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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)