. 2014 Mar 7;9(3):e90568. doi: 10.1371/journal.pone.0090568

Table 1. Extracellular matrix proteins novel in the zebrafish skeleton.

		Craniofacial skeleton			Axial skeleton			Caudal fin region
Uniprot	Protein name	Ratio 28/14	Ratio 358/28	Ratio 358/14	Ratio 28/14	Ratio 358/28	Ratio 358/14	Ratio 358/28	References
Bone-related proteins
F1QR30	Bgnb^a	0.44	0.94	1.38**	0.02	0.51	0.54	0.73	[29], [30], [32]
Q803H7	Itm2ba^a	1.48**	–0.27	1.21**	0.96*	0.02	0.98	–0.31	[48]
F1R0N0	Lrrc17^a	1.72**	0.26	1.98**	0.14	–0.20	–0.06	–0.79	[49]
Q6NXA5	Pon2^a	–0.47	–2.08*	–2.55**	–0.26	–1.69**	–1.96**	n.s.	[50]
B0S6K5	Tnw^a	–0.49	0.03	–0.46	–1.23**	–0.55	–1.78**	–0.03	[51]
B0S525	Igfbp5b^a	2.45**	0.28	2.73**	0.81*	0.15	0.95	–0.38	[31], [32], [52], [53]
F1RDU8	Fcgrt	0.73	–1.33*	–0.60	0.20	–1.35**	–1.15**	n.s.	[32]
E9QG22	Spp2	2.19**	0.96	3.15**	2.13**	0.30	2.43**	0.33	[44]
F1QXC6	Tgfb2l	1.14*	0.07	1.21*	1.42**	0.28	1.70**	0.01	[54], [55]
Cartilage-related proteins
B7SDQ7	Ccdc80^a	1.74**	0.15	1.89**	–0.06	0.28	0.21	0.00	[29]
F1Q775	Cilp^a	0.48	–0.25	0.23	–1.24**	–1.29	–2.53**	n.s.	[29]
F1Q924	Col6a6^a	–0.47	–0.51	–0.98*	–1.53**	0.32	–1.21**	0.06	[56]
F1QLW6	Ogn^a	1.80**	0.86	2.66**	2.20**	0.79	3.00**	1.11*	[29], [30], [32]
F1QKL1	Thbs3a^a	n.s.	n.s.	n.s.	0.72	0.34	1.06**	–0.93	[29]
F1R1P9	Thbs4b^a	n.s.	n.s.	n.s.	0.56	0.91	1.47**	0.10	[29], [30]
E7F6W5	Cmn^a	n.s.	n.s.	n.s.	–0.10	–2.29**	–2.39**	n.s.	[57]
F1RAC0	Aebp1 (2/2)	1.68**	0.53	2.21**	1.85**	0.66	2.51**	0.41	[29], [30]
F1Q5N7	Cilp2	1.16*	0.78	1.94**	0.54	0.60	1.14**	1.01*	[29], [58]
E7FB76	Col21a1	n.s.	n.s.	n.s.	–0.59	–1.26	–1.85**	n.s.	[30]
E7FF99	Fbn2	–0.10	–0.76	–0.86	–0.59	–0.56	–1.15**	–0.57	[29]
F1QLT3	Fgfbp2	1.50**	0.41	1.91**	0.26	–0.22	0.03	n.s.	[30]
F1R5Z2	Fndc1	1.80**	0.05	1.85**	1.24**	–0.48	0.76	–0.55	[59], [60]
F1Q5C3	Itih6	1.61**	–0.44	1.16	0.00	–0.55	–0.55	n.s.	[29]
E7F8X0	Srpx2	0.82	0.72	1.55*	0.83*	0.39	1.22**	0.88*	[29]
E7F1S4	Thbs2b	0.80	0.11	0.90	1.07**	–0.31	0.75	–0.75	[29]
E7EXE8	Tnxb	2.24**	0.50	2.74**	0.73	0.58	1.31*	0.56	[29]
Bone- and cartilage-related proteins
Q804H0	Anxa1c^a	–0.22	–1.52*	–1.74**	n.s.	n.s.	n.s.	n.s.	[29], [30], [32]
Q6IQP3	Calua^a	n.s.	n.s.	n.s.	2.93**	–1.23	1.69*	–1.35	[29], [32]
Q5SPR2	Clu^a	n.s.	n.s.	n.s.	1.58**	1.19**	2.77**	0.35	[29], [30], [32]
Q6AXL0	Cthrc1a^a	1.92**	0.37	2.29**	n.s.	n.s.	n.s.	n.s.	[29], [32]
Q6NYE1	Fgb^a	1.22**	–0.43	0.79	n.s.	n.s.	n.s.	n.s.	[29], [30], [32]
F1QG51	Fmoda^a	–0.22	–0.32	–0.53	–1.21**	–0.42	–1.63**	–1.29	[29], [30], [32]
F1REI0	Htra3^a	0.70	–1.09	–0.40	1.20**	–1.01*	0.19	–0.74	[61]
Q6GMI5	Bgna^a	0.92*	0.67	1.59**	0.71*	0.52	1.23**	0.37	[30], [31], [32]
F1R6R2	Apcs	n.s.	n.s.	n.s.	–1.69**	–0.35	–2.04**	n.s.	[30], [32]
A9JRB3	Htra1b	1.64**	0.26	1.90**	0.68*	0.28	0.95*	–0.34	[62] [63]
F1QFZ8	Mmp13b	1.24**	0.07	1.31**	0.88*	0.72	1.61**	0.64	[64] [65]
F1QLH9	Nucb1	0.88	–0.13	0.75	1.36**	–0.93	0.43	–1.00*	[29]
Q29RB4	Olfml3a	0.69	0.60	1.29**	0.81*	0.55	1.37**	0.27	[29], [32]
B3DJG2	Pcolce (2/2)	1.62*	0.16	1.78**	2.48**	0.33	2.81**	0.32	[29], [30], [32]
Novel proteins
F1QW52	Habp2	1.62**	0.04	1.67**	–0.22	–0.32	–0.54	–0.31	–
E7F8L7	Otos	0.28	–2.20*	–1.91**	–0.68*	–2.56**	–3.24**	n.s.	–
F1Q9N5	Metrnl	n.s.	n.s.	n.s.	1.28**	–0.34	0.94	–0.62	–
B0UXN0	Qsox1	n.s.	n.s.	n.s.	0.98**	1.30**	2.28**	n.s.	–
F1QK57	Tecta	1.10	0.96	2.07**	n.s.	n.s.	n.s.	n.s.	–
B0S6C1	Tfpia	1.85**	–0.67	1.18	0.92*	–0.86	0.06	–1.46*	–

Of the 123 extracellular proteins that were differentially abundant during zebrafish skeletal development, a subset of 40 proteins was identified as novel proteins in zebrafish skeletal development based on whether they were previously characterized or identified in skeletal tissues of other vertebrate species (mouse, rat, human). In addittion, 6 were considered as novel in vertebrate skeletogenesis in general (bottom). ^a Indicates proteins previously studied based on their gene expression pattern by in situ hybridization in stages up to 5 dpf. Proteins that were not selected for relative quantification based on described criteria (Materials and Methods section) are marked (N.S.). ^* Significantly differential abundant proteins based on their significance at a threshold of FDR = 0.05. ^** Significantly differential abundant proteins based on their significance at a threshold of FDR = 0.01.