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Table 1 Gene Ontology annotations of the differentially expressed hepatic genes with the Panther Classification Systema

From: Supplements of vitamins B9 and B12 affect hepatic and mammary gland gene expression profiles in lactating dairy cows

Treatment Gene symbol Gene name Treatment effect Molecular function Biological process Protein class
B9
DLK1 Delta-like 1 homolog (Drosophila) Down-regulated receptor activity
extracellular matrix structural constituent
receptor binding
transcription from RNA polymerase II promoter
cell communication
ectoderm development
nervous system development
intracellular protein transport
receptor-mediated endocytosis
regulation of transcription from RNA polymerase II promoter
membrane-bound signaling molecule
receptor
extracellular matrix structural protein
MYOM1 Myomesin-1 Down-regulated protein kinase activity
structural constituent of cytoskeleton
protein binding
small GTPase regulator activity
guanyl-nucleotide exchange factor activity
protein phosphorylation
cell communication
cell adhesion
muscle contraction
mesoderm development
muscle organ development
regulation of catalytic activity
non-receptor serine/threonine protein kinase
non-receptor serine/threonine protein kinase
guanyl-nucleotide exchange factor
actin family cytoskeletal protein
cell adhesion molecule
B12
HERC6 HECT and RLD domain containing E3 ubiquitin protein ligase family member 6 Up-regulated ligase activity catabolic process
cellular protein modification process
proteolysis
cellular process
ubiquitin-protein ligase
SESN2 Sestrin-2 Up-regulated oxidoreductase activity
peroxidase activity
metabolic process
cell cycle
Peroxidase
GPNMB glycoprotein (transmembrane) nmb Up-regulated receptor binding cellular process membrane-bound signaling molecule
cell adhesion molecule
IFI6 Interferon alpha-inducible protein 6 Up-regulated Unassigned Unassigned Unassigned
PPP1R3B Protein phosphatase 1 regulatory subunit 3B Up-regulated phosphatase activity
protein binding
phosphatase regulator activity
glycogen metabolic process
regulation of catalytic activity
phosphatase modulator
ID1 ID1 protein Up-regulated sequence-specific DNA binding transcription factor activity transcription from RNA polymerase II promoter
regulation of transcription from RNA polymerase II promoter
transcription factor
IFI27 interferon, alpha-inducible protein 27 Up-regulated Unassigned Unassigned Unassigned
MEP1B meprin A, beta Up-regulated oxidoreductase activity
serine-type peptidase activity
metallopeptidase activity
receptor activity
lipid transporter activity
transmembrane transporter activity
receptor binding
enzyme regulator activity
immune system process
proteolysis
synaptic transmission
cell-cell adhesion
visual perception
sensory perception
ectoderm development
mesoderm development
skeletal system development
angiogenesis
nervous system development
heart development
blood coagulation
lipid transport
intracellular protein transport
endocytosis
vitamin transport
regulation of catalytic activity
transporter
apolipoprotein
membrane-bound signaling molecule
receptor
metalloprotease
serine protease
oxidase
metalloprotease
serine protease
extracellular matrix protein
enzyme modulator
cell adhesion molecule
FUT5 fucosyltransferase 5 (alpha (1,3) fucosyltransferase Up-regulated transferase activity, transferring glycosyl groups protein glycosylation glycosyltransferase
G0S2 G0/G1switch 2 Up-regulated Unassigned Unassigned Unassigned
CDK5R1 Cyclin-dependent kinase 5 activator 1 Up-regulated kinase activity
protein binding
kinase activator activity
kinase regulator activity
protein phosphorylation
cell cycle
regulation of catalytic activity
kinase activator
ISG15 Ubiquitin-like protein ISG15 Up-regulated structural constituent of ribosome
nucleic acid binding
proteolysis ribosomal protein
 LOC515676 NFX1-type zinc finger-containing protein 1-like Up-regulated peptidase activity
protein binding
serine-type endopeptidase inhibitor activity
proteolysis
regulation of catalytic activity
serine protease inhibitor
SPP1 Osteopontin Up-regulated cytokine activity immune system process
cellular process
cell adhesion
cellular component morphogenesis
cellular component organization
cytokine
extracellular matrix protein
defense/immunity protein
cell adhesion molecule
DLK1 Delta-like 1 homolog (Drosophila) Down-regulated receptor activity
extracellular matrix structural constituent
receptor binding
transcription from RNA polymerase II promoter
cell communication
ectoderm development
nervous system development
intracellular protein transport
receptor-mediated endocytosis
regulation of transcription from RNA polymerase II promoter
membrane-bound signaling molecule
receptor
extracellular matrix structural protein
MYOM1 Myomesin-1 Down-regulated protein kinase activity
structural constituent of cytoskeleton
protein binding
small GTPase regulator activity
guanyl-nucleotide exchange factor activity
protein phosphorylation
cell communication
cell adhesion
muscle contraction
mesoderm development
muscle organ development
regulation of catalytic activity
non-receptor serine/threonine protein kinase
non-receptor serine/threonine protein kinase
guanyl-nucleotide exchange factor
actin family cytoskeletal protein
cell adhesion molecule
MT1E Metallothionein
MT1E
Down-regulated Unassigned Unassigned Unassigned
NEFH ortholog
Uncharacterized protein (Fragment)
NEFH
ortholog
Down-regulated Unassigned Unassigned Unassigned
SFRP1 Secreted frizzled-related protein 1 Down-regulated receptor activity
protein binding
reproduction
cell communication
single-multicellular organism process
nervous system development
response to stimulus
regulation of biological process
signaling molecule
G-protein coupled receptor
KIAA1324 KIAA1324 ortholog Down-regulated Unassigned Unassigned Unassigned
MGC126945 Uncharacterized protein Down-regulated receptor activity B cell mediated immunity
antigen processing and presentation
cellular defense response
immunoglobulin receptor superfamily
immunoglobulin receptor superfamily
major histocompatibility complex antigen
MT1A Metallothionein-1A
MT1A
Down-regulated Unassigned Unassigned Unassigned
B9 + B12
SAA3 Serum amyloid A protein Down-regulated lipid transporter activity
transmembrane transporter activity
immune system process
lipid transport
transporter
apolipoprotein
defense/immunity protein
 LOC100126815 MHC class I-like family A1 Down-regulated receptor activity B cell mediated immunity
antigen processing and presentation
cellular defense response
immunoglobulin receptor superfamily
immunoglobulin receptor superfamily
major histocompatibility complex antigen
ACMSD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase Down-regulated Unassigned Unassigned Unassigned
THRSP THRSP protein Down-regulated Unassigned Unassigned Unassigned
MGC126945 Uncharacterized protein Down-regulated receptor activity B cell mediated immunity
antigen processing and presentation
cellular defense response
immunoglobulin receptor superfamily
immunoglobulin receptor superfamily
major histocompatibility complex antigen
MT1A Metallothionein-1A
MT1A
Down-regulated Unassigned Unassigned Unassigned
C4H7orf57 chromosome 4 open reading frame, human C7orf57 Down-regulated Unassigned Unassigned Unassigned
CACNA2D1 calcium channel, voltage-dependent, alpha 2/delta subunit Down-regulated cation transmembrane transporter activity cation transport
protein targeting
Unassigned
GSTA5 Glutathione S-transferase Down-regulated Unassigned Unassigned Unassigned
 LOC509034 feline leukemia virus subgroup C receptor-related protein 2-like Down-regulated transmembrane transporter activity transport transporter
NHEDC1 solute carrier family 9, subfamily B (cation proton antiporter 2), member 1 Down-regulated Unassigned Unassigned Unassigned
SH3YL1 SH3 domain-containing YSC84-like protein 1 Down-regulated structural constituent of cytoskeleton
actin binding
cellular process non-motor actin binding protein
HP Haptoglobin Down-regulated serine-type peptidase activity
calcium ion binding
calmodulin binding
calcium-dependent phospholipid binding
gamete generation
complement activation
proteolysis
cellular process
blood circulation
response to stress
blood coagulation
serine protease
serine protease
complement component
annexin
calmodulin
NGEF neuronal guanine nucleotide exchange factor Down-regulated Unassigned Unassigned Unassigned
LGALS3 Lectin, galactoside-binding, soluble, 3 Up-regulated receptor binding cellular process signaling molecule
cell adhesion molecule
 LOC524810 IgM Up-regulated Unassigned Unassigned Unassigned
LOXL4 Lysyl oxidase homolog 4 Up-regulated oxidoreductase activity
serine-type peptidase activity
receptor activity
macrophage activation
apoptotic process
proteolysis
cell communication
cell-cell adhesion
neurological system process
cellular defense response
extracellular transport
negative regulation of apoptotic process
receptor
serine protease
oxidase
serine protease
PYCR1 Pyrroline-5-carboxylate reductase 1, mitochondrial Up-regulated oxidoreductase activity cellular amino acid biosynthetic process reductase
MSMB Uncharacterized protein Up-regulated hormone activity   peptide hormone
IGLL1 immunoglobulin lambda-like polypeptide 1 Up-regulated antigen binding B cell mediated immunity
hemopoiesis
response to stimulus
Immunoglobulin
MT1E Metallothionein
MT1E
Down-regulated Unassigned Unassigned Unassigned
GPNMB glycoprotein (transmembrane) nmb Up-regulated receptor binding cellular process membrane-bound signaling molecule
cell adhesion molecule
  1. All genes differentially expressed in liver were classified using the Gene Ontology annotations with the Panther Classification System. Some of these genes were not found by Panther genes list analysing system and some could not be classified. Only three ontology categories are presented: Molecular Function, Biological Process and Protein Class
  2. aPanther gene list classification system of the genes differentially expressed in hepatic tissue of cows receiving vitamin supplements (vitamin B9 alone: B9, vitamin B12 alone: B12 or both vitamins: B9 + B12) as compared to no vitamins treatment (Control)