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Table 2 Functional enrichment analysis of the DEGs in different transcriptomes by the DAVID functional annotation clustering tool

From: Transcriptomic analyses of regenerating adult feathers in chicken

Comparison

Tissue

Up-regulated

Representative annotation terms

Enrichment score

Genes

A

cEB vs. cLB

cEB

Translation

11.57

COG8, RPL22, HARS, RPL19, RPL10A, YARS, DENR, RPS14, RPS4, MRPL16, RPL13, MRPL23, RPL30, MRPL2, RPL18A, RPS8, RPL37A, RPSA, MRPL24, RPS15, EEF1D, RPLP1, RPL8, RPS7, RPL31, RPL17, MRPS12, RPLP0, RPS28

   

Oxidative phosphorylation

2.99

NDUFA2, UQCR11, NDUFA8, ATP5A1W, NDUFB6, NDUFS5, PPA1, COX4I1, NDUFAB1, UQCRQ, COX6A1, COX15, ATP5H, UQCR10, NDUFB3, NDUFA1, NDUFS6, COX8A, COX5A, ATP5O, UQCRH, COX6C, NDUFA11

   

Hydrogen ion transmembrane transporter activity

2.78

ATP5A1W, ATP5O, COX4I1, COX6C, COX5A, LOC770937, UQCRH, UQCRQ

   

Pyrimidine metabolism

1.61

NME2, ITPA, POLR2L, POLR2H, POLR1C, CANT1, POLR3H, RPB6

   

Contractile fiber part

1.37

MYL4, TNNC1, HSPB1, CRYAB

   

Ribosomal subunit

1.24

RPL19, RPS14, RPSA, RPS15, RPL17, MRPS12

   

Peptidyl-prolyl cis-trans isomerase activity

1.22

PPIB, FKBP25, FKBP1B

   

Inorganic cation transmembrane transporter activity

1.10

ATP5A1W, COX4I1, UQCRQ, UQCR10, RHBG, COX5A, ATP5O, UQCRH, COX6C

  

cLB

Amino acid transmembrane transporter activity

2.33

SLC38A2, SLC6A6, SLC7A5, SLC7A11

   

Transmembrane

1.72

ATP1B3, ELOVL6, ST8SIA5, BMPR2, EGFR, FZD10, GJA1, ITGA6, ITGAV, LAMP2, NRP1, SLC2A1, SLC38A2, SLC6A6, SLC7A5, SCD, TSPAN18, TFRC, TMEM41B, TYR

   

Lysosome

1.64

LAPTM5, CTSD, ARL8A, LAMP2

   

Tube development

1.43

SP3, NRP1, EPAS1, TP63, BMPR-II, BMPR1A

   

Enzyme linked receptor protein signaling pathway

1.33

SMAD5, MADH2, BMPR1A, NRP1, BMPR-II, EGFR

   

Carboxylic acid biosynthetic process

1.22

SCD, QKI, ELOVL6, CBS

   

Plasma membrane

1.15

LAPTM5, BMPR1A, ITGAV, TJP1, SLC2A1, SLC6A6, BMPR-II, SLC38A2, LAMP2, ITGA6, QKI, EGFR, GJA1, PANX1, DSC1

B

cEB vs. cEF

cEB

Translation

20.68

RPL22, HARS, RPL35, RPL19, MRPL17, RPL10A, RPL27, RPL26, YARS, DENR, RPS14, RPL6, RPS4, RPS24, MRPL16, EF1A, RPL27A, RPL13, MRPL23, MRPS11, RPL4, RPS27A, EIF3J, RPL30, MRPL2, RPL18A, RPS8, RPL14, RPSA, RPL3, MRPL24, RPL37, RPS15, EEF1D, RPLP1, RPL8, RPS7, RPL31, RPS3, MRPS12, RPLP0, RPS28, COG8, RPL17

   

Oxidative phosphorylation

3.83

NDUFA2, UQCR11, NDUFA8, ATP5A1W, NDUFB6, NDUFS5, COX4I1, NDUFAB1, COX6A1, COX15, ATP5H, UQCR10, NDUFB3, NDUFA1, NDUFB5, NDUFS6, COX5A, UQCRH, COX6C, ATP5B, ATP5G1, UQCRQ, COX7B, COX8A, ATP5O, NDUFA11

   

Ribosomal subunit

3.39

RPL19, RPL26, RPS14, RPS27A, RPSA, RPS15, RPS3, DAP3, MRPS12, RPL17

   

Pyrimidine metabolism

2.07

POLR2C, NME2, ITPA, POLR2L, POLR1D, POLR2H, POLR1C, CANT1, RPB6, POLR2I

   

Ubiquinol-cytochrome-c reductase activity

2.00

UQCRH, UQCR10, UQCRQ

   

RNA polymerase

1.36

POLR2H, RPB6, POLR1D, POLR2I, POLR1C, POLR2L, POLR2C

   

Transmembrance

2.76

ATP1A1, ATP1B3, EPHB6, FAT, GPR177, ST8SIA5, ACVR1, CXCR7, EGFR, FGFR2, FGFR3, FZD10,GJA1, ITGA6, ITGAV, LAMP2, LAPTM4A, PTPLAD1, SLC22A5, SLC16A9, SLC2A1, SLC26A5, SLC39A13, SLC6A6, SLC7A5, SCD, SDC3, TSPAN18, TMEM121, TMEM175, TMEM41B, TYR, TYRP1

  

cEF

Tissue morphogenesis

1.59

PRKAR1A, LMO4, TP63, TWSG1, JAG1, FGFR2, ACVR1, CA2

   

Regulation of ossification

1.58

SMAD5, JAG1, FGFR2, HIF1A, ACVR1, WNT7B

   

Ossification

1.28

SMAD5, TWSG1, FGFR2, MGP

   

Carboxylic acid transport

1.25

SLC7A5, SLC6A6, SLC7A11, PLIN2

   

Glycoprotein metabolic process

1.18

ST8SIA5, B3GNT5, B3GALNT1, HIF1A, B3GNT9

   

Transmembrane receptor protein serine/threonine kinase signaling pathway

1.13

SMAD5, TWSG1, ACVR1, MADH2

   

Enzyme linked receptor protein signaling pathway

1.13

EPHB6, JAK1, SMAD2, ACVR1, EGFR, FGFR2, FGFR3, RHOQ, SMAD5, TWSG1,

C

cEF vs. cMF

cEF

Skeletal system development

2.81

MGP, GLI1, WWOX, IGFBP5, GJA5, SHH, SOX14, SMAD1, CBFB

   

Signal peptide

2.29

KITLG, NELL2, ADCYAP1, AGRN, APOA1, CTSD, CHRNA4, CRH, FMOD, FZD10, FRZB, IGFBP2, MGP, MXRA8, NFASC, NPY, PON2, PLTP, SFRP2, SEMA3A, SILV, SHH, TTR, TSKU, TYR, TYRP1, KIT

   

Tube development

1.62

WNT5A, LMO4, LIPA, SHH, EDNRA, RARB, GJA5, CRH, GLI1

   

Melanin biosynthetic process

1.53

TYR, TYRP1, PMEL

   

Drug metabolism

1.48

GSTO1, GSTA, MGST2, ALDH3B1

   

Lytic vacuole

1.38

CTSD, NAGA, CTSL2, SLC48A1

   

Developmental protein

1.38

LFNG, BASP1, FZD10, FRZB, GLI1, MGP, MSX1, SFRP2, SEMA3A, SHH, TSKU, WNT2B, WNT5A

   

Regulation of transcription, DNA-dependent

1.26

PKNOX2, POU2F3, SMAD1, SMAD2, SOX10, SOX14, AGRN, CBFB, DLX6, FOXI3, GLI1, HMGA2, MED22, MSX1, RHOQ, RBBP7, RARB, LOC425662, IRX5, SHH, THRB, TCEA2, TFAP2B, MYCL1, MYCN

   

Respiratory tube development

1.23

WNT5A, LIPA, SHH, CRH, GLI1

  

cMF

Extracellular region

7.81

HBEGF, COL3A1, STC2, CTGF, SS2, FN1, MMP2, ANXA2, QSOX1, SPARC, LAMC2, ST6GAL1, DKK3, ADIPOQ, ADM, COL6A1, GPC4, COL6A2, JSC, CD44, MDK, CYR61, SERPINI1, COL1A2, EREG, THBS2, LUM, IGFBP7, APOLD1, EPDR1, PLA2G12A, INHBA, LGALS1, TIMP3, FBLN1, LAMA3, COL8A1, ADAMTS1, CD109, NOV, COL4A1, COL4A2, OSF-2, AVD, ENSGALG00000016682, ENSGALG00000011930

   

Carbohydrate binding

2.99

MRC2, HBEGF, CTGF, FN1, LAMC2, CD44, MDK, THBS2, CLEC3B, LGALS1, OSF-2

   

Signal peptide

2.62

CD3E, GFRA4, K123, TIMP3, CDH5, COL1A2, COL3A1, COL6A1, COL6A2, COL8A1, CTGF, CYR61, DKK3, FBLN1, INHBA, ITGA6, LEPREL1, LUM, MMP2, LOC769899, MDK, PTGS2, QSOX1, SPARC, SERPINI1, SDK2, NOV, THBS2

   

Cell adhesion

2.25

ITGB3, PPARD, CTGF, FN1, SDK2, CDH5, COL6A1, COL6A2, CD44, ITGA6, THBS2, EPDR1, COL8A1, EDIL3, OSF-2

   

Vasculature development

2.17

CTGF, PRRX1, MMP2, ANXA2, CDH5, CYR61, CAV1, COL1A2, EPAS1, MYH9

   

Collagen

2.12

ADIPOQ, COL1A2, COL3A1, COL4A1, COL6A1, COL6A2, COL8A1,

   

Phospholipid binding

1.50

ANXA1, ANXA2, ANXA5

   

Vascular smooth muscle contraction

1.85

ADRA1A, ITPR3, PLA2G4A, ACTG2, ARHGEF12, PLCB4, PLA2G12A, ITPR2, PLA2G10, RAMP2, PLA2G4C

   

Cell-substrate adhesion

1.40

ITGB3, PPARD, CTGF, FN1, ITGA6, EPDR1

   

Regulation of cell growth

1.34

CTGF, BCL6, CYR61, IGFBP7, INHBA, NOV

   

Cell surface

1.03

ITGB3, HSPB1, II, CD3E, CD44, MDK, ITGA6

D

cMF vs. cLF

cMF

Secondary metabolic process

2.33

PMEL, TYRP1, ALDOB, TYR

   

Organic acid transport

2.16

SLC6A6, CD36, PLIN2, OCA2

   

Signal peptide

1.53

C1ORF187, FZD10, GSN, LY75, LOC769899, MDK, NPY, OVM, PLTP, QSOX1, SOSTDC1, SILV, SHH, TYR, TYRP1, KIT

  

cLF

Extracellular region part

5.09

HBEGF, LAMB3, COL5A2, COL5A1, CTGF, FN1, SPARC, LAMC2, ADIPOQ, OSTN, LAMB1, THBS1, INHBA, LAMA3, COL12A1, COL4A1, OSF-2, MMP27, COL1A1, OVOS2

   

Structural molecule activity

3.43

LOC395532, COL4A1, COL5A1, COL5A2, COL7A1, LOC395906, NEFL, RPL36, LOC771066, THBS1

   

Blood vessel development

2.47

THY1, CDH2, CAV1, COL5A1, CTGF, THBS1

   

Glycoprotein

2.09

ST6GALNAC2, ST6GAL1, THY1, ADORA1, ALPL, LOC395532, CDH2, CHST3, ENSGALG00000015908, FN1, HSP90B1, INHBA, LAMB1, NTM, P4HA2, SPARC, SERPINH1, MOXD1

   

Regulation of cell migration

1.98

THY1, ADORA1, HBEGF, THBS1, LAMA3

   

Calcium binding

1.31

ACTN1, CDH2, CALM1, SPARC, TNNC1

   

Glycoprotein biosynthetic process

1.31

ST6GALNAC2, ST3GAL2, ST6GAL1, B3GNT2, GALNT1, CHST3

   

Cell adhesion

1.30

THY1, NTM, COL5A1, COL7A1,CTGF, FN1, LAMB1, THBS1, CDH2, DSG2, EDIL3, POSTN

   

Negative regulation of molecular function

1.26

THY1, ENSGALG00000014471, CAV1, HSPA5

   

Endoplasmic reticulum

1.22

HSPA5, MOXD1, ITPR3, ADIPOQ, P4HA2, THY1, CAV1, SERPINH1, HSP90B1, DUOXA1

   

Identical protein binding

1.20

TNNC1, HSPB1, ADIPOQ, INHBA, CAT, MTMR2

   

Regulation of cellular protein metabolic process

1.11

ADIPOQ, PACSIN3, CAV1, THBS1NN BDKRB2

  1. The genes were analyzed by the Functional Annotation Clustering Tool. The top annotation clusters that had group enrichment scores greater than 1 were listed. The representative biology terms associated with the top annotation clusters are manually summarized
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BMC Genomics

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