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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