Table 3.

R-square values and fold-change for differentially expressed cis-regulated genes by microarray analysis within 4q22-q34 region on chromosome 4 in NP, NP.P, P.NP and P rats^ab

		R-square values												Fold change
Gene symbol	Gene name	Average BMC	Whole body BMC/BW	Cranial BMC/BW	Femur BMC/BW	L1-6 BMC/BW	Whole body aBMD	Cranial aBMD	Femur Midshaft Total vBMD	Distal Femur Total vBMD	L5 Total vBMD	Femur Ultimate Force	Femur Neck Ultimate Force	NP vs P	NP vs NP.P	P vs P.NP	NP.P vs P.NP	ANOVA p-value	FDR-Chr 4c	FDR-Chr alld
Candidate genes	Candidate genes
Snca	Synuclein, alpha	0.89	0.90	0.98	0.85	0.83	0.95	0.96	0.73	0.59	0.56	0.88	0.46	1.7	1.3	0.8	1.0	0	0	0.00006
Spr	Sepiapterin reductase	0.86	0.86	0.97	0.83	0.79	0.94	0.89	0.62	0.47	0.44	0.95	0.34	1.5	1.3	0.8	0.9	0.0007	0.008	0.009
Npy	Neuropeptide Y	0.73	0.73	0.76	0.75	0.67	0.82	0.62	0.28	0.23	0.20	0.97	0.13	1.5	1.4	0.9	0.9	0.00001	0.0009	0.0009
Arf5	ADP-ribosylation factor 5	0.65	0.63	0.89	0.54	0.55	0.67	0.91	0.95	0.58	0.59	0.59	0.51	0.8	0.9	1.2	1.1	0.00001	0.0003	0.07
Tmem209	Transmembrane protein 209	0.64	0.72	0.28	0.77	0.81	0.61	0.44	0.26	0.72	0.68	0.27	0.66	1.2	1.0	1.0	1.2	0.002	0.02	0.02
Slc25a26	Solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 26	0.60	0.68	0.26	0.70	0.76	0.55	0.45	0.33	0.82	0.79	0.20	0.79	1.1	1.0	1.0	1.2	0.0004	0.008	0.09
Gpnmb	Glycoprotein (transmembrane) nmb	0.56	0.50	0.88	0.45	0.40	0.62	0.69	0.53	0.19	0.17	0.84	0.11	0.7	0.7	1.3	1.2	0.006	0.07	0.06
Fkbp14	FK506 binding protein 14	0.52	0.58	0.17	0.66	0.67	0.50	0.26	0.07	0.43	0.39	0.26	0.36	0.9	0.9	0.9	0.8	0.002	0.03	0.03
Isy1	ISY1 splicing factor homolog	0.51	0.58	0.16	0.62	0.67	0.46	0.32	0.20	0.69	0.66	0.14	0.66	1.2	1.0	1.0	1.2	0.002	0.02	0.02
Ghrhr	Growth hormone releasing hormone receptor	0.48	0.42	0.84	0.35	0.32	0.51	0.71	0.69	0.24	0.24	0.65	0.17	0.6	0.7	1.6	1.4	0.003	0.04	0.04
Nup205	Nucleoporin 205	0.47	0.53	0.13	0.57	0.63	0.41	0.28	0.17	0.66	0.63	0.11	0.64	1.1	1.0	1.0	1.2	0.004	0.03	0.03
Skap2	Src family associated phosphoprotein 2	0.46	0.43	0.64	0.43	0.35	0.55	0.42	0.17	0.05	0.03	0.89	0.01	1.3	1.5	0.9	0.8	0.00004	0.0003	0.0005
Ruvbl1	RuvB-like protein 1	0.45	0.51	0.12	0.56	0.61	0.39	0.26	0.14	0.63	0.60	0.10	0.61	1.1	1.0	1.1	1.2	0.002	0.02	0.02
Tmem43	Transmembrane protein 43	0.44	0.50	0.10	0.57	0.60	0.41	0.20	0.06	0.45	0.41	0.16	0.40	0.9	1.0	0.9	0.8	0.006	0.05	0.05
Wdr91	WD repeat domain 91	0.44	0.37	0.80	0.30	0.28	0.46	0.64	0.62	0.18	0.17	0.64	0.12	1.4	1.3	0.7	0.8	0.0006	0.007	0.008
Tmem176b	Transmembrane protein 176B or Torid	0.38	0.33	0.60	0.33	0.26	0.46	0.36	0.15	0.02	0.01	0.82	0.00	1.3	1.4	0.9	0.8	0.0004	0.006	0.006
Sec61a1	Sec61 alpha 1 subunit	0.36	0.41	0.06	0.48	0.51	0.31	0.14	0.04	0.42	0.39	0.09	0.40	1.1	1.0	1.1	1.3	0.003	0.03	0.03
Bpgm	2,3-bisphosphoglycerate mutase	0.36	0.42	0.09	0.43	0.51	0.30	0.26	0.23	0.73	0.73	0.04	0.77	1.2	0.9	1.0	1.4	0.0003	0.01	0.01
Cald1	Caldesmon 1	0.32	0.37	0.07	0.38	0.45	0.25	0.22	0.21	0.71	0.70	0.02	0.75	0.9	1.1	1.0	0.8	0.003	0.03	0.03
Abtb1	Ankyrin repeat and BTB (POZ) domain containing 1	0.27	0.31	0.02	0.34	0.40	0.20	0.13	0.09	0.55	0.53	0.01	0.58	1.1	0.9	1.1	1.3	0.001	0.01	0.01
Add2	Adducin 2 (beta)	0.26	0.30	0.06	0.29	0.37	0.19	0.22	0.27	0.72	0.73	0.00	0.80	1.2	0.8	1.0	1.3	0.0004	0.008	0.009
Gars	Glycyl-tRNA synthetase	0.22	0.25	0.10	0.22	0.29	0.16	0.28	0.46	0.75	0.79	0.00	0.86	1.1	0.9	0.9	1.1	0.01	0.09	0.08
Gadd45a	Growth arrest and DNA-damage-inducible 45 alpha	0.20	0.24	0.01	0.25	0.32	0.14	0.11	0.11	0.56	0.56	0.00	0.62	1.1	0.8	1.1	1.5	0.00005	0.001	0.001
Cnbp	Cellular nucleic acid binding protein	0.19	0.22	0.02	0.22	0.29	0.12	0.15	0.21	0.64	0.65	0.00	0.73	1.1	0.9	1.0	1.1	0.008	0.06	0.06
Chn2	Chimerin (chimaerin) 2	0.16	0.12	0.29	0.14	0.08	0.22	0.11	0.01	0.02	0.03	0.58	0.08	1.1	1.4	1.0	0.8	0.008	0.06	0.05
Podxl	Podocalyxin-like	0.12	0.14	0.01	0.13	0.20	0.07	0.10	0.19	0.57	0.60	0.02	0.68	1.2	0.7	0.9	1.6	0.002	0.02	0.02
Eif4e3	Eukaryotic translation initiation factor 4E member 3	0.12	0.14	0.01	0.14	0.20	0.07	0.10	0.18	0.57	0.59	0.02	0.68	0.9	1.2	1.0	0.8	0.002	0.02	0.02
Tmem140	Transmembrane protein 140	0.10	0.04	0.31	0.03	0.01	0.11	0.12	0.06	0.03	0.04	0.43	0.08	0.7	0.5	1.4	2.0	0	0	0.00001
Kel	Kel Kell blood group	0.10	0.10	0.01	0.12	0.17	0.04	0.02	0.02	0.36	0.36	0.03	0.43	1.1	0.8	1.2	1.6	0	0	0.00001
Abcg2	ATP-binding cassette, sub-family G (WHITE), member 2	0.09	0.03	0.29	0.02	0.01	0.09	0.11	0.05	0.04	0.04	0.40	0.09	0.9	0.8	1.1	1.2	0.005	0.06	0.05
Tia1	Cytotoxic granule-associated RNA binding protein 1	0.06	0.06	0.00	0.11	0.07	0.08	0.00	0.15	0.03	0.05	0.17	0.08	1.0	1.2	1.3	1.1	0.001	0.02	0.02
Serbp1	Serpine1 mRNA binding protein 1	0.05	0.05	0.02	0.05	0.09	0.01	0.01	0.04	0.36	0.37	0.08	0.46	1.0	0.9	1.0	1.2	0.0007	0.01	0.01
Hoxa5	Homeo box A5	0.05	0.00	0.17	0.00	0.01	0.01	0.05	0.05	0.08	0.08	0.18	0.12	1.2	1.6	0.7	0.5	0	0	0.00004
Foxp1	Forkhead box P1	0.05	0.02	0.08	0.03	0.05	0.00	0.01	0.00	0.18	0.18	0.11	0.23	1.0	1.2	0.9	0.7	0.01	0.06	0.05
Bola3	BolA homolog 3	0.02	0.00	0.09	0.00	0.00	0.03	0.00	0.02	0.19	0.22	0.28	0.30	1.0	0.9	1.0	1.1	0.009	0.08	0.07
Predicted genes	Predicted genes
Ppp4r2	Protein phosphatase 4, regulatory subunit 2	0.74	0.76	0.80	0.68	0.72	0.74	0.94	0.97	0.85	0.86	0.49	0.80	1.1	1.0	0.9	1.0	0.004	0.03	0.03
Mpp6	Membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	0.73	0.76	0.76	0.68	0.72	0.72	0.92	0.96	0.89	0.89	0.44	0.84	0.7	1.0	1.3	1.0	0.00008	0.001	0.002
Baiap1	BAI1-associated protein 1	0.43	0.45	0.49	0.37	0.43	0.39	0.67	0.91	0.80	0.83	0.17	0.83	0.7	1.1	1.4	0.9	0.001	0.05	0.04
Cct7	Chaperonin subunit 7	0.39	0.45	0.14	0.45	0.53	0.32	0.33	0.34	0.82	0.82	0.05	0.86	1.1	0.9	1.0	1.2	0.00007	0.001	0.002
Chchd6	Coiled-coil-helix-coiled-coil-helix domain containing 6	0.38	0.44	0.08	0.47	0.53	0.32	0.23	0.17	0.67	0.65	0.05	0.68	1.2	0.9	1.1	1.4	0.004	0.03	0.03
MGC94941	Similar to Mkrn1 protein	0.31	0.35	0.04	0.39	0.44	0.24	0.14	0.08	0.54	0.52	0.02	0.55	1.2	0.9	1.2	1.7	0	0	0.0002
Slc35b4	Predicted solute carrier family 35, member B4	0.19	0.12	0.50	0.09	0.06	0.21	0.29	0.24	0.00	0.00	0.50	0.00	1.2	1.2	0.9	0.8	0.0006	0.007	0.008
RGD1563542	Similar to Kell protein	0.14	0.15	0.00	0.18	0.23	0.08	0.03	0.01	0.36	0.35	0.01	0.40	1.1	0.8	1.3	1.8	0.00003	0.0006	0.0007
Nt5c3	Predicted 5′-nucleotidase, cytosolic III	0.14	0.07	0.41	0.05	0.03	0.14	0.21	0.16	0.00	0.00	0.43	0.02	0.7	0.6	1.5	1.8	0	0	0
RGD1311080	Similar to RIKEN cDNA A930038C07	0.12	0.12	0.01	0.16	0.19	0.06	0.01	0.00	0.22	0.21	0.00	0.24	1.0	1.2	0.8	0.7	0.00008	0.001	0.002
Ube2h	ubiquitin-conjugating enzyme E2H	0.09	0.11	0.00	0.11	0.16	0.04	0.06	0.13	0.50	0.52	0.03	0.61	1.1	0.8	1.0	1.3	0.008	0.07	0.06
RGD1306936	Similar to chromosome 7 open reading frame 30	0.06	0.00	0.25	0.00	0.00	0.03	0.12	0.19	0.01	0.00	0.17	0.01	1.1	1.2	0.8	0.8	0.003	0.03	0.02

^aGenes (r² > 0.50) are indicated in bold face.

^bP allele is high bone mass expressing genotype.

^cFDR-Chr 4: False discovery rate from the analysis of 460 probe sets in the chromosome 4 QTL region.

^dFDR-Chr all: False discovery rate from the analysis of all probe sets in all chromosomes.