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Table 2 Enriched biological process GO terms (P < 0.01) obtained by the Gene Ontology Tree Machine (GOTM).

From: Pathway results from the chicken data set using GOTM, Pathway Studio and Ingenuity softwares

Enriched biological process GO terms

P < 0.01

Time effect

Species effect

Injection effect

organelle organization and biogenesis:

P = 0.005

   

ARPC3 KATNB1 DCTN6 KIF3A JMJD2A HDAC4 MTSS1

    

CBX3 ADRB2 TIMM8A GOLGB1 RHOA RHOB NEDD9 SPTBN5 PEX1 H2AFY2 FMN2 RHOJ

MM8-MM24

MM8-MA8

 

EP400 NSD1 SOX2 BRCA2 YWHAH DDX54 NOC4L ATG9A SUV39H2 SMC3 CDC42BPB

   

gluconeogenesis:

P = 0.008

   

ATF4 ACN9 TPI1

    

glutamine biosynthesis:

P = 0.005

   

GLUL CORO2A

    

nervous system development:

P = 0.005

MM8-MM24

  

SPON2 NCKAP1 CHRNA4 CNTF DAB1 TIMM8A EFNB1 NEUROG1 PAX5 RPS6KA3

    

YWHAH SEMA6D ST8SIA2 PARD6B LGI1 NOG CD9 ECE2 HDAC4 MTSS1

    

organelle organization and biogenesis:

P = 0.009

   

NSD1 L3MBTL DST NEDD9 SPTBN5 PFN2

  

MM8-MA8

 

pyruvate metabolism:

P = 0.001

   

ATF4 TPI1

    

G-protein signaling\, coupled to IP3 second messenger phospholipase C activating:

P = 0.008

   

NMUR1 DGKG P2RY4 AVPR1A DGKZ SPHK1

    

UDP-N-acetylglucosamine metabolism:

P = 0.006

   

UAP1 GNE

    

negative regulation of DNA replication:

P = 0.0009

  

MM8-PM8

ENPP7 S100A11 CDT1

    

endocytosis:

P = 0.0047

  

genes down-regulated

ADRB2 AP1B1 DOCK1 PACSIN3 PACSIN1 LRP6 NECAP2 ELMO3 SNX4

    

tissue development:

P = 0.004

   

APOA5 EDA ELF3 LAMB3 LAMC2 BMP4 SOX9 TFAP2A TGFB2 TUFT1

    

ectoderm development

P = 0.003

   

EDA ELF3 LAMB3 LAMC2 TFAP2A TGFB2

    

immune response-regulating signal transduction:

P = 0.003

   

FYN SPG21 PTPRC

    

caspase activation:

P = 0.004

   

DIABLO STAT1 CASP9 CASP8AP2

    

Golgi vesicle transport:

P = 0.006

   

SEC23A EXOC5 TMED2 COPE COPB1 SEC22A SAR1A MCFD2 COPB2 GOSR1

   

MM8-PM8

protein targeting to mitochondrion:

P = 0.008

  

genes up-regulated

TIMM44 TOMM34 TSPO GRPEL1

    

chromatin assembly or disassembly:

P = 0.002

   

CBX3 HMGB2 HP1BP3 HDAC8 SMARCE1 CHAF1B SMARCA5 TLK1

    

modification-dependent protein catabolism:

P = 0.008

   

FBXO21 RNF11 PSMA2 PSMA5 PSMB1 PSMB3 PSMC5 UBE2E1 UBE3A USP7 PSMF1 USP3

    

protein transport:

P = 0.002

   

34 genes

    
  1. For each set of data, the enriched biological processes found with GOTM analysis are listed, with their probability and representative genes.