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

From: Longissimus dorsi transcriptome analysis of purebred and crossbred Iberian pigs differing in muscle characteristics

Annotation Cluster 1 Enrichment Score: 6.94 Count P value+ Genes
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
  1. +P-value from modified Fisher exact score.