Identification of Critical Genes and Signaling Pathways in Human Monocytes Following High-Intensity Exercise
Abstract
:1. Introduction
2. Materials and Methods
2.1. Microarray Data
2.2. Microarray Data Pre-Processing
2.3. Screening Differentially Expressed Genes and Hierarchical Clustering Analysis
2.4. Enrichment Analyses of Differentially Expressed Genes
2.5. PPI Network and Module Analysis
2.6. TF Target Regulation Prediction
3. Results
3.1. Normalization and DEGs Screening
3.2. Enrichment Analyses of DEGs
3.3. PPI Network and Module Analysis
3.4. TF Target Regulation Prediction
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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GO-ID | Term | Gene Counts | p-Value |
---|---|---|---|
GO-BP terms | |||
GO:0070301 | cellular response to hydrogen peroxide | 6 | 2.81 × 10−5 |
GO:0006986 | response to unfolded protein | 5 | 1.35 × 10−4 |
GO:0008285 | negative regulation of cell proliferation | 10 | 8.43 × 10−4 |
GO:0071499 | cellular response to laminar fluid shear stress | 3 | 0.001058 |
GO:0051247 | positive regulation of protein metabolic process | 3 | 0.001058 |
GO-CC terms | |||
GO:0005634 | Nucleus | 52 | 6.68 × 10−5 |
GO:0043227 | membrane-bounded organelle | 67 | 0.00014 |
GO:0043231 | intracellular membrane-bounded organelle | 62 | 0.0009 |
GO:0005737 | Cytoplasm | 45 | 0.003735 |
GO:0005654 | Nucleoplasm | 26 | 0.017733 |
GO-MF terms | |||
GO:0051087 | chaperone binding | 6 | 1.70 × 10−4 |
GO:0005515 | protein binding | 75 | 3.58 × 10−4 |
GO:0003700 | transcription factor activity sequence-specific DNA binding | 16 | 0.001167 |
GO:0030544 | Hsp70 protein binding | 4 | 0.001208 |
GO:0043130 | ubiquitin binding | 5 | 0.001571 |
Pathway | ID | Gene Counts | p-Value | Genes |
---|---|---|---|---|
FoxO signaling pathway | hsa04068 | 5 | 1.69 × 10−5 | PLK2, CDKN1B, TNFSF10, GABARAPL1, KLF2 |
Protein processing in endoplasmic reticulum | hsa04141 | 5 | 4.75 × 10−5 | DNAJB1, PLAA, DNAJA1, HERPUD1, HSPH1 |
Influenza A | hsa05164 | 5 | 5.02 × 10−5 | DNAJB1, TNFSF10, NXT1, SOCS3, TNF |
ErbB signaling pathway | hsa04012 | 4 | 5.46 × 10−5 | CDKN1B, EREG, HBEGF, AREG |
MAPK signaling pathway | hsa04010 | 6 | 7.17 × 10−5 | AREG, NR4A1, TNF, MAPK7, DUSP2, EREG |
MicroRNAs in cancer | hsa05206 | 6 | 7.71 × 10−5 | DDIT4, CDKN1B, MAPK7, CYP1B1, mir-223, MCL1 |
Parathyroid hormone synthesis, secretion and action | hsa04928 | 4 | 0.000124 | NR4A2, HBEGF, PDE4B, GNA13 |
PI3K-Akt signaling pathway | hsa04151 | 6 | 0.00019 | AREG, DDIT4, CDKN1B, NR4A1, MCL1, EREG |
Pathways in cancer | hsa05200 | 7 | 0.000249 | PIM2, CDKN1B, CXCR4, RASSF5, CKS1B, GNA13, CKS2 |
Adipocytokine signaling pathway | hsa04920 | 3 | 0.000619 | TNF, SOCS3, CD36 |
Epstein–Barr virus infection | hsa05169 | 4 | 0.001303 | CDKN1B, TNF, TNFAIP3, RUNX3 |
IL-17 signaling pathway | hsa04657 | 3 | 0.001425 | TNF, MAPK7, TNFAIP3 |
Small-cell lung cancer | hsa05222 | 3 | 0.001425 | CDKN1B, CKS1B, CKS2 |
Viral protein interaction with cytokine and cytokine receptor | hsa04061 | 3 | 0.001744 | TNFSF10, TNF, CXCR4 |
Glycosylphosphatidylinositol (GPI)-anchor biosynthesis | hsa00563 | 2 | 0.001751 | PIGM, PIGW |
Gene Symbol | Gene Description | Degree |
---|---|---|
TNF | Tumor necrosis factor | 56 |
DUSP1 | Dual-specificity protein phosphatase 1 | 47 |
ATF3 | Cyclic AMP-dependent transcription factor ATF-3 | 47 |
CXCR4 | C-X-C chemokine receptor type 4 | 40 |
NR4A1 | Nuclear receptor subfamily 4 group A member 1 | 37 |
BHLHE40 | Class E basic helix-loop-helix protein 40 | 35 |
CDKN1B | Cyclin-dependent kinase inhibitor 1B | 34 |
SOCS3 | Suppressor of cytokine signaling 3 | 34 |
TNFAIP3 | Tumor necrosis factor alpha-induced protein 3 | 31 |
MCL1 | Induced myeloid leukemia cell differentiation protein Mcl-1 | 31 |
GO-ID | Term | Gene Counts | p-Value |
---|---|---|---|
GO-BP terms | |||
GO:0048523 | negative regulation of cellular process | 20 | 3.59 × 10−9 |
GO:0031324 | negative regulation of cellular metabolic process | 16 | 2.26 × 10−8 |
GO:0010604 | positive regulation of macromolecule metabolic process | 17 | 2.77 × 10−8 |
GO:0009968 | negative regulation of signal transduction | 12 | 7.14 × 10−8 |
GO:0051172 | negative regulation of nitrogen compound metabolic process | 15 | 7.14 × 10−8 |
GO-CC terms | |||
GO:0005634 | Nucleus | 16 | 0.0185 |
GO:0044428 | nuclear part | 12 | 0.0337 |
GO-MF terms | |||
GO:0000977 | RNA polymerase II regulatory region sequence-specific DNA binding | 9 | 7.56 × 10−7 |
GO:0001012 | RNA polymerase II regulatory region DNA binding | 9 | 7.56 × 10−7 |
GO:0044212 | transcription regulatory region DNA binding | 10 | 7.56 × 10−7 |
GO:0043565 | sequence-specific DNA binding | 10 | 9.79 × 10−7 |
GO:0003677 | DNA binding | 13 | 2.79 × 10−6 |
Pathway | ID | Gene Counts | p-Value | Genes |
---|---|---|---|---|
MAPK signaling pathway | hsa04010 | 5 | 7.84 × 10−8 | AREG, NR4A1, MAPK7, TNF, DUSP2 |
IL-17 signaling pathway | hsa04657 | 3 | 6.23 × 10−6 | TNF, MAPK7, TNFAIP3 |
TNF signaling pathway | hsa04668 | 3 | 1.07 × 10−5 | TNF, TNFAIP3, SOCS3 |
Osteoclast differentiation | hsa04380 | 3 | 1.58 × 10−5 | TNF, SOCS3, FOSL2 |
Apoptosis | hsa04210 | 3 | 1.89 × 10−5 | TNFSF10, MCL1, TNF |
Fluid shear stress and atherosclerosis | hsa05418 | 3 | 2.01 × 10−5 | TNF, KLF2, MAPK7 |
Necroptosis | hsa04217 | 3 | 3.15 × 10−5 | TNFSF10, TNF, TNFAIP3 |
Influenza A | hsa05164 | 3 | 3.45 × 10−5 | TNFSF10, TNF, SOCS3 |
Epstein–Barr virus infection | hsa05169 | 3 | 5.92 × 10−5 | RUNX3, TNF, TNFAIP3 |
Type 2 diabetes mellitus | hsa04930 | 2 | 0.000148 | TNF, SOCS3 |
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Li, P.; Luo, L. Identification of Critical Genes and Signaling Pathways in Human Monocytes Following High-Intensity Exercise. Healthcare 2021, 9, 618. https://doi.org/10.3390/healthcare9060618
Li P, Luo L. Identification of Critical Genes and Signaling Pathways in Human Monocytes Following High-Intensity Exercise. Healthcare. 2021; 9(6):618. https://doi.org/10.3390/healthcare9060618
Chicago/Turabian StyleLi, Pengda, and Li Luo. 2021. "Identification of Critical Genes and Signaling Pathways in Human Monocytes Following High-Intensity Exercise" Healthcare 9, no. 6: 618. https://doi.org/10.3390/healthcare9060618