Identification of potential key genes associated with glioblastoma based on the gene expression profile.

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The GSE31262 gene expression profile data, which included 9 glioblastoma stem cells (GSCs) samples and 5 neural stem cell samples from adult humans, were downloaded from Gene Expression Omnibus (GEO) database. limma package was used to identify differentially expressed genes (DEGs). Based on STRING database and Pearson Correlation Coefficient (PCC), a co-expression network was constructed to comprehensively understand the interactions between DEGs, and function analysis of genes in the network was conducted. Furthermore, the DEGs that were associated with prognosis were analyzed. A total of 431 DEGs were identified, including 98 upregulated DEGs and 333 downregulated DEGs. Genes including PDZ binding kinase, topoisomerase (DNA) II α (TOP2A), cyclin dependent kinase (CDK) 1, cell division cycle 6 and NIMA related kinase 2 had a relatively high degree in the co-expression network. A set of genes including cyclin D1, CDK1 and CDK2 were significantly enriched in the cell cycle and p53 signaling pathway. Additionally, 69 DEGs were identified as genes involved in glioblastoma prognosis, such as CDK2 and TOP2A. The genes that had a higher degree and were associated with cell cycle and p53 signaling pathway may play pivotal roles in the progress of glioblastoma.", "claims": [{"id": "claim-method", "statement": "Cox proportional hazard model (30,31) was utilized to predict the association of DEGs and patient prognosis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28789435", "locator": "sections[9] \"Analysis of DEGs associated with glioblastoma prognosis\" paragraph 3", "quote": "Cox proportional hazard model (30,31) was utilized to predict the association of DEGs and patient prognosis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mRNA expression profile dataset GSE31262 was downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/), which derived from 9 individual samples of GSCs and 5 individual samples of ahNSCs taken from the adult human brain (16).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28789435", "locator": "sections[4] \"Obtaining and preprocessing of mRNA expression profile data\" paragraph 2", "quote": "The mRNA expression profile dataset GSE31262 was downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/), which derived from 9 individual samples of GSCs and 5 individual samples of ahNSCs taken from the adult human brain (16)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using the limma package on GSE31262 expression data downloaded from the Gene Expression Omnibus (GEO) database, the study identified 431 DEGs in glioblastoma stem-cell samples, including 98 upregulated and 333 downregulated DEGs.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28789435", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The GSE31262 gene expression profile data, which included 9 glioblastoma stem cells (GSCs) samples and 5 neural stem cell samples from adult humans, were downloaded from Gene Expression Omnibus (GEO) database. limma package was used to identify differentially expressed genes (DEGs)."}, {"asset": "source:pmid:28789435", "locator": "sections[13] \"Identification of DEGs and hierarchical clustering analysis\" paragraph 2", "quote": "Based on the criteria of FDR <0.05 and |log2 FC| ≥1, a total of 431 DEGs were identified in the GSC samples, including 98 upregulated DEGs and 333 downregulated DEGs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using the limma package on GSE31262 expression data downloaded from the Gene Expression Omnibus (GEO) database, the study identified 431 DEGs in glioblastoma stem-cell samples, including 98 upregulated and 333 downregulated DEGs.", "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:28789435"], "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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