Bioinformatics analysis of microarray data to reveal the pathogenesis of brain ischemia
Open accessAbstract
Brain ischemia leads to energy depletion, mitochondrial dysfunction and neuronal cell death. The present study was designed to identify key genes and pathways associated with brain ischemia. The gene expression profile GSE52001, including 3 normal brain samples and 3 cerebral ischemia samples, was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified using the limma package. Then functional and pathway enrichment analyses were performed by the MATHT tool. Protein‑protein interaction (PPI) network, module selection and microRNA (miRNA)‑target gene network were constructed utilizing Cytoscape software. A total of 488 DEGs were identified (including 281 upregulated and 207 downregulated genes). In the PPI network, Rac family small GTPase 2 (RAC2) had higher degrees. RAC2 was significantly enriched in the FcγR‑mediated phagocytosis pathway. miR‑29A/B/C had a higher degree in the miRNA‑target gene network. Insulin like growth factor 1 (Igf1) was identified as the target gene for miR‑29A/B/C. RAC2 may function in brain ischemia through mediating the FcγR‑mediated phagocytosis pathway. Meanwhile, miR‑29A/B/C and their targets gene Igf1 may serve important roles in the development and progression of brain ischemia.
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FcγR-mediated phagocytosis may be modulated by miR-29a/b/c, and Igf1 is a target gene for miR-29a/b/c.
“Interestingly, FcγR-mediated phagocytosis may also be modulated by miR-29a/b/c. Insulin like growth factor 1 (Igf1) was identified as the target gene for miR-29a/b/c”
From MicroRNAs as Regulators of Phagocytosis (2022) · cites this paper as [215]
The Discussion identifies Igf1 as a target gene regulated by miR-29A/B/C, although it says the relationship in brain ischemia has not been experimentally validated. It associates FcγR-mediated phagocytosis with RAC2, not miR-29A/B/C, so the proposed modulation of that pathway by miR-29A/B/C is unsupported. (LLM, conf=0.90)
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- Authors
- He, J., Gao, Y., Wu, G., Lei, X., Zhang, Y., Pan, W., & Yu, H.
- Affiliations
- Department of Anesthesia, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
- Second Affiliated Hospital of Xi'an Jiaotong University (CN)
- Corresponding author
- Gao, Ya
- Venue
- Molecular Medicine Reports
- Publisher
- Spandidos Publications
- Published
- 2018-05-09
- Volume
- 18
- Issue
- 1
- Pages
- 333-341
- ISSN
- 1791-2997 (ISSN-L)
- 1791-3004
- PMC
- PMC6059688
- OpenAlex
- W2802681141
- Cited by
- 11
- References
- 50
- Citations by year
- 2025: 1 · 2024: 1 · 2023: 1 · 2022: 1 · 2021: 2 · 2020: 2 · 2019: 2 · 2018: 1
- FWCI
- 0.62
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc-nd
- Locations
- Molecular Medicine Reports (publishedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- National Natural Science Foundation of China (81270435)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › MicroRNA in disease regulation
- Life Sciences › Neuroscience › Neurology › Neuroinflammation and Neurodegeneration Mechanisms
- Keywords
- cerebral ischemia, differentially expressed genes, Rac2, insulin-like growth factor I, protein-protein interaction network, gene expression profiling, pathogenesis
- MeSH terms
- RAC2 GTP-Binding Protein, Animals, Brain Ischemia, Gene Expression Regulation, Rats, Sprague-Dawley, Computational Biology, Oligonucleotide Array Sequence Analysis, rac GTP-Binding Proteins, Gene Expression Profiling, Databases, Genetic, MicroRNAs, Rats
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