Integrated Analysis of Expression Profile Based on Differentially Expressed Genes in Middle Cerebral Artery Occlusion Animal Models
Abstract
:1. Introduction
2. Results
2.1. Microarray Data Search and Data Preprocessing
2.1.1. Microarray Data Search
2.1.2. Data Preprocessing
2.2. Meta-Analysis
2.2.1. Mus Function Annotation and Pathway Enrichment Analysis
2.2.2. Rat Function Annotation and Pathway Enrichment Analysis
2.3. Differential Expression Analysis in Each Study
2.4. Integrated Analysis
3. Discussion
4. Materials and Methods
4.1. Microarray Data Search
4.2. Included and Excluded Criteria
4.3. Data Preprocessing
4.4. Meta-Analysis
4.5. Differential Expression Analysis in Each Study
4.6. Integrated Analysis
4.7. Functional Annotation
5. Conclusions
Acknowledgments
Author Contributions
Conflicts of Interest
Abbreviations
GO | Gene ontology |
DEGs | Differentially expressed genes |
ROS | Reactive oxygen species |
CNS | Central neural system |
RLE | Relative log expression |
NUSE | Normalized unscaled standard errors |
KNN | k-nearest neighbors |
DAVID | Database for Annotation, Visualization and Integrated Discovery |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
PPI | Protein-protein interaction |
NGAL | Neutrophil gelatinase-associated lipocalin |
MCAO | Middle cerebral artery occlusion |
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Series Dataset | Ischemic Period (min) | Reperfusion Period (h) | No. of Samples | Platform | |
---|---|---|---|---|---|
MCAO | Sham | ||||
Mus musculus | |||||
E-MEXP-2547 [8] | 30 | 24, 240 | 5 | 5 | Affymetrix GeneChip Mouse Gene 1.0 ST Array |
GSE23160 [9] | 120 | 2, 8, 24 | 24 | 8 | Illumina MouseRef-8 v2.0 expression beadchip |
GSE30655 [10] | 60 | 24 | 7 | 3 | Affymetrix Mouse Genome 430 2.0 Array |
GSE58720 [11] | 90 | 24 | 3 | 3 | Agilent-028005 SurePrint G3 Mouse GE 8 × 60 K Microarray |
Rattus norvegicus | |||||
E-MEXP-2222 [12] | 90 | 6, 24 | 12 | 3 | Affymetrix Rat Genome 230 2.0 Array |
GSE33725 [13] | NA | 2, 6 | 6 | 6 | Agilent-014879 Whole Rat Genome Microarray 4 × 44 K G4131F |
GSE52001 [14] | 120 | 144 | 3 | 3 | Agilent-028282 Whole Rat Genome Microarray 4 × 44 K v3 |
GSE61616 [15] | 120 | 168 | 5 | 5 | Affymetrix Rat Genome 230 2.0 Array |
GO ID | GO Term | % | p-Value |
---|---|---|---|
Biological Process | |||
GO:0002237 | response to molecule of bacterial origin | 1.67 | 2.10 × 10−3 |
GO:0032655 | regulation of interleukin-12 production | 1.11 | 2.46 × 10−3 |
GO:0043086 | negative regulation of catalytic activity | 2.22 | 2.78 × 10−3 |
GO:0010033 | response to organic substance | 5.56 | 2.92 × 10−3 |
GO:0044092 | negative regulation of molecular | 2.50 | 3.28 × 10−3 |
Cellular Component | |||
GO:0044445 | cytosolic part | 1.67 | 5.75 × 10−3 |
GO:0031974 | membrane-enclosed lumen | 8.89 | 2.27 × 10−2 |
GO:0005829 | cytosol | 5.00 | 2.33 × 10−2 |
GO:0005886 | plasma membrane | 18.61 | 2.59 × 10−2 |
GO:0005938 | cell cortex | 1.94 | 2.78 × 10−2 |
Molecular Function | |||
GO:0005509 | calcium ion binding | 7.50 | 1.03 × 10−2 |
GO:0019838 | growth factor binding | 1.67 | 1.21 × 10−2 |
GO:0043167 | ion binding | 25.28 | 2.49 × 10−2 |
GO:0046872 | metal ion binding | 24.72 | 2.75 × 10−2 |
GO:0003677 | DNA binding | 12.78 | 2.92 × 10−2 |
ID | Term | % | p-Value |
---|---|---|---|
Mus musculus | |||
mmu04010 | MAPK signaling pathway | 4.72 | 8.14 × 10−5 |
mmu04060 | Cytokine-cytokine receptor interaction | 3.06 | 2.65 × 10−2 |
mmu04062 | Chemokine signaling pathway | 2.50 | 3.18 × 10−2 |
mmu04722 | Neurotrophin signaling pathway | 1.94 | 4.90 × 10−2 |
mmu05410 | Hypertrophic cardiomyopathy (HCM) | 1.39 | 9.16 × 10−2 |
Rattus norvegicus | |||
rno04730 | Long-term depression | 2.77 | 1.44 × 10−6 |
rno04010 | MAPK signaling pathway | 5.14 | 1.52 × 10−6 |
rno04070 | Phosphatidylinositol signaling system | 2.37 | 1.82 × 10−6 |
rno04540 | Gap junction | 2.37 | 2.29 × 10−6 |
rno04670 | Leukocyte transendothelial migration | 2.77 | 3.29 × 10−6 |
GO ID | GO Term | % | p-Value |
---|---|---|---|
Biological Process | |||
GO:0009611 | response to wounding | 9.49 | 1.91 × 10−7 |
GO:0022604 | regulation of cell morphogenesis | 4.74 | 5.44 × 10−6 |
GO:0006954 | inflammatory response | 5.53 | 3.57 × 10−5 |
GO:0006813 | potassium ion transport | 4.35 | 7.65 × 10−5 |
GO:0006811 | ion transport | 9.88 | 1.16 × 10−4 |
Cellular Component | |||
GO:0044456 | synapse part | 6.72 | 1.44 × 10−6 |
GO:0005886 | plasma membrane | 24.90 | 1.52 × 10−6 |
GO:0043005 | neuron projection | 8.70 | 1.82 × 10−6 |
GO:0005856 | cytoskeleton | 13.44 | 2.29 × 10−6 |
GO:0045202 | synapse | 7.91 | 3.29 × 10−6 |
Molecular Function | |||
GO:0005509 | calcium ion binding | 9.49 | 5.33 × 10−5 |
GO:0005216 | ion channel activity | 6.32 | 6.73 × 10−5 |
GO:0043167 | ion binding | 25.30 | 8.37 × 10−5 |
GO:0022838 | substrate specific channel activity | 6.32 | 9.35 × 10−5 |
GO:0022836 | gated channel activity | 5.53 | 9.48 × 10−5 |
Study | Count | Up-Regulated | Down-Regulated |
---|---|---|---|
Mus musculus | |||
E-MEXP-2547 | 179 | 179 | 0 |
GSE23160 | 22 | 22 | 0 |
GSE30655 | 341 | 128 | 213 |
GSE58720 | 1162 | 841 | 321 |
Rattus norvegicus | |||
E-MEXP-2222 | 83 | 81 | 2 |
GSE33725 | 38 | 38 | 0 |
GSE52001 | 94 | 66 | 28 |
GSE61616 | 827 | 695 | 132 |
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Zhou, H.; Qiu, Z.; Gao, S.; Chen, Q.; Li, S.; Tan, W.; Liu, X.; Wang, Z. Integrated Analysis of Expression Profile Based on Differentially Expressed Genes in Middle Cerebral Artery Occlusion Animal Models. Int. J. Mol. Sci. 2016, 17, 776. https://doi.org/10.3390/ijms17050776
Zhou H, Qiu Z, Gao S, Chen Q, Li S, Tan W, Liu X, Wang Z. Integrated Analysis of Expression Profile Based on Differentially Expressed Genes in Middle Cerebral Artery Occlusion Animal Models. International Journal of Molecular Sciences. 2016; 17(5):776. https://doi.org/10.3390/ijms17050776
Chicago/Turabian StyleZhou, Huaqiang, Zeting Qiu, Shaowei Gao, Qinchang Chen, Si Li, Wulin Tan, Xiaochen Liu, and Zhongxing Wang. 2016. "Integrated Analysis of Expression Profile Based on Differentially Expressed Genes in Middle Cerebral Artery Occlusion Animal Models" International Journal of Molecular Sciences 17, no. 5: 776. https://doi.org/10.3390/ijms17050776
APA StyleZhou, H., Qiu, Z., Gao, S., Chen, Q., Li, S., Tan, W., Liu, X., & Wang, Z. (2016). Integrated Analysis of Expression Profile Based on Differentially Expressed Genes in Middle Cerebral Artery Occlusion Animal Models. International Journal of Molecular Sciences, 17(5), 776. https://doi.org/10.3390/ijms17050776