Gene expression profiles and pathway enrichment analysis of human osteosarcoma cells exposed to sorafenib.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29744300", "kind": "science-record", "revision": 9, "content_hash": "sha256:0d33c0b63e2e39bbd8205f60dc9e91768ebdf91861f943592436dea13c03ab97", "created_at": "2026-11-01T15:40:33Z", "updated_at": "2026-11-01T22:43:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene expression profiles and pathway enrichment analysis of human osteosarcoma cells exposed to sorafenib.", "doi": "10.1002/2211-5463.12428", "pmid": "29744300", "authors": ["Zhehao Dai", "Haoyu Tang", "Yue Pan", "Junquan Chen", "Yongping Li", "Jun Zhu"], "journal": "FEBS open bio", "year": 2018, "abstract": "Sorafenib is an inhibitor of a variety of tyrosine kinase receptors used to treat various cancers including hepatocellular, renal cell and thyroid carcinoma. It has been shown to change various targets associated with osteosarcoma, but the detailed mechanism remains unclear. In order to identify key genes, enriched pathways and important modules during the exposure of human osteosarcoma cells to sorafenib, data for gene expression profiles (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53155) were downloaded from the GEO database. In total, 61 differentially expressed genes (DEGs) were identified by the R bioconductor packages. Functional and enrichment analyses of DEGs were performed using the DAVID database. These revealed that DEGs were enriched in biological processes, molecular function and KEGG pathway of inflammatory immune response and angiogenesis. A protein-protein interaction network was constructed by string and visualized in cytoscape, and eight genes were selected as hubs: IL8,CXCL2,PTGS2,FOS,CXCL1, C3,EHMT2 and PGF. Subsequently, only one cluster was identified by mcode, which consisted of six nodes (CXCL1,CXCL2,PTGS2,FOS, C3 and PGF) and nine edges. PGF was the seed gene in this cluster. In conclusion, the results of this data mining and integration should help in revealing new mechanisms and targets of sorafenib in inhibiting osteosarcoma.", "claims": [{"id": "claim-method", "statement": "The dataset was analyzed with R bioconductor packages, and raw datasets were normalized based on the preprocesscore package and the DEGs were screened out via the limma package through the cut‐off criteria of P‐value < 0.01 and |log2(fold change) |>2.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29744300", "locator": "sections[7] \"Identification of differentially expressed genes from public microarray data\" paragraph 2", "quote": "The dataset was analyzed with R bioconductor packages, and raw datasets were normalized based on the preprocesscore package and the DEGs were screened out via the limma package through the cut‐off criteria of P‐value < 0.01 and |log2(fold change) |>2."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The public gene expression profiles of http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53155 were downloaded from the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo). These profiles were deposited by Birgit Gallé in 2013 and comprised three untreated replicates of human osteosarcoma cells (ATCC CRL‐1543™), and three replicates of the same cells treated with 4 μm sorafenib.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29744300", "locator": "sections[7] \"Identification of differentially expressed genes from public microarray data\" paragraph 2", "quote": "The public gene expression profiles of http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53155 were downloaded from the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo). These profiles were deposited by Birgit Gallé in 2013 and comprised three untreated replicates of human osteosarcoma cells (ATCC CRL‐1543™), and three replicates of the same cells treated with 4 μm sorafenib."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used limma through R Bioconductor after preprocesscore normalization to screen differentially expressed genes from the GEO dataset GSE53155. The headline result was the identification of 61 DEGs in sorafenib-treated human osteosarcoma cells.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29744300", "locator": "sections[7] \"Identification of differentially expressed genes from public microarray data\" paragraph 2", "quote": "The public gene expression profiles of http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53155 were downloaded from the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo)."}, {"asset": "source:pmid:29744300", "locator": "sections[7] \"Identification of differentially expressed genes from public microarray data\" paragraph 2", "quote": "The dataset was analyzed with R bioconductor packages, and raw datasets were normalized based on the preprocesscore package and the DEGs were screened out via the limma package through the cut‐off criteria of P‐value < 0.01 and |log2(fold change) |>2."}, {"asset": "source:pmid:29744300", "locator": "sections[11] \"Identification of DEGs\" paragraph 2", "quote": "Compared with untreated human osteosarcoma cells, a total of 61 DEGs were identified in human osteosarcoma cells treated with sorafenib, consisting of 18 up‐regulated and 43 down‐regulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used limma through R Bioconductor after preprocesscore normalization to screen differentially expressed genes from the GEO dataset GSE53155. The headline result was the identification of 61 DEGs in sorafenib-treated human osteosarcoma cells.", "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:29744300"], "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:GSE53155"], "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:GSE53155"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29744300", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/2211-5463.12428", "sha256": "sha256:a75aa4928476d0c10959ff1a3852cd4c6b5e35d0e6dc967f9a234f3d7d56962d", "bytes": 18437, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/2211-5463.12428", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5929930", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE53155", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53155", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE53155", "version": null, "note": "The public gene expression profiles of http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53155 were downloaded from the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo). 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CXCL2, CXCL8, SCG2"], ["0006955: immune response", "7", "3.88 × 10−4", "CXCL1, C3, CXCL2, RFX1, CXCL8, CTSS, IFI6"], ["0050930: induction of positive chemotaxis", "3", "5.41 × 10−4", "PGF, CXCL8, SCG2"], ["0090023: positive regulation of neutrophil chemotaxis", "3", "0.001179039", "CXCL1, CXCL2, CXCL8"], ["0001525: angiogenesis", "5", "0.00172978", "PTGS2, PGF, CXCL8, SCG2, ANGPTL4"], ["0045766: positive regulation of angiogenesis", "4", "0.002389639", "C3, PGF, CXCL8, ANGPTL4"], ["0032496: response to lipopolysaccharide", "4", "0.006460182", "CXCL1, FOS, PTGS2, CXCL2"], ["0060326: cell chemotaxis", "3", "0.009969718", "CXCL1, CXCL2, PDGFRA"], ["0070098: chemokine‐mediated signaling pathway", "3", "0.011807301", "CXCL1, CXCL2, CXCL8"], ["0008285: negative regulation of cell proliferation", "5", "0.013070326", "CXCL1, RARRES3, NDN, PTGS2, CXCL8"], ["Molecular function ontology", "0008009: chemokine activity", "3", "0.005428355", "CXCL1, CXCL2, CXCL8"], ["0045236: CXCR chemokine receptor binding", "2", "0.020082714", "CXCL1, CXCL2"], ["0000978: RNA polymerase II core promoter proximal region sequence‐specific DNA binding", "4", "0.045260858", "FOS, NDN, SMARCE1, RFX1"]], "row_count": 19, "column_count": 5, "numeric_cells": 55, "header_rows": 1, "locator": "section[12]/table-wrap[1]#feb412428-tbl-0002"}}, {"id": "asset:table:pmid:29744300:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:86a8e2379075dc4e86429db246137201d7b7af0724d9258aee8f758f84c85de8", "bytes": 897, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#feb412428-tbl-0003", "version": null, "note": "The top 10 enriched KEGG pathways of the down‐regulated genes", "structure": {"pmcid": "PMC5929930", "section_index": 12, "section_title": "GO functional annotation and pathway enrichment", "row_count": 10, "column_count": 4}, "table": {"label": "Table 3", "caption": "The top 10 enriched KEGG pathways of the down‐regulated genes", "rows": [["Term", "Count", "P", "Genes"], ["Legionellosis", "4", "6.26 × 10−4", "CXCL1, C3, CXCL2, CXCL8"], ["Pertussis", "4", "0.001630681", "FOS, C3, CXCL8, C1S"], ["Salmonella infection", "4", "0.002182574", "CXCL1, FOS, CXCL2, CXCL8"], ["TNF signaling pathway", "4", "0.004370617", "CXCL1, FOS, PTGS2, CXCL2"], ["Pathways in cancer", "6", "0.006830986", "FOS, LAMA4, PTGS2, PGF, PDGFRA, CXCL8"], ["Leishmaniasis", "3", "0.021059667", "FOS, PTGS2, C3"], ["PI3K–Akt signaling pathway", "5", "0.021872858", "LAMA4, PGF, PDGFRA, IL3RA, DDIT4"], ["Antigen processing and presentation", "3", "0.023923045", "KLRC2, KLRC3, CTSS"], ["Chagas disease (American trypanosomiasis)", "3", "0.042619701", "FOS, C3, CXCL8"]], "row_count": 10, "column_count": 4, "numeric_cells": 18, "header_rows": 1, "locator": "section[12]/table-wrap[2]#feb412428-tbl-0003"}}], "gaps": ["asset:data:geo:GSE53155 not downloaded", 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