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pmid:32575108
Bioinformatics-Based Study to Investigate Potential Differentially Expressed Genes and miRNAs in Pediatric Sepsis.
Kexin Xie · Shan Kong · Fuxing Li · Yulin Zhang · Jing Wang · Weidong Zhao
Medical science monitor : international medical journal of experimental and clinical research · 2020 doi:10.12659/MSM.923881
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Complete file
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Our understanding about the pathogenic mechanisms of sepsis is limited. The aim of this study was to identify the differential expression genes (DEGs) in pediatric sepsis through comprehensive analysis, and to provide specific insights for the clinical sepsis therapies in children. MATERIAL AND METHODS Three pediatric gene expression profiles (GSE25504, GSE26378, GSE26440) were downloaded from the Gene Expression Omnibus (GEO) database. The difference expression genes (DEGs) between pediatric sepsis and normal control group were screened with the GEO2R online tool. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the DEGs were performed. Cytoscape with CytoHubba were used to identify the hub genes. Finally, NetworkAnalyst was used to construct the targeted microRNAs (miRNAs) of the hub genes. RESULTS Totally, 160 overlapping upward genes and 61 downward genes were identified. In addition, 5 KEGG pathways, including hematopoietic cell lineage, Staphylococcus aureus infection, starch and sucrose metabolism, osteoclast differentiation, and tumor necrosis factor (TNF) signaling pathway, were significantly enriched using a database for labeling, visualization, and synthetic discovery. In combination with the results of the protein-protein interaction (PPI) network and CytoHubba, 9 hub genes including ITGAM, TLR8, IL1ß, MMP9, MPO, FPR2, ELANE, SPI1, and C3AR1 were selected. Combined with DEG-miRNAs visualization, 5 miRNAs, including has-miR-204-5p, has-miR-211-5p, has-miR-590-5p, and has-miR-21-5p, were predicted as possibly the key miRNAs. CONCLUSIONS Our findings will contribute to identification of potential biomarkers and novel strategies for pediatric sepsis treatment.", "claims": [{"id": "claim-method", "statement": "GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r) was applied to perform DEGs analysis between serum samples from pediatric sepsis and control groups, and corrected P-value calculations to obtain |logFC|.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32575108", "locator": "sections[4] \"Differentially expressed genes (DEGs) selection\" paragraph 2", "quote": "GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r) was applied to perform DEGs analysis between serum samples from pediatric sepsis and control groups, and corrected P-value calculations to obtain |logFC|."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Three microarray datasets (GSE25504, GSE26378, GSE26440) of pediatric sepsis and control samples were collected from the GEO database (https://www.ncbi.nlm.nih.gov/geo/) after a careful review.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32575108", "locator": "sections[3] \"Microarray data processing\" paragraph 2", "quote": "Three microarray datasets (GSE25504, GSE26378, GSE26440) of pediatric sepsis and control samples were collected from the GEO database (https://www.ncbi.nlm.nih.gov/geo/) after a careful review."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:32575108"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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