Molecular Vision: Schippert, Mol Vis 2009; 15:2720-2739. Table 3

Table 3. List of genes that were differentially expressed between wild-type and homozygous Egr-1 knockout mice at the age of 42 days (wt/42 versus hm/42).

Affymetrix ID	Gene symbol	Gene title	FC (wt/p42 vs hm/p42)	p-value (wt/p42 vs hm/p42)	FC (wt/p30 vs hm/p30)	p-value (wt/p30 vs hm/p30)
Structural Molecule Activity (1)
1421811_at	Thbs1	thrombospondin 1	−2.09	0.0195	1.06	0.7630
Transporter Activity (4)
1458916_at	Slc12a6	Solute carrier family 12, member 6	1.61	0.0076	−1.08	0.6697
1457497_at	Syt1	Synaptotagmin I	1.64	0.0052	−1.16	0.6213
1436044_at	Scn7a	sodium channel, voltage-gated, type VII, alpha	−1.89	0.0003	−1.28	0.0383
1415844_at	Syt4	synaptotagmin IV	−2.26	0.0000	−2.55	0.0000
Enzyme Regulator Activity (7)
1444671_at	Rasal2	RAS protein activator like 2	1.53	0.0363	−1.30	0.2962
1446595_at	Itsn2	intersectin 2	1.53	0.0182	−1.26	0.4784
1440347_at	Arhgap10	Rho GTPase activating protein 10	1.57	0.0115	1.02	0.9324
1441386_at	Rapgef1	Rap guanine nucleotide exchange factor 1	1.61	0.0194	−1.12	0.1515
1445307_at	Auts2	Autism susceptibility candidate 2	1.86	0.0009	−1.13	0.7187
1442897_at	2610024E20Rik	RIKEN cDNA 2610024E20 gene	−1.50	0.0219	−1.39	0.0095
1416188_at	Gm2a	GM2 ganglioside activator protein	−1.79	0.0475	−1.02	0.8384
Molecular Transducer Activity (8)
1458469_at	Cblb	Casitas B-lineage lymphoma b	1.61	0.0089	−1.13	0.6019
1455967_at	Sorbs1	sorbin and SH3 domain containing 1	1.58	0.0111	1.10	0.7148
1445555_at	Trpm3	Transient receptor potential cation channel, subfamily M, member 3	1.64	0.0456	−1.13	0.5703
1443279_at	Nlk	Nemo like kinase	1.55	0.0307	−1.09	0.7229
1441498_at	Ptprd	Protein tyrosine phosphatase, receptor type, D	1.57	0.0499	1.12	0.8303
1441220_at	Magi2	Membrane associated guanylate kinase, WW and PDZ domain containing 2	1.93	0.0316	1.10	0.8184
1422723_at	Stra6	stimulated by retinoic acid gene 6	−1.59	0.0205	1.22	0.3171
1417205_at	Kdelr2	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2	−1.53	0.0027	1.14	0.3870
Transcription Regulator Activity (13)
1441615_at	Cbfa2t2	core-binding factor, runt domain, alpha subunit 2, translocated to, 2 (human)	1.53	0.0280	−1.02	0.92091
1445914_at	Nrf1	Nuclear respiratory factor 1	1.543	0.0016	1.31	0.5977
1441140_at	Rere	Arginine glutamic acid dipeptide (RE) repeats	1.55	0.0021	1.27	0.3524
1456686_at	Zfhx1a	Zinc finger homeobox 1a	1.56	0.0159	1.04	0.7871
1439946_at	Mef2c	Myocyte enhancer factor 2C	1.62	0.0041	−1.14	0.5653
1458661_at	Lcor	Ligand dependent nuclear receptor corepressor	1.63	0.0265	−1.04	0.9105
1446953_at	Tcf4	Transcription factor 4	1.63	0.0097	1.03	0.9567
1445695_at	Atxn1	Ataxin 1	1.73	0.0110	−1.40	0.3692
1417065_at	Egr1	early growth response 1	1.79	0.0004	1.99	0.0000
1443511_at	Rora	RAR-related orphan receptor alpha	1.96	0.0294	−1.18	0.5929
1436329_at	Egr3	early growth response 3	−1.51	0.0326	−1.30	0.1831
1443897_at	Ddit3	DNA-damage inducible transcript 3	−1.55	0.0297	1.11	0.6698
1417930_at	Nab2	Ngfi-A binding protein 2	−2.88	0.0001	−2.40	0.0035
Catalytic Activity (17)
1458663_at	Large	Like-glycosyltransferase	1.50	0.0298	1.37	0.2474
1442813_at	Dgki	Diacylglycerol kinase, iota	1.53	0.0448	−1.00	0.9982
1435273_at	Wars2	tryptophanyl tRNA synthetase 2 (mitochondrial)	1.53	0.0008	1.10	0.6011
1443445_at	Diap3	Diaphanous homolog 3 (Drosophila)	1.61	0.0162	−1.32	0.0682
1442163_at	Hace1	HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1	1.64	0.0043	−1.11	0.7030
1417024_at	Hars	histidyl-tRNA synthetase	1.66	0.0000	1.66	0.0000
1440066_at	Smarcad1	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a	1.69	0.0420	1.16	0.1397
1445395_at	Prkca	Protein kinase C, alpha	1.69	0.0030	1.04	0.9369
1438583_at	Ern1	Endoplasmic reticulum (ER) to nucleus signaling 1	1.71	0.0264	−1.50	0.0969
1446412_at	Wwox	WW domain-containing oxidoreductase	1.76	0.0152	1.104	0.6550
1445188_at	Gphn	Gephyrin	1.80	0.0010	−1.13	0.7227
1455905_at	2610507B11Rik	RIKEN cDNA 2610507B11 gene	−1.50	0.0435	−1.15	0.3423
1430177_at	Ube2b	ubiquitin-conjugating enzyme E2B, RAD6 homology (S. cerevisiae)	−1.52	0.0099	−1.33	0.2071
1439540_at	March2	membrane-associated ring finger (C3HC4) 2	−1.52	0.0115	−1.40	0.0493
1416613_at	Cyp1b1	cytochrome P450, family 1, subfamily b, polypeptide 1	−1.54	0.0402	−1.19	0.3717
1421024_at	Agpat1	1-acylglycerol-3-phosphate O-acyltransferase 1	−1.55	0.0048	1.02	0.8328
1439843_at	Camk4	calcium/calmodulin-dependent protein kinase IV	−1.95	0.0006	−2.19	0.0000
Binding (30)
1441567_at	Myo9a	Myosin IXa	1.50	0.0249	1.07	0.8016
1447381_at	Cpsf6	Cleavage and polyadenylation specific factor 6	1.51	0.0298	1.12	0.5466
1456773_at	Nupl2	nucleoporin like 2	1.51	0.0362	−1.07	0.6814
1441373_at	Msi2	Musashi homolog 2 (Drosophila)	1.53	0.0046	1.14	0.6634
1436382_at	Zbtb12	zinc finger and BTB domain containing 12	1.54	0.0359	−1.18	0.1262
1456303_at	Phf14	PHD finger protein 14	1.54	0.0178	1.07	0.8732
1443199_at	Lrch3	Leucine-rich repeats and calponin homology (CH) domain containing 3	1.55	0.0347	−1.29	0.2964
1443337_at	Grip1	Glutamate receptor interacting protein 1	1.55	0.0332	−1.30	0.5147
1447615_at	Fmn1	Formin 1	1.55	0.0082	−1.19	0.6470
1455893_at	Rspo2	R-spondin 2 homolog (Xenopus laevis)	1.55	0.0419	1.09	0.5464
1446279_at	Negr1	Neuronal growth regulator 1	1.58	0.0314	1.02	0.9288
1445329_at	Dtnb	dystrobrevin, beta	1.58	0.0214	−1.07	0.7944
1444384_at	Jazf1	JAZF zinc finger 1	1.58	0.0358	−1.34	0.2980
1439123_at	Phf21a	PHD finger protein 21A	1.60	0.0102	−1.14	0.6756
1441769_at	Arl15	ADP-ribosylation factor-like 15	1.61	0.0200	−1.03	0.9351
1442411_at	Glcci1	Glucocorticoid induced transcript 1	1.63	0.0068	−1.16	0.6206
1440551_at	Dnajc1	DnaJ (Hsp40) homolog, subfamily C, member 1	1.66	0.0280	1.21	0.5996
1440543_at	D930036F22Rik	RIKEN cDNA D930036F22 gene	1.66	0.0428	−1.02	0.9482
1443315_at	Dmd	Dystrophin	1.66	0.0103	−2.45	0.0492
1456351_at	Brd8	bromodomain containing 8	1.66	0.0005	1.67	0.0003
1446481_at	Apbb2	Amyloid beta (A4) precursor protein-binding, family B, member 2	1.68	0.0279	1.06	0.8385
1458263_at	Cugbp2	CUG triplet repeat, RNA binding protein 2	1.74	0.0041	−1.10	0.8176
1440067_at	Ncam1	Neural cell adhesion molecule 1	1.75	0.0171	1.03	0.9102
1444488_at	Cadps	Ca<2+>dependent activator protein for secretion	1.76	0.0054	1.01	0.9801
1441330_at	Crb1	crumbs homolog 1 (Drosophila)	1.99	0.0214	−1.12	0.4163
1429239_a_at	Stard4	StAR-related lipid transfer (START) domain containing 4	2.18	0.001991	1.79	0.0295
1451692_at	Tmco6	transmembrane and coiled-coil domains 6	2.73	0.0002	4.10	0.000
1449548_at	Efnb2	ephrin B2	−1.58	0.0436	−1.05	0.8291
1449527_at	Pcdhb7	protocadherin beta 7	−1.64	0.0016	−1.58	0.0155
1422640_at	Pcdhb9	protocadherin beta 9	−17.48	0.0000	−14.34	0.0000
Unknown (43)
1454397_at	4632418H02Rik	RIKEN cDNA 4632418H02 gene	1.50	0.0066	−1.05	0.8725
1432713_at	6430709C05Rik	RIKEN cDNA 6430709C05 gene	1.51	0.0031	−1.05	0.8923
1442509_at	Evi5	Ecotropic viral integration site 5	1.52	0.0156	−1.03	0.9005
1429900_at	5330406M23Rik	RIKEN cDNA 5330406M23 gene	1.52	0.0119	1.12	0.8002
1444651_at	LOC553089	hypothetical LOC553089	1.53	0.0230	−1.42	0.3710
1459409_at	Ccdc109a	coiled-coil domain containing 109A	1.53	0.0337	1.01	0.9616
1440570_at	Lhfpl3	Lipoma HMGIC fusion partner-like 3	1.53	0.010572	1.29	0.4440
1430195_at	2810043O03Rik	RIKEN cDNA 2810043O03 gene	1.54	0.0153	−1.16	0.7564
1438788_at	D5Wsu152e	DNA segment, Chr 5, Wayne State University 152	1.54	0.0060	1.15	0.7128
1444137_at	A430108G06Rik	RIKEN cDNA A430108G06 gene	1.54	0.0017	1.03	0.8671
1457781_at	Kcnq1ot1	KCNQ1 overlapping transcript 1	1.54	0.0013	−1.00	0.9993
1430096_at	2900017F05Rik	RIKEN cDNA 2900017F05 gene	1.56	0.0160	1.14	0.5974
1443088_at	9930031P18Rik	RIKEN cDNA 9930031P18 gene	1.56	0.0026	1.16	0.7326
1458706_at	2610035D17Rik	RIKEN cDNA 2610035D17 gene	1.56	0.0048	−1.08	0.5992
1453706_at	2900042A17Rik	RIKEN cDNA 2900042A17 gene	1.57	0.0272	1.02	0.9373
1443489_at	Vps13b	Vacuolar protein sorting 13B (yeast)	1.57	0.0012	1.01	0.9575
1440604_at	8030494B02Rik	Riken cDNA 8030494B02 gene	1.57	0.0255	−1.35	0.2507
1444445_at	C77648	expressed sequence C77648	1.57	0.0475	−1.10	0.6343
1433837_at	8430408G22Rik	RIKEN cDNA 8430408G22 gene	1.57	0.0226	−1.00	0.9943
1457508_at	C430003N24Rik	RIKEN cDNA C430003N24 gene	1.60	0.0022	−1.34	0.3974
1454558_at	5430416B10Rik	RIKEN cDNA 5430416B10 gene	1.60	0.0256	−1.07	0.8665
1440892_at	BC017647	CDNA sequence BC017647	1.63	0.0403	−1.06	0.8572
1441467_at	Tspan5	Tetraspanin 5	1.64	0.0438	−1.10	0.6658
1460101_at	NRXN3	Neurexin 3	1.67	0.0353	−1.05	0.9144
1444109_at	C130009A20Rik	RIKEN cDNA C130009A20 gene	1.67	0.0109	1.01	0.9683
1454424_at	2610040L17Rik	RIKEN cDNA 2610040L17 gene	1.68	0.0058	1.06	0.8692
1433266_at	2810416A17Rik	RIKEN cDNA 2810416A17 gene	1.66	0.0005	−1.14	0.7660
1442561_at	Mamdc1	MAM domain containing 1	1.69	0.0202	−1.06	0.9040
1453906_at	Med13l	mediator complex subunit 13-like	1.69	0.0010	1.02	0.9415
1443201_at	Gpc6	Glypican 6	1.70	0.0288	−1.20	0.6594
1458309_at	Dip2c	disco-interacting protein 2 homolog C	1.73	0.0250	−1.04	0.8794
1458505_at	LOC552901	hypothetical LOC552901	1.75	0.0206	−1.20	0.5693
1429977_at	9030425L15Rik	RIKEN cDNA 9030425L15 gene	1.76	0.0068	−1.07	0.9202
1440513_at	C80258	expressed sequence C80258	1.79	0.0100	−1.20	0.6384
1429870_at	C630040K21Rik	RIKEN cDNA C630040K21 gene	1.79	0.0029	−1.01	0.9797
1446102_at	D9Ertd292e	DNA segment, Chr 9, ERATO Doi 292, expressed	1.81	0.0028	−1.23	0.2711
1458779_at	8030445P17Rik	RIKEN cDNA 8030445P17 gene	1.83	0.0154	−1.17	0.763599
1453897_at	C030014A21Rik	RIKEN cDNA C030014A21 gene	1.85	0.0025	−1.46	0.265201
1446606_at	LOC625175	hypothetical protein A630054D14	1.86	0.0062	1.30	0.187229
1432757_at	2900011L18Rik	RIKEN cDNA 2900011L18 gene	1.90	0.0232	1.30	0.623096
1441231_at	LOC100042016	hypothetical protein LOC100042016	1.92	0.0002	−1.06	0.840764
1439086_at	A930009L07Rik	RIKEN cDNA A930009L07 gene	−1.58	0.0294	1.19	0.34015
1428909_at	A130040M12Rik	RIKEN cDNA A130040M12 gene	−1.62	0.0368	−1.90	0.0001
Not Annotated (12)
1446799_at			1.50	0.0030	−1.10	0.8224
1443271_at			1.51	0.0384	−1.46	0.3101
1441740_at			1.52	0.0284	−1.22	0.5593
1443526_at			1.52	0.0062	1.03	0.9444
1458077_at			1.55	0.0148	−1.01	0.9758
1445740_at			1.56	0.0456	−1.00	0.9998
1435409_at			1.61	0.0220	1.59	0.0878
1439999_at			1.63	0.0223	−1.11	0.7133
1443744_at			1.72	0.0128	−1.14	0.7148
1444622_at			1.82	0.0224	−1.02	0.9539
1457479_at			1.95	0.0060	−1.00	0.9815
1459595_at			2.18	0.0019	1.07	0.8169

Shown are Affymetrix ID, gene symbol, gene title, fold change (FC) and p-values that indicate the differences in gene expression levels between the wild-type and the homozygous Egr-1 knockout mice both at the age of 42 days and 30 days. Genes were sorted after GO annotations. Genes that were significantly changed (with a FC > 1.5 and p-value < 0.05) in both the 42 days old mice and the 30 days old mice are shown in italics and are underlined. The gene that showed the highest differences in mRNA expression levels between the homozygous and the wild-type mice (Pcdhb9 [shown in bold]) was further investigated using real-time PCR.