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pmid:29921304
Identification of hub genes with prognostic values in gastric cancer by bioinformatics analysis.
Ting Li · Xujie Gao · Lei Han · Jinpu Yu · Hui Li
World journal of surgical oncology · 2018 doi:10.1186/s12957-018-1409-3
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Complete file
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To identify key genes in GC, mRNA microarray GSE27342, GSE29272, and GSE33335 were downloaded from GEO database.\nMETHODS: Differentially expressed genes (DEGs) were obtained using GEO2R. DAVID database was used to analyze function and pathways enrichment of DEGs. Protein-protein interaction (PPI) network was established by STRING and visualized by Cytoscape software. Then, the influence of hub genes on overall survival (OS) was performed by the Kaplan-Meier plotter online tool. Module analysis of the PPI network was performed using MCODE. Additionally, potential stem loop miRNAs of hub genes were predicted by miRecords and screened by TCGA dataset. Transcription factors (TFs) of hub genes were detected by NetworkAnalyst.\nRESULTS: In total, 67 DEGs were identified; upregulated DEGs were mainly enriched in biological process (BP) related to angiogenesis and extracellular matrix organization and the downregulated DEGs were mainly enriched in BP related to ion transport and response to bacterium. KEGG pathways analysis showed that the upregulated DEGs were enriched in ECM-receptor interaction and the downregulated DEGs were enriched in gastric acid secretion. A PPI network of DEGs was constructed, consisting of 43 nodes and 87 edges. Twelve genes were considered as hub genes owing to high degrees in the network. Hsa-miR-29c, hsa-miR-30c, hsa-miR-335, hsa-miR-33b, and hsa-miR-101 might play a crucial role in hub genes regulation. In addition, the transcription factors-hub genes pairs were displayed with 182 edges and 102 nodes. The high expression of 7 out of 12 hub genes was associated with worse OS, including COL4A1, VCAN, THBS2, TIMP1, COL1A2, SERPINH1, and COL6A3.\nCONCLUSIONS: The miRNA and TFs regulation network of hub genes in GC may promote understanding of the molecular mechanisms underlying the development of gastric cancer and provide potential targets for GC diagnosis and treatment.", "claims": [{"id": "claim-method", "statement": "DEG was obtained from GEO database by a way of GEO2R analysis (http://www.ncbi.nlm.nih.gov/geo/geo2r/). The adj. P < 0.05 and |logFC| > 1.5 were set as DEGs cutoff criterion.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29921304", "locator": "sections[3] \"Identification of DEGs\" paragraph 2", "quote": "DEG was obtained from GEO database by a way of GEO2R analysis (http://www.ncbi.nlm.nih.gov/geo/geo2r/). The adj. 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"reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[3]#Tab6", "version": null, "note": "Hub genes’ negatively correlated stem loop miRNAs in predicted miRNAs", "structure": {"pmcid": "PMC6009060", "section_index": 14, "section_title": "MiRNA-hub genes pairs", "row_count": 12, "column_count": 3}, "table": {"label": "Table 6", "caption": "Hub genes’ negatively correlated stem loop miRNAs in predicted miRNAs", "rows": [["Genes", "Negatively correlated stem loop miRNAs", "Total"], ["COL1A1", "hsa-miR-378 hsa-miR-29c hsa-miR-592 hsa-miR-30c hsa-miR-19a hsa-miR-18a hsa-miR-96 hsa-miR-802 hsa-miR-101 hsa-miR-182 hsa-miR-577 hsa-miR-335 hsa-miR-877 hsa-miR-130b hsa-miR-33b", "15"], ["COL1A2", "hsa-miR-7 hsa-miR-200c hsa-miR-19a hsa-miR-96 hsa-miR-200a hsa-miR-200b hsa-miR-429 hsa-miR-29c hsa-miR-130b hsa-miR-30c hsa-miR-182 hsa-miR-194 hsa-miR-301b hsa-miR-335 hsa-miR-577 hsa-miR-1304 hsa-miR-105 hsa-miR-196a hsa-miR-579 hsa-miR-9 hsa-miR-135b", "21"], 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hsa-miR-182 hsa-miR-222 hsa-miR-188-3p hsa-miR-192 hsa-miR-877 hsa-miR-29c hsa-miR-144 hsa-miR-200a hsa-miR-200c hsa-miR-200b hsa-miR-96 hsa-miR-19a hsa-miR-18a hsa-miR-378", "28"], ["SPP1", "hsa-miR-195 hsa-miR-101", "2"], ["THBS2", "hsa-miR-509 hsa-miR-504 hsa-miR-767 hsa-miR-579 hsa-miR-509 hsa-miR-135b hsa-miR-335 hsa-miR-196a hsa-miR-101 hsa-miR-33bhsa-miR-577 hsa-miR-802 hsa-miR-29c hsa-miR-222 hsa-miR-301b hsa-miR-188 hsa-miR-182 hsa-miR-30c hsa-miR-194 hsa-miR-877hsa-miR-192 hsa-miR-130b hsa-miR-206 hsa-miR-429 hsa-miR-96 hsa-miR-19a hsa-miR-200b hsa-miR-18a hsa-miR-486 hsa-miR-556 hsa-miR-592 hsa-miR-200c hsa-miR-144", "33"], ["VCAN", "hsa-mir-605 hsa-mir-135b hsa-mir-579 hsa-mir-33b hsa-mir-206 hsa-mir-192 hsa-mir-222 hsa-mir-200b hsa-mir-429 hsa-mir-200a hsa-mir-19a hsa-mir-144 hsa-mir-18a hsa-mir-200c", "14"]], "row_count": 12, "column_count": 3, "numeric_cells": 22, "header_rows": 1, "locator": "section[14]/table-wrap[3]#Tab6"}}, {"id": "asset:table:pmid:29921304:7", 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