Table S4. Tags down in P10.5 crx-/- retina. 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, INL=inner nuclear layer, MG=Muller glia, ONL=outer nuclear layer.
Tag	Gene	Crx+/+	Crx-/-	P-value	Expression in retina	Function
TATCAAGATT	22584 serine/threonine kinase receptor associated protein	9	0	0.0012	AC	SYNAPTIC
CTGCCTGAGA	46379 syntrophin associated serine/threonine kinase	10	0	0.0006	AC	SYNAPTIC
TAGATTGAGG	32545 ESTs	8	0	0.0027	AC	OTHER
GCAATGCAAA	35817 ESTs	10	0	0.0006	MG	OTHER
CAACTTAGCA	20465 G protein-coupled receptor 37	29	8	0.0002	MG	SIGNAL TRANSDUCTION
GGAGGGATCA	8131 integrin linked kinase	19	6	0.0042	MG	SIGNAL TRANSDUCTION
GAAGTACGTC	21383 ESTs/CGI-145	10	0	0.0006	ONL	CYTOSKELETAL
GTGTGAGAAT	26828 ESTs/erb2-interacting protein ERBIN	9	0	0.0012	ONL	CYTOSKELETAL
TAGATTTCCC	81416 novel retinol dehydrogenase	18	2	0.0001	ONL	LIPID METABOLISM/TRANSPORT
AAGGTGCACG	28147 Mus musculus Dp1l1 mRNA for polyposis locus protein 1-like 1 (TB2 protein-like 1), complete cds	13	1	0.0006	ONL	LIPID METABOLISM/TRANSPORT
GGGCCTGCTC	38763 ESTs/IMP dehydrogenase 1	13	2	0.0023	ONL	METABOLIC
GCATACCGTT	152952 ESTs	19	0	0.0000	ONL	OTHER
ATTGGCCCCA	26633 PH domain containing protein in retina 1	110	25	0.0000	ONL	OTHER
GCAGGGGCGG	24847 thymic dendritic cell-derived factor 1 36242 membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2)	16	1	0.0001	ONL	OTHER
TCTTTCAAGA	40852 ESTs	17	2	0.0002	ONL	OTHER
CTGTTGGCTA	41982 retinoschisis 1 homolog (human)	10	0	0.0006	ONL	OTHER
AGCATTCCTC	1276 retinal S-antigen	595	114	0.0000	ONL	PHOTOTRANSDUCTION
ACAAGTGTCC	2965 rhodopsin	93	12	0.0000	ONL	PHOTOTRANSDUCTION
TCCTTGCAAA	39200 phosphodiesterase 6G, cGMP-specific, rod, gamma 18962 catenin alpha 1	129	17	0.0000	ONL	PHOTOTRANSDUCTION
TTGTCCCTCC	69061 guanine nucleotide binding protein, alpha transducing 1	23	0	0.0000	ONL	PHOTOTRANSDUCTION
GCGACTGGAA	2344 guanine nucleotide binding protein, beta 1	35	12	0.0002	ONL	PHOTOTRANSDUCTION
GCTATCTTCA	29878 recoverin 33709 ESTs, Weakly similar to pregnancy specific glycoprotein 19 [M.musculus]	11	0	0.0003	ONL	PHOTOTRANSDUCTION
AGAGCTGGTT	95398 ESTs, Moderately similar to GBG1_MOUSE GUANINE NUCLEOTIDE-BINDING PROTEIN G(T) GAMMA-1 SUBUNIT [M.musculus]	26	7	0.0003	ONL	PHOTOTRANSDUCTION
TCTGGCTGGA	2965 rhodopsin	28	4	0.0000	ONL	PHOTOTRANSDUCTION
AAACCCCACT	2965 rhodopsin 110329 ESTs	30	2	0.0000	ONL	PHOTOTRANSDUCTION
GGGACAGAGG	2965 rhodopsin 44195 ESTs, Moderately similar to KIAA1173 protein [H.sapiens]	139	3	0.0000	ONL	PHOTOTRANSDUCTION
GCTTTGGGTC	1372 phosphodiesterase, cGMP, rod receptor, beta polypeptide	64	31	0.0001	ONL	PHOTOTRANSDUCTION
CAGAGTTGGG	2965 rhodopsin 23836 ESTs, Weakly similar to AF218940_1 formin-2 [M.musculus]	8	0	0.0027	ONL	PHOTOTRANSDUCTION
GAAAATCAAA	95707 AILP1	19	3	0.0002	ONL	POST-TRANSLATIONAL PROCESSING
TTCTTTCCGC	141993 muscleblind-like (Drosophila)	8	0	0.0027	ONL	RNA BINDING PROTEINS
CACCCGCAGC	7919 HGF-regulated tyrosine kinase substrate	21	6	0.0015	ONL	SYNAPTIC
TGGTTACGTA	1561 BCL2/adenovirus E1B 19 kDa-interacting protein 1, NIP2	12	2	0.0043	ONL	TRANSCRIPTION
TCCTTGCATA	2965 rhodopsin	54	23	0.0000	ONL	UNKNOWN
GATGTGTAAA	38890 ESTs/Daxx	26	5	0.0000	ONL/BP	CELL DEATH
GCTGCATAGC	21662 Mus musculus RPGR-interacting protein mRNA, complete cds	42	7	0.0000	ONL/BP	CYTOSKELETAL
AAGGTCTGCC	2400 glutathione peroxidase 4 8180 dihydropyrimidinase-like 3	78	26	0.0000	ONL/BP	METABOLIC
ATCCTTCCCC	911 HMG-17	27	4	0.0000	ONL+AC	TRANSCRIPTION
CAGTTGCAAT	41500 ESTs/NeuroD	72	36	0.0001	ONL+AC	TRANSCRIPTION
AGGGAAAAAA	41649 ESTs/KIAA0515 ubiquitin-like motif?	27	11	0.0035	ONL+BP	PROTEOLYSIS
GTGGACCCCA	44123 DNA segment, Chr 8, ERATO Doi 713, expressed	8	0	0.0027	ONL+INL	OTHER
ACACGACGTA	50 ESTs	27	11	0.0035	ONL+INL	OTHER
GCTGCTGGTG	26168 ESTs, Weakly similar to contains transmembrane [M.musculus] 3746 nascent polypeptide-associated complex alpha polypeptide	15	2	0.0007	widespread	OTHER
GACACTCAAT	43678 ESTs	60	17	0.0000	widespread	OTHER
TTTGTCACCA	38912 ESTs	19	3	0.0002	widespread	OTHER
GCGTTGGTCT	22121 DNA segment, Chr 7, ERATO Doi 156, expressed	10	1	0.0037	widespread	OTHER
GGAGGGTGTG	28873 phosphatidic acid phosphatase type 2c	26	4	0.0000	widespread	SIGNAL TRANSDUCTION
TTGGATTTAA	16533 RNA polymerase II 1	11	1	0.0021	widespread	TRANSCRIPTION
CGCGCGCGCA	30928 ESTs, Weakly similar to mCAC [M.musculus] 24214 forkhead box K1	64	5	0.0000	widespread	TRANSPORTERS
GCTGCCAGGG	688 Bcl2-associated athanogene 1	13	2	0.0023		CELL DEATH
GAAGCAGGAC	4024 cofilin 1, non-muscle	81	24	0.0000		CYTOSKELETAL
GGATGGGGAG	4024 cofilin 1, non-muscle	39	9	0.0000		CYTOSKELETAL
GCAGGCACTC	1703 tubulin, beta 5	204	69	0.0000		CYTOSKELETAL
GGCTGGGGGC	2647 profilin 1	20	1	0.0000		CYTOSKELETAL
ATGTCTCAAA	4591 tubulin alpha 2	138	96	0.0006		CYTOSKELETAL
TATGCAACCC	7089 necdin	49	25	0.0011		CYTOSKELETAL
GCCCGGGAAT	5290 Mus musculus chromosome 10 popeye protein 3 (Pop3) mRNA, complete cds 157045 hexokinase 1	128	27	0.0000		METABOLIC
GGGGCTCAGC	589 glucose phosphate isomerase 1 complex	38	11	0.0000		METABOLIC
TGACCGGCTG	1776 ferritin heavy chain	17	2	0.0002		METABOLIC
AATGGATGAA	24635 ESTs, Moderately similar to phosphoenolpyruvate carboxykinase [M.musculus]	11	0	0.0003		METABOLIC
GAATAGGGGT	3913 enolase 2, gamma neuronal	10	0	0.0006		METABOLIC
CCAAATAAAA	26504 lactate dehydrogenase 1, A chain	111	78	0.0021		METABOLIC
TTCCAGCTGC	16783 Mus musculus phosphoglycerate mutase 1 (Pgam1) mRNA, complete cds	45	24	0.0031		METABOLIC
TCAGAGGCCT	22801 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 1	26	5	0.0000		METABOLIC
GTGGCTCACA	10098 non-selective cation channel 1 1114 galactosidase, alpha 117043 transcription termination factor 1 11756 chemokine (C-X-C) receptor 2 1378 cannabinoid receptor 2 (macrophage) 138634 hypothetical protein (MNCb-0628) 143758 similar to RAP1 protein 1664 RAB33B, member of RAS oncogene family 21758 cytochrome P450, 2e1, ethanol inducible 2913 solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1 3159 phosphorylase kinase gamma 33263 histocompatibility 2, D region locus 1 35016 histocompatibility 2, T region locus 23 38151 adenylosuccinate lyase 38241 interleukin 1 receptor-associated kinase 4184 zinc finger protein 1 42032 cofactor required for Sp1 transcriptional activation subunit 2 (150 kDa) 42046 parkin 502 interferon (alpha and beta) receptor 6666 zinc finger protein 316 87812 18S RNA 88535 f-box only protein 17	866	718	0.0000		OTHER
AGCAATTCAA	156913 Mus musculus domesticus mitochondrial DNA, complete genome	53	17	0.0000		OTHER
TAGTCAGGGA	2875 DNA segment, Chr 8, ERATO Doi 325, expressed	31	7	0.0000		OTHER
ACGCCACAAT	29642 ESTs, Highly  similar to HYPOTHETICAL 46.6 KD PROTEIN IN DAL80-GAP1 INTERGENIC REGION [Saccharomyces cerevisiae]	44	15	0.0000		OTHER
GCAGGGTGGG	22103 thymine DNA glycosylase	20	2	0.0000		OTHER
TGTGTCTGTG	140725 ESTs 86439 ESTs, Weakly similar to AF209931_1 7h3 protein [H.sapiens]	16	1	0.0001		OTHER
CCGAAGCTGA	139674 ESTs	18	2	0.0001		OTHER
ACACCCTGGA	391 Mus musculus brain cDNA, clone MNCb-1039	18	2	0.0001		OTHER
TGCAAATGGA	25148 ESTs, Highly similar to T08667 hypothetical protein DKFZp547O0510.1 - human [H.sapiens]	19	3	0.0002		OTHER
CCCTTCTTCT	16820 hemoglobin alpha, adult chain 1	10	0	0.0006		OTHER
GTGATGAAGC	26287 DNA segment, Chr 8, ERATO Doi 503, expressed 27756 ESTs	10	0	0.0006		OTHER
TGCTGTGCAT	18459 fibroblast growth factor inducible 14	25	8	0.0010		OTHER
GCTCCCCCAC	24998 ESTs 2509 procollagen, type VI, alpha 1	9	0	0.0012		OTHER
GTAGCAAAAG	156690 retibindin 23876 ESTs, Highly  similar to PROPIONYL-COA CARBOXYLASE ALPHA CHAIN PRECURSOR [Rattus norvegicus]	22	7	0.0021		OTHER
GTCACACCAC	19187 prothymosin alpha	11	1	0.0021		OTHER
TCTGCCTGCA	22123 DNA segment, Chr 15, Wayne State University 75, expressed 39090 glutamate receptor, ionotropic, NMDA2C (epsilon 3)	11	1	0.0021		OTHER
GGCTGCAGCC	44493 pale ear	48	26	0.0027		OTHER
GAATGGCGGG	4095 inactive X specific transcripts	8	0	0.0027		OTHER
CGCTGATAGG	29190 ESTs, Highly similar to Y176_HUMAN HYPOTHETICAL PROTEIN KIAA0176 [H.sapiens]	14	3	0.0038		OTHER
GTGGAAGCGA	155235 open reading frame 12 44244 Mus musculus EST from clone 555961, full insert	12	2	0.0043		OTHER
TGCTCTGCCT	20929 hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 2 2856 interleukin 6 receptor, alpha 44493 pale ear 86541 intracisternal A particles	12	2	0.0043		OTHER
GCACCAACTG	38228 ESTs	12	2	0.0043		OTHER
CTGTAAATGT	43696 ESTs	12	2	0.0043		OTHER
TGGTGTAGGA	918 heat shock 70kD protein 5 (glucose-regulated protein, 78kD)	33	11	0.0003		PROTEIN PROCESSING
GATTGTCAAA	3371 FK506-binding protein 3 (25kD)	9	0	0.0012		PROTEIN PROCESSING
GTTGTAAAGT	29186 DNA J protein	8	0	0.0027		PROTEIN PROCESSING
TGGTGACAAA	10706 cyclin ania-6a	78	29	0.0000		PROTEIN SYNTHESIS
GCGAAGCTCA	265 ESTs, Highly  similar to 40S RIBOSOMAL PROTEIN S25 [Homo sapiens; Rattus norvegicus]	67	20	0.0000		PROTEIN SYNTHESIS
GTGAAACTAA	66 ribosomal protein S4, X-linked	59	20	0.0000		PROTEIN SYNTHESIS
TGGGTTGTCT	254 translationally regulated transcript (21 kDa)	165	113	0.0001		PROTEIN SYNTHESIS
GTGACCGAAG	12858 eukaryotic translation initiation factor 4A1	17	3	0.0007		PROTEIN SYNTHESIS
TCTTCTCACA	23 ESTs, Moderately  similar to 60S RIBOSOMAL PROTEIN L39 [Rattus norvegicus]	12	1	0.0011		PROTEIN SYNTHESIS
GCGAAGGCTG	2718 eukaryotic translation elongation factor 1-beta homolog	9	0	0.0012		PROTEIN SYNTHESIS
AGAGCGAAGT	13859 ribosomal protein L41	34	14	0.0014		PROTEIN SYNTHESIS
TATGTTGCGG	28753 ESTs, Highly  similar to PROTEIN TRANSLATION FACTOR SUI1 HOMOLOG [Anopheles gambiae]	35	16	0.0026		PROTEIN SYNTHESIS
AGGGAGTGGG	28378 ESTs, Moderately  similar to CYANELLE 30S RIBOSOMAL PROTEIN S11 [Cyanophora paradoxa] 41554 ESTs, Weakly similar to OZF_MOUSE ZINC FINGER PROTEIN OZF [M.musculus]	10	1	0.0037		PROTEIN SYNTHESIS
GTAAGCATAA	235 ubiquitin B	136	64	0.0000		PROTEOLYSIS
TGACCCCGGG	43005 ubiquitin A-52 residue ribosomal protein fusion product 1	240	132	0.0000		PROTEOLYSIS
CCTTGCTCAA	4263 cystatin C	106	70	0.0008		PROTEOLYSIS
GTAAGCAAAA	235 ubiquitin B	81	50	0.0011		PROTEOLYSIS
GAACGCGACG	98 proteasome (prosome, macropain) subunit, beta type 6	9	0	0.0012		PROTEOLYSIS
TGAGTGGACA	21306 matrix metalloproteinase 24	19	6	0.0042		PROTEOLYSIS
GCCTTCCAAT	19101 DEAD (aspartate-glutamate-alanine-aspartate) box polypeptide 5	58	25	0.0000		RNA BINDING PROTEINS
TGTGTTGTGT	19101 DEAD (aspartate-glutamate-alanine-aspartate) box polypeptide 5	39	17	0.0009		RNA BINDING PROTEINS
GCCTCAGTTC	5082 DEAD (aspartate-glutamate-alanine-aspartate) box polypeptide 6 99752 EST	9	0	0.0012		RNA BINDING PROTEINS
CAGCATCACC	21559 ESTs, Moderately  similar to PTB-ASSOCIATED SPLICING FACTOR [Homo sapiens]	41	20	0.0022		RNA BINDING PROTEINS
GAGAAGTGTG	2635 pyruvate kinase 3 26391 ESTs	22	4	0.0001		SIGNAL TRANSDUCTION
TGCTGAGAAT	7793 protein phosphatase 1, catalytic subunit, gamma isoform	55	28	0.0007		SIGNAL TRANSDUCTION
GGCCGCTGCT	142697 ESTs, Highly  similar to SERINE/THREONINE PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT, BETA ISOFORM [Homo sapiens]	54	28	0.0009		SIGNAL TRANSDUCTION
CTGGGCCCAG	6483 phospholipase D3	12	1	0.0011		SIGNAL TRANSDUCTION
TGTAGACGGA	152772 ESTs, Highly  similar to TYROSINE-PROTEIN KINASE JAK1 [Homo sapiens] 666 ESTs, Moderately  similar to NADH-UBIQUINONE OXIDOREDUCTASE KFYI SUBUNIT PRECURSOR [Bos taurus]	21	6	0.0015		SIGNAL TRANSDUCTION
GCACAACTTG	18041 calmodulin 2	150	111	0.0015		SIGNAL TRANSDUCTION
CTAACTAGTT	153637 ESTs, Moderately similar to 1615347A ras p21 GTPase activating protein [M.musculus]	12	2	0.0043		SIGNAL TRANSDUCTION
GGGCCCAACT	21149 CRIPT protein	12	2	0.0043		SYNAPTIC
TAATAAAAAT	2756 high mobility group nucleosomal binding domain 1 35166 ESTs	15	3	0.0024		TRANSCRIPTION
GCCAGAAAAA	19788 Kruppel-like factor 9	8	0	0.0027		TRANSCRIPTION
GGGGCTCTGT	1635 ESTs, Highly similar to PIAS3 [M.musculus] 5856 NY-REN-18 antigen	18	5	0.0031		TRANSCRIPTION
ACAGCCCACC	4550 ATPase, Na+/K+ transporting, beta 1 polypeptide	10	1	0.0037		TRANSPORTERS
GCTGCCCTCC		292	166	0.0000		UNKNOWN
GCCACCGTCC		45	7	0.0000		UNKNOWN
CCGACGGGCG		28	2	0.0000		UNKNOWN
GCCGTTCTTA		28	2	0.0000		UNKNOWN
GTGACCACGG		102	6	0.0000		UNKNOWN
ACCCGCCGGG		50	1	0.0000		UNKNOWN
AGCAGTCCCC		110	63	0.0000		UNKNOWN
GCACGACCTG		28	5	0.0000		UNKNOWN
GTAATCCTGC		12	0	0.0001		UNKNOWN
CTGCGGCTTC		16	2	0.0003		UNKNOWN
CAAACCTCCA		13	1	0.0006		UNKNOWN
AACGAGGAAT		12	1	0.0011		UNKNOWN
GGAGTGCCTT		9	0	0.0012		UNKNOWN
TGTTGGTACG		26	9	0.0014		UNKNOWN
GGTCAGTCGG		33	2	0.0000		UNKNOWN
TCGGACGAGG		8	0	0.0027		UNKNOWN