Table 4 Functional clustering of differentially expressed genes between ICSI BCB+ and ICSI BCB−; mICSI BCB− and ICSI BCB−; and mICSI BCB− and ICSI BCB+ blastocysts following unpaired t-tests, with FC > 2 (abs) and significance of p < 0.01.

From: Restoration of normal embryogenesis by mitochondrial supplementation in pig oocytes exhibiting mitochondrial DNA deficiency

Clustering of differentially expressed genes (T-Test, p value < 0.01, abs. FC > 2)

Top Diseases and Functions

Network(s)

Predicted upstream Regulator

Molecule Type

Regulation

Activation z-score (abs. Fold-change > 1.5)

p-value of overlap (p < 0.05)

ICSI BCB − vs ICSI BCB + blastocysts

 BAG3, CCBL1, CGREF1, CREM, EDN1, FAM73A, JUN, KLF5, OXNAD1, PITPNB, SMN1/SMN2

Cellular Assembly and Organization, Cellular Function and Maintenance, Cell Death and Survival

Supp. Figs 7, 8, 9, 12, 17 and 18

CREB1

transcription regulator

Activation

2.617

1.57E-03

 BCAT2, EDN1, EPHX2, JUN, MXD3, PGK1, PRDX2, SMTN, SPINT1, UCK1

Cancer, Cellular Movement, Organismal Development

Supp. Figs 7, 8 and 18

ERBB2

kinase

Activation

2.236

1.51E-02

 EDN1, JUN, KLF5, SRF

Inflammatory Disease, Inflammatory Response, Organismal Injury and Abnormalities

Supp. Figs 7, 12 and 18

lysophosphatidic acid

chemical - other

Activation

1.958

2.04E-03

 CALU, CELF2, CERS4, EPHX2, JUN, LARGE, LTBP1, VAV3

Cancer, Cellular Movement, Organismal Development

Supp. Fig. 7

FOS

transcription regulator

Activation

1.698

3.59E-02

 AEBP1, EDN1, JUN, PGK1, PTPN11, SLC25A11

Cell Morphology, Cellular Assembly and Organization, Cellular Function and Maintenance

Supp. Figs 8 and 18

Insulin

hormone

Activation

1.513

3.02E-02

 EDN1, JUN, MIOX, PRDX2

Cell To Cell Signaling and Interaction, Reproductive System Development and Function, Cell Signaling

Supp. Fig. 16

N-acetyl-L-cysteine

chemical drug

Inhibition

−1.941

5.0E-02

mICSI BCB − vs ICSI BCB − blastocysts

 CCND2, EDN1, IL18, TRAF2

Cellular Development, Cellular Growth and Proliferation, Hematological System Development and Function

Supp. Figs 8, 12, 17 and 18

Resveratrol

Chemical drug

Activation

1.954

1.19E-02

 CCND2, CGREF1, EDN1, IL18, TRAF2

Cellular Development, Cellular Growth and Proliferation, Hematological System Development and Function

Supp. Figs 7, 8, 12, 17 and 18

NFkB (complex)

Complex

Inhibition

−2.208

3.62E-02

 CCND2, LIMK2, NABP1, UPB1

Cellular Movement, Hematological System Development and Function, Immune Cell Trafficking

Supp. Figs 11 and 16

IL5

Cytokine

Inhibition

−2.000

9.57E-03

mICSI BCB − vs ICSI BCB + blastocysts

 ATF4, CLDN7, CYTH2, DDIT4, FTH1, LDHB, MCL1, SMN1/SMN2, TP53I3, UBE2S

Lipid Metabolism, Small Molecule Biochemistry, Vitamin and Mineral Metabolism

Not displayed

MYC

Transcription regulator

Activation

2.156

3.13E-02

 AP2A2, ATF4, DPM3, LRRFIP1

Cellular Compromise, Infectious Disease, Drug Metabolism

Supp. Fig. 7

STAT4

Transcription regulator

Activation

2

4.01E-02

 ADIPOR2, FABP3, MIOX, STUB1

Carbohydrate Metabolism, Cell Cycle, Developmental Disorder

Supp. Fig. 16

Streptozocin

Chemical drug

Activation

1.98

3.46E-02

  1. DEGs were clustered according to their predicted upstream regulators based on prior knowledge of expected regulation from the Ingenuity® Knowledge Base.
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