Bioinformatics analysis of differentially expressed pathways related to the metastatic characteristics of osteosarcoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27353415", "kind": "science-record", "revision": 8, "content_hash": "sha256:c2f6195ea9b19de4c5d2a3b4b0d2be995afa2d5265b1dfc5ca58cf5ef0f22140", "created_at": "2026-11-01T15:40:18Z", "updated_at": "2026-11-01T21:59:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis of differentially expressed pathways related to the metastatic characteristics of osteosarcoma.", "doi": "10.3892/ijmm.2016.2657", "pmid": "27353415", "authors": ["Wei Sun", "Xiaojun Ma", "Jiakang Shen", "Fei Yin", "Chongren Wang", "Zhengdong Cai"], "journal": "International journal of molecular medicine", "year": 2016, "abstract": "In this study, gene expression data of osteosarcoma (OSA) were analyzed to identify metastasis-related biological pathways. Four gene expression data sets (GSE21257, GSE9508, GSE49003 and GSE66673) were downloaded from Gene Expression Omnibus (GEO). An analysis of differentially expressed genes (DEGs) was performed using the Significance Analysis of Microarray (SAM) method. Gene expression levels were converted into scores of pathways by the Functional Analysis of Individual Microarray Expression (FAIME) algorithm and the differentially expressed pathways (DEPs) were then disclosed by a t-test. The distinguishing and prediction ability of the DEPs for metastatic and non-metastatic OSA was further confirmed using the principal component analysis (PCA) method and 3 gene expression data sets (GSE9508, GSE49003 and GSE66673) based on the support vector machines (SVM) model. A total of 616 downregulated and 681 upregulated genes were identified in the data set, GSE21257. The DEGs could not be used to distinguish metastatic OSA from non-metastatic OSA, as shown by PCA. Thus, an analysis of DEPs was further performed, resulting in 14 DEPs, such as NRAS signaling, Toll-like receptor (TLR) signaling, matrix metalloproteinase (MMP) regulation of cytokines and tumor necrosis factor receptor-associated factor (TRAF)-mediated interferon regulatory factor 7 (IRF7) activation. Cluster analysis indicated that these pathways could be used to distinguish between metastatic OSA from non-metastatic OSA. The prediction accuracy was 91, 66.7 and 87.5% for the data sets, GSE9508, GSE49003 and GSE66673, respectively. The results of PCA further validated that the DEPs could be used to distinguish metastatic OSA from non-metastatic OSA. On the whole, several DEPs were identified in metastatic OSA compared with non-metastatic OSA. Further studies on these pathways and relevant genes may help to enhance our understanding of the molecular mechanisms underlying metastasis and may thus aid in the development of novel therapies.", "claims": [{"id": "claim-method", "statement": "Following normalization and log2 transformation, differential analysis was performed using the significance analysis of microarray (SAM) method based on the t-test, as previously described (21).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27353415", "locator": "sections[4] \"Data pre-processing and differential analysis of GSE21257\" paragraph 3", "quote": "Following normalization and log2 transformation, differential analysis was performed using the significance analysis of microarray (SAM) method based on the t-test, as previously described (21)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Four gene expression data sets (GSE21257, GSE9508, GSE49003 and GSE66673) were downloaded from Gene Expression Omnibus (GEO). Data set GSE21257 (17) contained 34 metastatic OSA tissue samples (from 34 patients, 18.1±12.5 years, 9 females and 25 males) and 19 non-metastatic OSA tissue samples (from 19 patients, 19.4±12.2 years, 10 females and 9 males) that were collected with Illumina Human-6 v2.0 Expression BeadChip (Illumina Inc., San Diego, CA, USA).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27353415", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Four gene expression data sets (GSE21257, GSE9508, GSE49003 and GSE66673) were downloaded from Gene Expression Omnibus (GEO)."}, {"asset": "source:pmid:27353415", "locator": "sections[3] \"Gene expression data\" paragraph 3", "quote": "Data set GSE21257 (17) contained 34 metastatic OSA tissue samples (from 34 patients, 18.1±12.5 years, 9 females and 25 males) and 19 non-metastatic OSA tissue samples (from 19 patients, 19.4±12.2 years, 10 females and 9 males) that were collected with Illumina Human-6 v2.0 Expression BeadChip (Illumina Inc., San Diego, CA, USA)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used the Significance Analysis of Microarray (SAM) method to analyze GSE21257 gene-expression data downloaded from Gene Expression Omnibus (GEO), identifying 616 downregulated and 681 upregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27353415", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Four gene expression data sets (GSE21257, GSE9508, GSE49003 and GSE66673) were downloaded from Gene Expression Omnibus (GEO)."}, {"asset": "source:pmid:27353415", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "An analysis of differentially expressed genes (DEGs) was performed using the Significance Analysis of Microarray (SAM) method."}, {"asset": "source:pmid:27353415", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 616 downregulated and 681 upregulated genes were identified in the data set, GSE21257."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used the Significance Analysis of Microarray (SAM) method to analyze GSE21257 gene-expression data downloaded from Gene Expression Omnibus (GEO), identifying 616 downregulated and 681 upregulated genes.", "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:27353415"], "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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