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Table 2 Overrepresented GO terms from functional annotation clustering in DAVID corresponding to those categories of terms with enrichment fold greater than 3.0.

From: Transcription profiling provides insights into gene pathways involved in horn and scurs development in cattle

Contrast

Description of change

GO Term

Enriched gene category

Gene number

P-value

Genes

PvH

Genes down regulated in horned versus polled animals

GOTERM_BP_5

epidermis development

18

2.10E-12

COL17A1, KLK5, SPINK5, GJB5, KLK7, IVL, GRHL3, CALML5, KRT5, SPRR3, TCHH, LAMC2, DSP, KRT17, S100A7, LOR, BARX2, KRT10,

  

GOTERM_BP_5

striated muscle contraction

8

2.40E-07

MYOM2, SMPX, MYBPC1, MYH7, PGAM2, MYH2, KBTBD10, TTN

  

KEGG_PATHWAY

cell communication

16

2.20E-08

DSC1, KRT40, KRT33A, COL17A1, DSC3, KRT25, GJB5, GJB4, KRT23, KRT5, DSG1, LAMC2, KRT27, KRT17, GJA3, KRT10,

  

GOTERM_CC_5

intermediate filament

13

6.40E-06

KRT40, KRT33A, KRT25, KRTAP1-1, KRT23, KRTAP1-5, KRT5, KRT26, DSP, KRT27, KRT17, KRT10, PKP1

  

GOTERM_CC_5

cytoskeleton

41

1.00E-08

ACTN2, KRT40, DSC1, MYL1, PKP3, DSC3, LMOD2, MYH7, NEB, KRTAP1-1, KRT25, CSTA, MYH2, MYOZ2, KRT23, KRTAP1-5, SPRR3, KRT26, MYL3, KRT10, PKP1, KRT33A, ACTA1, KBTBD10, CGN, IVL, ELMOD1, DST, PDLIM3, MC1R, MYOM2, ELMO3, KRT5, MYBPC1, MYOT, SPTBN2, TCHH, KRT27, DSP, KRT17, LOR

  

GOTERM_CC_5

intercellular junctions

14

1.50E-07

DSC1, COL17A1, PKP3, DSC3, GJB5, CLDN8, CGN, GJB4, DST, CLDN23, DSG1, DSP, GJA3, PKP1

 

Genes upregulated in horned versus polled animals

GOTERM_CC_ALL

extracellular region

28

4.80E-11

GDF6, IGF1, PROC, ANG, DLK1, PTN, SCUBE1, FMOD, PLA2G7, CHI3L1, SPP2, CCL8, CP, HP, MASP1, SFRP4, SPON1, CFI, COL8A1, APOL3, CRLF1, PRSS2, PI15, FGG, FGF11, CCL19, TF, EPDR1

PvS

Genes down regulated in scurred versus polled animals

GOTERM_CC_5

intermediate filament cytoskeleton

11

7.50E-08

KRT40, KRT33A, KRT15, KRTAP1-5, KRTAP2-1, KRT85, NEFH, KRT26, KRTAP1-1, KRT25, KRT27

 

Genes upregulated in scurred versus polled animals

GOTERM_CC_5

fibrillar collagen

5

2.40E-07

COL1A2, COL5A2, LUM, COL1A1, COL5A1

  

GOTERM_BP_5

skeletal development

13

2.80E-08

COMP, PHEX, IBSP, DMP1, OSTN, ALX1, MEPE, COL1A2, SPP1, POSTN, SPP2, COL1A1, MMP9

  

KEGG_PATHWAY

ECM-receptor interaction

11

1.30E-08

TNC, LAMA1, TNN, COL1A2, COL5A2, SPP1, COL6A6, COL1A1, ITGA11, IBSP, COL5A1

  1. GO term = gene ontology term, BP = biological process, CC = cellular compartment, KEGG = Kyoto encyclopedia of genes and genomes, ECM = extracellular matrix, PvH = polled versus horned and PvS = Polled versus scurs. Down-regulated indicates genes that showing lower expression in one versus the other and up-regulated indicates genes showing higher normalised expression in one versus the other.
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