Microarray analysis of the molecular mechanisms associated with age and body mass index in human meniscal injury.

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The GSE45233 gene expression dataset with 12 injured meniscus samples associated with age and BMI and GSE66635 dataset with 12 injured and 12 normal meniscus samples were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified based on age or BMI in GSE45233. DEGs between injured and normal meniscus samples in GSE66635 were also identified. Common DEGs between GSE45233 and GSE66635 were identified as feature genes associated with age or BMI, followed by protein‑protein interaction (PPI) network and functional pathway enrichment analyses for the feature genes. Finally, the GSE51588 genome‑wide expression profile was then downloaded from the GEO database to validate the results. A total of 1,328 DEGs were identified. Of these, 28 age‑associated and 20 BMI‑associated meniscal injury genes were obtained. B‑cell lymphoma‑2 (Bcl‑2) and matrix metalloproteinase‑14 were identified as hub genes in the PPI networks. Functional pathway enrichment analysis revealed that vascular endothelial growth factor A (VEGFA), transferrin (TF) and Bcl‑2 were involved in the hypoxia‑inducible factor 1 signaling pathway. TF was involved in the mineral absorption function pathway associated with BMI. Additionally, TF and VEGFA were identified to be overlapping candidate genes of GSE45233 and GSE66635, and DEGs in GSE51588. Therefore, VEGFA, TF, and Bcl‑2 may be important genes for human meniscal injuries. Additional evaluations of these results are required.", "claims": [{"id": "claim-method", "statement": "The significances of average expression level differences for feature genes extracted from the two new groups were analyzed by t-test using the Limma package (23).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30483788", "locator": "sections[6] \"Integrative analysis of feature gene expression levels\" paragraph 2", "quote": "The significances of average expression level differences for feature genes extracted from the two new groups were analyzed by t-test using the Limma package (23)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The analyzed data sets generated during the study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30483788", "locator": "sections[22] \"Availability of data and materials\" paragraph 2", "quote": "The analyzed data sets generated during the study are available from the corresponding author on reasonable request."}], "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:30483788"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE45233"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE45233"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30483788", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/mmr.2018.9685", "sha256": 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the age and body mass index groups.", "structure": {"pmcid": "PMC6297773", "section_index": 16, "section_title": "PPI network analysis", "row_count": 28, "column_count": 4}, "table": {"label": "Table II.", "caption": "List of top 10 highest degree nodes of the age and body mass index groups.", "rows": [["A, Age group"], [""], ["Gene", "P-value", "log2FC", "Degree"], ["BCL2", "0.0345", "−1.30", "74"], ["CCNB1", "0.0030", "1.31", "30"], ["S100A1", "0.0004", "−5.64", "18"], ["VEGFA", "0.0173", "−1.66", "18"], ["TF", "0.0281", "−1.40", "14"], ["CD36", "0.0010", "9.33", "13"], ["PBK", "0.0043", "1.39", "12"], ["CTSS", "0.0222", "1.48", "8"], ["HAPLN1", "0.0031", "−2.21", "7"], ["CALCRL", "0.0198", "2.61", "6"], [""], ["B, Body mass index group"], [""], ["Gene", "P-value", "log2FC", "Degree"], [""], ["MMP14", "0.0398", "−1.26", "20"], ["S100A8", "0.0042", "2.74", "16"], ["TF", "0.0325", "1.45", "14"], ["CXCL12", "0.0113", "−2.19", "7"], ["EDNRA", "0.0084", "−3.18", "6"], ["IGFBP1", "0.0157", 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