIS
AACAGGTTCA	265 ESTs, Highly  similar to 40S RIBOSOMAL PROTEIN S25 [Homo sapiens; Rattus norvegicus]	42	93	0.0000		PROTEIN SYNTHESIS
AGATCTATAC	37835 ribosomal protein L7	5	29	0.0001		PROTEIN SYNTHESIS
ATACTGAAGC	42578 ribosomal protein L13	6	31	0.0001		PROTEIN SYNTHESIS
CTAGTCTTTG	154915 ribosomal protein S29	64	123	0.0001		PROTEIN SYNTHESIS
GCTGCCAGCA	29383 ESTs, Highly  similar to TRANSLATION INITIATION FACTOR EIF-2B-EPSILON SUBUNIT [Oryctolagus cuniculus]	1	17	0.0001		PROTEIN SYNTHESIS
CTGTAGGTGA	30011 ESTs, Highly  similar to 40S RIBOSOMAL PROTEIN S23 [Homo sapiens; Rattus norvegicus]	19	50	0.0003		PROTEIN SYNTHESIS
CCTTTGAGAT	5291 ribosomal protein S5	6	27	0.0004		PROTEIN SYNTHESIS
TTCAGCTCGA	5281 ribosomal protein S7	10	34	0.0005		PROTEIN SYNTHESIS
AGTTACTTGA	29452 ESTs, Moderately  similar to SIGNAL RECOGNITION PARTICLE 19 KD PROTEIN [Homo sapiens]	0	11	0.0008		PROTEIN SYNTHESIS
CACAGACTGT	30120 ribosomal protein S27	3	18	0.0012		PROTEIN SYNTHESIS
ACTGCTTGCC	29815 ESTs, Highly  similar to S-ADENOSYLMETHIONINE SYNTHETASE GAMMA FORM [Rattus norvegicus]	9	30	0.0013		PROTEIN SYNTHESIS
TTCCAATACA	19187 prothymosin alpha 22387 eukaryotic translation initiation factor 2, subunit 3, structural gene X-linked	0	10	0.0014		PROTEIN SYNTHESIS
AAAACAGTGG	21529 ribosomal protein L37a	31	64	0.0015		PROTEIN SYNTHESIS
TCTGTGCACC	164 ribosomal protein S11 90529 RAD21 homolog (S. pombe)	13	36	0.0017		PROTEIN SYNTHESIS
TCGCAAGCAA	3746 nascent polypeptide-associated complex alpha polypeptide	15	38	0.0026		PROTEIN SYNTHESIS
GATGTGACCA	104828 eukaryotic translation initiation factor 3, subunit 2 (beta, 36kD)	1	12	0.0026		PROTEIN SYNTHESIS
AAGGCAAAGA	43749 ESTs, Highly  similar to PROBABLE 60S RIBOSOMAL PROTEIN L14EB [Saccharomyces cerevisiae]	2	14	0.0033		PROTEIN SYNTHESIS
AGCTGGGGTT	13020 ribosomal protein L13a	1	11	0.0042		PROTEIN SYNTHESIS
CACCACCGTT	725 ribosomal protein L7a	25	52	0.0043		PROTEIN SYNTHESIS
TGGTTGCTGG	156953 Mus musculus ubiquitin-conjugating enzyme MHR6BN (Hr6bn) gene, complete cds 2296 peptidyl arginine deiminase, type II 30314 neuropilin 2	53	151	0.0000		PROTEOLYSIS
CCCTGGGTTC	34374 ESTs, Highly  similar to CHYMOTRYPSINOGEN B PRECURSOR [Rattus norvegicus] 7500 ferritin light chain 1	3	45	0.0000		PROTEOLYSIS
GTGTTAACCA	2050 ubiquitin conjugating enzyme 2e	13	42	0.0001		PROTEOLYSIS
CCACCTCTCA	235 ubiquitin B	4	20	0.0014		PROTEOLYSIS
CAACAAAACC	235 ubiquitin B	4	18	0.0039		PROTEOLYSIS
GTGGAAAATG	2830 ESTs, Weakly similar to DDX8_HUMAN PROBABLE ATP-DEPENDENT RNA HELICASE HRH1 [H.sapiens]	1	20	0.0000		RNA BINDING PROTEINS
CCTCCTCCAG	43721 small nuclear ribonucleoprotein N 46814 M.musculus SmN pseudogene	5	21	0.0020		RNA BINDING PROTEINS
CCTACCAAGA	21938 protein tyrosine phosphatase, receptor type, C	14	52	0.0000		SIGNAL TRANSDUCTION
GAACAGAACC	29724 ESTs, Moderately similar to TOK-1alpha [H.sapiens]	2	18	0.0003		SIGNAL TRANSDUCTION
GTTGTGATTT	22691 Ewing sarcoma homolog	7	27	0.0009		SIGNAL TRANSDUCTION
AAAATGTACT	130120 EST 3752 RAN binding protein 1	3	18	0.0012		SIGNAL TRANSDUCTION
ATCACTCCAA	30126 membrane interacting protein of RGS16	5	20	0.0036		SIGNAL TRANSDUCTION
ATTTAGAGGT	103632 RAS-like, family 2, locus 9 7521 RAN, member RAS oncogene family	1	11	0.0042		SIGNAL TRANSDUCTION
GAAAGCAAAC	3475 retinoid X receptor gamma	0	11	0.0008		TRANSCRIPTION
ATGGTGGATT	2137 transcriptional regulator, SIN3B (yeast)	5	22	0.0014		TRANSCRIPTION
CCGTGTCCGA	28022 ESTs, Highly  similar to HISTONE H2B [Rattus norvegicus]	8	28	0.0014		TRANSCRIPTION
ACCCAGGCTG	21069 ESTs, Moderately similar to heat shock factor binding protein 1 HSBP1 [H.sapiens]	3	17	0.0019		TRANSCRIPTION
GGTGGTGCTT	16228 solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4	29	86	0.0000		TRANSPORTERS
CCACAGAGCT	18300 solute carrier family 3, member 1 2144 Ena-vasodilator stimulated phosphoprotein	8	33	0.0002		TRANSPORTERS
GAACTATGTT	30718 translocase of inner mitochondrial membrane 8 homolog b (yeast)	4	23	0.0003		TRANSPORTERS
TTGTATAATA	658 solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5	2	15	0.0020		TRANSPORTERS
AGGCCACAGC		1	15	0.0004		UNKNOWN
ACAATGCAGA		0	11	0.0008		UNKNOWN
AAGCAAGCGT		1	12	0.0026		UNKNOWN