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Table 2 Identification of the major biological processes of the genes differentially expressed in hepatic tissuea

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

Biological process Genes
Level 1 Level 2/3 Symbol Fold Change
apoptotic process negative regulation of apoptotic process LOXL4 1.6
biological adhesion cell adhesion MYOM1
SPP1
MEP1B
LOXL4
−2.5
0.9
1.3
1.6
biological regulation regulation of biological process DLK1
SFRP1
ID1
LOXL4
−2.5
−1.8
1.1
1.6
  regulation of molecular function MYOM1
CDK5R1
PPP1R3B
MEP1B
LOC515676
−2.5
0.8
1.1
1.3
1.9
cellular component organization or biogenesis cellular component organization SPP1 0.9
cellular process cell communication DLK1
MYOM1
SFRP1
MEP1B
LOXL4
−2.5
−2.5
−1.8
1.3
1.6
cell cycle CDK5R1
SESN2
0.8
0.9
developmental process anatomical structure morphogenesis SPP1 0.9
death LOXL4 1.6
ectoderm development DLK1
MEP1B
−2.5
1.3
mesoderm development MYOM1
MEP1B
−2.5
1.3
system development DLK1
MYOM1
SFRP1
MEP1B
IGLL1
−2.5
−2.5
−1.8
1.3
2.1
immune system process antigen processing and presentation LOC100126815
MGC126945
−2.4
−1.8
immune response LOC100126815
MGC126945
HP
IGLL1
−2.4
−1.8
−1.6
2.1
macrophage activation LOXL4 1.6
localization transport DLK1
LOC509034
SAA3
CACNA2D1
MEP1B
LOXL4
−2.5
−1.5
−1.1
−1.0
1.3
1.6
metabolic process catabolic process HERC6 1.8
carbohydrate metabolic process PPP1R3B 1.1
cellular amino acid metabolic process PYCR1 1.5
nucleobase-containing compound metabolic process DLK1
ID1
−2.5
1.1
protein metabolic process MYOM1
HP
CDK5R1
MEP1B
LOXL4
FUT5
HERC6
LOC515676
ISG15
−2.5
−1.6
0.8
1.3
1.6
1.6
1.8
1.9
2.5
multicellular organismal process single-multicellular organism process MYOM1
SFRP1
HP
MEP1B
LOXL4
−2.5
−1.8
−1.6
1.3
1.6
reproduction gamete generation HP −1.6
response to stimulus cellular defense response LOC100126815
MGC126945
LOXL4
−2.4
−1.8
1.6
immune response LOC100126815
MGC126945
HP
IGLL1
−2.4
−1.8
−1.6
2.1
response to external stimulus HP
MEP1B
−1.6
1.3
response to stress HP −1.6
Not found   C20H5orf49 LOC789904
SLC22A9
CFH
SLC26A10
SAA2
M-SAA3
LOC100847494
LOC100335975
LOC617654
−1.9
−1.8
−1.7
−1.5
−1.4
−1.2
−1.1
−0.9
1.4
4.2
Unassigned C4H7orf57
MT1E
MT1A
THRSP
KIAA1324
NGEF
GSTA5
ACMSD
NHEDC1
NEFH
G0S2
LOC524810
IFI27
IFI6
−4.4
−3.4
−3.3
−1.7
−1.6
−1.4
−1.3
−1.2
−1.1
−1.1
1.9
2.6
3.3
3.7
  1. All genes modulated in the liver by the vitamins treatment, including those that were not found or classified by the Panther system are listed. The fold change observed by microarray analysis varies from −4.4 to 4.2 and only significantly (FDR ≤ 0.05) expressed genes (compared to control) are shown
  2. aIdentification of the major biological processes 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)