Table 4 Functional annotation clustering of genes upregulated in muscle from DU×IB piglets

GO:0032501 ~ multicellular organismal process

54

6.61E-13

S100A6, AEBP1, KERA, UTRN, POSTN, REST, ENPEP, GPX2, APP, ROBO1, SEMA3E, S1PR5, COL12A1, LOX, SLC22A2, USH2A, EGFL6, CHODL, CTNNBIP1, MAN2A1, ALDH7A1, DACT1, GRN, SORT1, VCAN, COL1A1, CNTN3, PROS1, CASQ2, MYL6, HUS1, AKAP9, GPM6B, FKBP1A, APLNR, PTK2, ITGAV, SYN3, PPP3CB, SCARB1, FBN2, DCLK1, MAP1B, ITGA2, IGF2, COL5A1, DKK3, ITGA6, SFRP2, CD59, TCF12, MYH10, CDH11, CLCN5

GO:0048856 ~ anatomical structure development

41

9.60E-10

MYL6, AEBP1, S100A6, UTRN, GPM6B, POSTN, FKBP1A, ENPEP, REST, PTK2, APP, ROBO1, ITGAV, S1PR5, SEMA3E, PPP3CB, COL12A1, FBN2, LOX, USH2A, DCLK1, MYOC, MAP1B, CHODL, ITGA2, IGF2, COL5A1, DKK3, MAN2A1, ITGA6, SFRP2, GRN, SORT1, VCAN, ANTXR1, CNTN3, COL1A1, TCF12, CASQ2, MYH10, CDH11

GO:0007275 ~ multicellular organismal development

43

2.42E-09

MYL6, AEBP1, S100A6, HUS1, UTRN, GPM6B, POSTN, FKBP1A, ENPEP, REST, PTK2, APP, ROBO1, ITGAV, S1PR5, SEMA3E, PPP3CB, COL12A1, FBN2, LOX, USH2A, DCLK1, EGFL6, MAP1B, CHODL, ITGA2, IGF2, COL5A1, CTNNBIP1, DKK3, MAN2A1, DACT1, ITGA6, SFRP2, GRN, SORT1, VCAN, CNTN3, COL1A1, TCF12, CASQ2, MYH10, CDH11

GO:0032502 ~ developmental process

45

4.28E-09

MYL6, S100A6, AEBP1, HUS1, UTRN, GPM6B, POSTN, FKBP1A, ENPEP, REST, PTK2, APP, ROBO1, ITGAV, S1PR5, SEMA3E, PPP3CB, COL12A1, FBN2, LOX, USH2A, DCLK1, MYOC, EGFL6, MAP1B, CHODL, ITGA2, IGF2, COL5A1, CTNNBIP1, DKK3, MAN2A1, DACT1, ITGA6, SFRP2, GRN, SORT1, VCAN, ANTXR1, CNTN3, COL1A1, TCF12, CASQ2, MYH10, CDH11

GO:0048731 ~ system development

35

1.36E-07

MYL6, AEBP1, S100A6, UTRN, GPM6B, POSTN, FKBP1A, ENPEP, REST, APP, PTK2, ROBO1, ITGAV, S1PR5, SEMA3E, PPP3CB, COL12A1, LOX, USH2A, DCLK1, MAP1B, CHODL, ITGA2, IGF2, COL5A1, MAN2A1, ITGA6, SORT1, VCAN, CNTN3, COL1A1, TCF12, CASQ2, CDH11, MYH10

GO:0030154 ~ cell differentiation

22

2.12E-04

S100A6, EGFL6, UTRN, MAP1B, ITGA2, IGF2, GPM6B, REST, PTK2, APP, ITGA6, ROBO1, SFRP2, SEMA3E, S1PR5, PPP3CB, SORT1, VCAN, ANTXR1, COL1A1, DCLK1, MYH10

GO:0048869 ~ cellular developmental process

22

3.88E-04

S100A6, EGFL6, UTRN, MAP1B, ITGA2, IGF2, GPM6B, REST, PTK2, APP, ITGA6, ROBO1, SFRP2, SEMA3E, S1PR5, PPP3CB, SORT1, VCAN, ANTXR1, COL1A1, DCLK1, MYH10

GO:0048513 ~ organ development

24

4.09E-04

MYL6, AEBP1, UTRN, ITGA2, CHODL, FKBP1A, IGF2, POSTN, ENPEP, COL5A1, MAN2A1, PTK2, APP, ITGA6, ROBO1, ITGAV, PPP3CB, COL1A1, LOX, TCF12, CASQ2, USH2A, DCLK1, MYH10

Annotation Cluster 2 Enrichment Score: 4.70

Count

P value ⁺

Genes

GO:0043062 ~ extracellular structure organization

11

7.37E-08

APP, PTK2, COL14A1, UTRN, MAP1B, COL12A1, FKBP1A, POSTN, COL1A1, LOX, COL5A1

GO:0030198 ~ extracellular matrix organization

9

5.04E-07

APP, PTK2, COL14A1, COL12A1, FKBP1A, POSTN, COL1A1, LOX, COL5A1

GO:0030199 ~ collagen fibril organization

5

7.49E-05

COL14A1, COL12A1, COL1A1, LOX, COL5A1

Annotation Cluster 3 Enrichment Score: 2.37

Count

P value ⁺

Genes

GO:0009605 ~ response to external stimulus

15

1.56E-04

MAP1B, ITGA2, IGF2, ENSA, COL5A1, ITGA6, SFRP2, ROBO1, CD59, SCARB1, VCAN, LOX, COL1A1, PROS1, MYH10

GO:0042060 ~ wound healing

8

2.23E-04

CD59, ITGA2, SCARB1, IGF2, LOX, PROS1, COL5A1, MYH10

GO:0009611 ~ response to wounding

10

0.0011093

CD59, MAP1B, ITGA2, VCAN, SCARB1, IGF2, LOX, PROS1, COL5A1, MYH10

GO:0051128 ~ regulation of cellular component organization

9

0.011086

PTK2, ROBO1, MAP1B, ITGA2, SCARB1, IGF2, COL5A1, MYH10, DSTN

GO:0050896 ~ response to stimulus

28

0.0134512

KERA, HUS1, TIPIN, FKBP1A, ENSA, GPX2, APP, ROBO1, PPP3CB, SCARB1, GNG2, LOX, FAM129A, USH2A, MAP1B, ITGA2, IGF2, COL5A1, ABCG2, ITGA6, SFRP2, CD59, SORT1, VCAN, COL1A1, TCF12, PROS1, MYH10

GO:0042221 ~ response to chemical stimulus

14

0.0284588

MAP1B, ITGA2, FKBP1A, IGF2, ENSA, ABCG2, GPX2, ROBO1, PPP3CB, SORT1, SCARB1, GNG2, LOX, COL1A1

Annotation Cluster 4 Enrichment Score: 2.26

Count

P value ⁺

Genes

GO:0006928 ~ cell motion

13

1.17E-05

ITGA2, ENPEP, COL5A1, DSTN, PTK2, APP, ITGA6, ROBO1, SCARB1, VCAN, DCLK1, THBS4, MYH10

GO:0016477 ~ cell migration

10

1.09E-04

PTK2, ITGA6, ROBO1, VCAN, SCARB1, ENPEP, COL5A1, DCLK1, MYH10, THBS4

GO:0007409 ~ axonogenesis

8

1.21E-04

APP, S100A6, PTK2, ROBO1, MAP1B, VCAN, DCLK1, MYH10

GO:0000904 ~ cell morphogenesis involved in differentiation

9

1.61E-04

APP, S100A6, PTK2, ROBO1, MAP1B, VCAN, ANTXR1, DCLK1, MYH10

GO:0048870 ~ cell motility

10

1.61E-04

PTK2, ITGA6, ROBO1, VCAN, SCARB1, ENPEP, COL5A1, DCLK1, MYH10, THBS4

GO:0051674 ~ localization of cell

10

1.64E-04

PTK2, ITGA6, ROBO1, VCAN, SCARB1, ENPEP, COL5A1, DCLK1, MYH10, THBS4

GO:0030154 ~ cell differentiation

22

2.12E-04

S100A6, EGFL6, UTRN, MAP1B, ITGA2, IGF2, GPM6B, REST, PTK2, APP, ITGA6, ROBO1, SFRP2, SEMA3E, S1PR5, PPP3CB, SORT1, VCAN, ANTXR1, COL1A1, DCLK1, MYH10

GO:0009653 ~ anatomical structure morphogenesis

20

2.24E-04

S100A6, MAP1B, ITGA2, FKBP1A, IGF2, ENPEP, COL5A1, DKK3, PTK2, APP, ITGA6, ROBO1, SFRP2, VCAN, ANTXR1, FBN2, COL1A1, MYOC, DCLK1, MYH10

GO:0048869 ~ cellular developmental process

22

3.88E-04

S100A6, EGFL6, UTRN, MAP1B, ITGA2, IGF2, GPM6B, REST, PTK2, APP, ITGA6, ROBO1, SFRP2, SEMA3E, S1PR5, PPP3CB, SORT1, VCAN, ANTXR1, COL1A1, DCLK1, MYH10

GO:0030030 ~ cell projection organization

10

5.27E-04

APP, S100A6, PTK2, ITGA6, ROBO1, MAP1B, VCAN, DCLK1, MYH10, THBS4

GO:0040011 ~ locomotion

10

5.63E-04

PTK2, ITGA6, ROBO1, VCAN, SCARB1, ENPEP, COL5A1, DCLK1, MYH10, THBS4

GO:0048858 ~ cell projection morphogenesis

8

5.68E-04

APP, S100A6, PTK2, ROBO1, MAP1B, VCAN, DCLK1, MYH10

GO:0032990 ~ cell part morphogenesis

8

9.16E-04

APP, S100A6, PTK2, ROBO1, MAP1B, VCAN, DCLK1, MYH10

GO:0000902 ~ cell morphogenesis

9

0.0013059

APP, S100A6, PTK2, ROBO1, MAP1B, VCAN, ANTXR1, DCLK1, MYH10

GO:0048699 ~ generation of neurons

10

0.0021025

APP, S100A6, PTK2, ROBO1, S1PR5, MAP1B, VCAN, REST, DCLK1, MYH10

GO:0048666 ~ neuron development

8

0.0025921

APP, S100A6, PTK2, ROBO1, MAP1B, VCAN, DCLK1, MYH10

GO:0022008 ~ neurogenesis

10

0.0031988

APP, S100A6, PTK2, ROBO1, S1PR5, MAP1B, VCAN, REST, DCLK1, MYH10

GO:0032989 ~ cellular component morphogenesis

9

0.0032876

APP, S100A6, PTK2, ROBO1, MAP1B, VCAN, ANTXR1, DCLK1, MYH10

GO:0045664 ~ regulation of neuron differentiation

5

0.0042345

PTK2, ROBO1, S1PR5, MAP1B, REST

GO:0007399 ~ nervous system development

13

0.0054731

S100A6, MAP1B, GPM6B, REST, PTK2, APP, ROBO1, S1PR5, SEMA3E, VCAN, CNTN3, DCLK1, MYH10

GO:0048468 ~ cell development

11

0.005626

APP, S100A6, PTK2, ROBO1, UTRN, MAP1B, PPP3CB, VCAN, ANTXR1, DCLK1, MYH10

GO:0030182 ~ neuron differentiation

8

0.0057725

APP, S100A6, PTK2, ROBO1, MAP1B, VCAN, DCLK1, MYH10

GO:0060284 ~ regulation of cell development

6

0.0067586

PTK2, ROBO1, S1PR5, MAP1B, IGF2, REST

GO:0050767 ~ regulation of neurogenesis

5

0.0122736

PTK2, ROBO1, S1PR5, MAP1B, REST

GO:0031344 ~ regulation of cell projection organization

4

0.0132242

PTK2, ROBO1, MAP1B, ITGA2

GO:0051960 ~ regulation of nervous system development

5

0.0177634

PTK2, ROBO1, S1PR5, MAP1B, REST

GO:0045595 ~ regulation of cell differentiation

8

0.0186936

PTK2, ROBO1, ITGAV, S1PR5, MAP1B, IGF2, REST, USH2A

GO:0022604 ~ regulation of cell morphogenesis

4

0.037216

PTK2, ROBO1, MAP1B, MYH10

GO:0050793 ~ regulation of developmental process

9

0.0379454

PTK2, ROBO1, ITGAV, S1PR5, MAP1B, IGF2, REST, USH2A, MYH10