Identification of potential crucial genes and key pathways in osteosarcoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32665038", "kind": "science-record", "revision": 8, "content_hash": "sha256:e553945f7a3373d4665f092bcb6a86fd2bd026cc97e8a4349903e85d80f6561c", "created_at": "2026-11-01T15:41:06Z", "updated_at": "2026-11-01T22:45:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of potential crucial genes and key pathways in osteosarcoma.", "doi": "10.1186/s41065-020-00142-0", "pmid": "32665038", "authors": ["Junwei Liu", "Siyu Wu", "Xiaoyu Xie", "Ziming Wang", "Qianqian Lei"], "journal": "Hereditas", "year": 2020, "abstract": "BACKGROUND: The aim of this study is to identify the potential pathogenic and metastasis-related differentially expressed genes (DEGs) in osteosarcoma through bioinformatic analysis of Gene Expression Omnibus (GEO) database.\nRESULTS: Gene expression profiles of GSE14359, GSE16088, and GSE33383, in total 112 osteosarcoma tissue samples and 7 osteoblasts, were analyzed. Seventy-four normal-primary DEGs (NPDEGs) and 764 primary-metastatic DEGs (PMDEGs) were screened. VAMP8, A2M, HLA-DRA, SPARCL1, HLA-DQA1, APOC1 and AQP1 were identified continuously upregulating during the oncogenesis and metastasis of osteosarcoma. The enriched functions and pathways of NPDEGs include procession and presentation of antigens, activation of MHC class II receptors and phagocytosis. The enriched functions and pathways of PMDEGs include mitotic nuclear division, cell adhesion molecules (CAMs) and focal adhesion. With protein-protein interaction (PPI) network analyzed by Molecular Complex Detection (MCODE) plug-in of Cytoscape software, one hub NPDEG (HLA-DRA) and 7 hub PMDEGs (CDK1, CDK20, CCNB1, MTIF2, MRPS7, VEGFA and EGF) were eventually selected, and the most significant pathways in NPDEGs module and PMDEGs module were enriched in the procession and presentation of exogenous peptide antigen via MHC class II and the nuclear division, respectively.\nCONCLUSIONS: By integrated bioinformatic analysis, numerous DEGs related to osteosarcoma were screened, and the hub DEGs identified in this study are possibly part of the potential biomarkers for osteosarcoma. However, further experimental studies are still necessary to elucidate the biological function and mechanism of these genes.", "claims": [{"id": "claim-method", "statement": "Identification of DEGs was performed using the LIMMA package of R [21]. The adjusted P-values (adj P-value) were adopted to avoid the occurrence of false-positive results. Using the Benjamini-Hochberg method [22] via the multtest package in R, the FDR (that is, adjusted p-value) < 0.05 and |log2fold-change (FC)| > 1 were used as the cut-off criteria, as previously reported [7–11]. The three gene expression profiles above were downloaded from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/) [18] for identification of DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32665038", "locator": "sections[5] \"Identification of DEGs\" paragraph 2", "quote": "Identification of DEGs was performed using the LIMMA package of R [21]."}, {"asset": "source:pmid:32665038", "locator": "sections[5] \"Identification of DEGs\" paragraph 2", "quote": "The adjusted P-values (adj P-value) were adopted to avoid the occurrence of false-positive results."}, {"asset": "source:pmid:32665038", "locator": "sections[5] \"Identification of DEGs\" paragraph 2", "quote": "Using the Benjamini-Hochberg method [22] via the multtest package in R, the FDR (that is, adjusted p-value) < 0.05 and |log2fold-change (FC)| > 1 were used as the cut-off criteria, as previously reported [7–11]."}, {"asset": "source:pmid:32665038", "locator": "sections[3] \"Osteosarcoma datasets\" paragraph 3", "quote": "The three gene expression profiles above were downloaded from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/) [18] for identification of DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and analyzed during the current study are available in the GEO repository (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32665038", "locator": "sections[23] \"notes\" paragraph 1", "quote": "The datasets generated and analyzed during the current study are available in the GEO repository (https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:32665038"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": {"fdr_threshold": "with Benjamini-Hochberg false discovery rate adjustment"}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32665038", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s41065-020-00142-0", "sha256": "sha256:d5a8e435265b37833113e7cb52e0c2b551cd575062da6019a98b3b1e10c02ac1", "bytes": 36463, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s41065-020-00142-0", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7362476", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:32665038:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8a0d42ffe144a83123e57f135073fc77f3c7fae92895b8a325ebbd46e8ff1287", "bytes": 622, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Characteristics of datasets in this study", "structure": {"pmcid": "PMC7362476", "section_index": 3, "section_title": "Osteosarcoma datasets", "row_count": 5, "column_count": 6}, "table": {"label": "Table 1", "caption": "Characteristics of datasets in this study", "rows": [["Dataset", "Platform", "Sample", "Country"], ["Normal", "Primary tumor", "Metastatic tumor"], ["GSE14359 [15]", "Affymetrix HG U133A", "1 osteoblasts (two duplication)", "10 tissue samples", "4 lung samples", "Germany"], ["GSE16088 [16]", "Affymetrix HG U133A", "3 osteoblasts (U2, HOS and MG63)", "14 tissue samples", "", "USA"], ["GSE33383 [17]", "Illumina human-6 v2.0", "3 osteoblasts (220-OB, 240-OB and Kaat-OB)", "84 tissue samples", "", "Norway"]], "row_count": 5, "column_count": 6, "numeric_cells": 13, "header_rows": 2, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:32665038:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1c6885ec23e0db61a9fd07ccc7152d3e37ccce27da051f572be544c2ef83dbe7", "bytes": 1835, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#Tab2", "version": null, "note": "DEGs continuous upregulating during the oncogenesis and metastasis of osteosarcoma", "structure": {"pmcid": "PMC7362476", "section_index": 11, "section_title": "Identification of DEGs between primary and metastatic osteosarcoma samples", "row_count": 8, "column_count": 4}, "table": {"label": "Table 2", "caption": "DEGs continuous upregulating during the oncogenesis and metastasis of osteosarcoma", "rows": [["Gene symbol", "Full name", "GO BP ID", "KEGG pathway"], ["HLA-DRA", "Major histocompatibility complex, class II, DR alpha", "GO:0002478, GO:0019884, GO:0019886, GO:0048002, GO:0002495, GO:0002504, GO:0019882, GO:0060333, GO:0002429, GO:0071346, GO:0002768, GO:0034341, GO:0050852, GO:0002503, GO:0050851, GO:0002399, GO:0002501, GO:0002396", "hsa04940, hsa05310, hsa05330, hsa05332, hsa05150, hsa05322, hsa04672, hsa05140, hsa04612, hsa04145, hsa05320, hsa05416, hsa05323, hsa05152, hsa04640, hsa05321, hsa04514, hsa04658, hsa04659, hsa05145, hsa05166, hsa05164, hsa05169"], ["VAMP8", "Vesicle Associated Membrane Protein 8", "GO:0002478, GO:0019884, GO:0048002, GO:0019882, GO:0043312, GO:0002283, GO:0042119, GO:0002446, GO:0002697, GO:0002696, GO:0050867, GO:0002699, GO:0043304, GO:0033006, GO:0042590", "/"], ["A2M", "Alpha-2-Macroglobulin", "GO:0002697", "hsa04610"], ["SPARCL1", "SPARC Like 1", "/", "/"], ["HLA-DQA1", "Major Histocompatibility Complex, Class II, DQ Alpha 1", "GO:0002478, GO:0019884, GO:0019886, GO:0048002, GO:0002495, GO:0002504, GO:0019882, GO:0060333, GO:0002429, GO:0071346, GO:0002768, GO:0034341, GO:0050852, GO:0050851", "hsa04940, hsa05310, hsa05330, hsa05332, hsa05150, hsa05322, hsa04672, hsa05140, hsa04612, hsa04145, hsa05320, hsa05416, hsa05323, hsa05152, hsa04640, hsa05321, hsa04514, hsa04658, hsa04659, hsa05145, hsa05166, hsa05164, hsa05169"], ["APOC1", "Apolipoprotein C1", "GO:0043062, GO:0051346, GO:0060627, GO:0030100", "/"], ["AQP1", "Aquaporin 1", "GO:0015669, GO:0015701, GO:0046677, GO:0030185, GO:0006979, GO:0015670, GO:0048545, GO:0042476, GO:0042542, GO:0097237", "hsa04964"]], "row_count": 8, "column_count": 4, "numeric_cells": 15, "header_rows": 1, "locator": "section[11]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:32665038:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:81c1ac4a9f24e22855d4647d75662d7f8b887069a04e7c8d030b21b340e5d65a", "bytes": 3548, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#Tab3", "version": null, "note": "Hub genes with high degree of connectivity in each module", "structure": {"pmcid": "PMC7362476", "section_index": 13, "section_title": "PPI (protein-protein interaction) network and module analysis", "row_count": 9, "column_count": 8}, "table": {"label": "Table 3", "caption": "Hub genes with high degree of connectivity in each module", "rows": [["Category", "MCODE module", "Gene symbol", "Degree", "Type", "Full name", "Go BP ID", "KEGG pathways"], ["NPDEG", "Module 1", "HLA-DRA", "7", "Up", "Major histocompatibility complex, class II, DR alpha", "GO:0002478, GO:0019884, GO:0019886, GO:0048002, GO:0002495, GO:0002504, GO:0019882, GO:0060333, GO:0002429, GO:0071346, GO:0002768, GO:0034341, GO:0050852, GO:0002503, GO:0050851, GO:0002399, GO:0002501, GO:0002396,", "hsa04940, hsa05310, hsa05330, hsa05332, hsa05150, hsa05322, hsa04672, hsa05140, hsa04612, hsa04145, hsa05320, hsa05416, hsa05323, hsa05152, hsa04640, hsa05321, hsa04514, hsa04658, hsa04659, hsa05145, hsa05166, hsa05164, hsa05169"], ["PMDEG", "Module 1", "CDK1", "74", "Up", "Cyclin dependent kinase 1", "GO:0010038, GO:1901988, GO:0045930, GO:1901991, GO:0010948, GO:0007093, GO:0007568, GO:0046677, GO:0031145, GO:0000075, GO:0042692, GO:0009123, GO:0009141, GO:0071103, GO:0045927,", "hsa04110"], ["PMDEG", "Module 1", "CDK20", "62", "Up", "Cyclin dependent kinase 20", "/", "/"], ["PMDEG", "Module 1", "CCNB1", "61", "Up", "Cyclin B1", "GO:0140014, GO:0000819, GO:0000070, GO:0010038, GO:0000280, GO:0007059, GO:0048285, GO:0045839, GO:0098813, GO:0007088, GO:0051784, GO:0051783, GO:0001701, GO:0010965, GO:2000816, GO:0051983, GO:1905819, GO:0051306, GO:0030071, GO:0033048, GO:1905818, GO:0007094, GO:0031577, GO:0071173, GO:0071174, GO:0033044, GO:1902099, GO:0071241, GO:0033046, GO:0007091, GO:0051985, GO:1901988, GO:0045841, GO:0051304, GO:0044784, GO:0071248, GO:1902100, GO:0033047, GO:0033045, GO:0045930, GO:0070482, GO:1901991, GO:0010948, GO:0007093, GO:0036293, GO:0001666, GO:0031145, GO:0051656, GO:0000075, GO:0071453, GO:0042692, GO:0009123, GO:0009141, GO:0048565, GO:0010639, GO:0071103, GO:0045927", "hsa04110"], ["PMDEG", "Module 2", "MTIF2", "25", "Up", "Mitochondrial translational initiation factor 2", "GO:0032543, GO:0140053", "/"], ["PMDEG", "Module 2", "MRPS7", "25", "Down", "Mitochondrial ribosomal protein S7", "GO:0032543, GO:0140053, GO:0070125, GO:0006414, GO:0022613, GO:0070126", "/"], ["PMDEG", "Module 3", "VEGFA", "38", "Down", "Vascular endothelial growth factor A", "GO:0043129, GO:0052547, GO:0048875, GO:0052548, GO:0050900, GO:0010466, GO:0010951, GO:0032103, GO:0010810, GO:0045785, GO:0048732, GO:0001701, GO:0010811, GO:0060249, GO:0033044, GO:0031589, GO:0045807, GO:0097529, GO:0045861, GO:0030595, GO:0070482, GO:0048871, GO:0051346, GO:0036293, GO:0001666, GO:0002576, GO:0001894, GO:0002685, GO:0002688, GO:0060627, GO:0071453, GO:0001954, GO:0042692, GO:0001952, GO:0050920, GO:0030100, GO:0060326, GO:0050678, GO:0002687, GO:0061138, GO:0016049, GO:0045927", "hsa05323, hsa04510, hsa04933"], ["PMDEG", "Module 3", "EGF", "34", "Up", "Epidermal growth factor", "GO:0140014, GO:0043129, GO:0052547, GO:0043062, GO:0030198, GO:0000280, GO:0048875, GO:0052548, GO:0048285, GO:0007088, GO:0050900, GO:0010466, GO:0010951, GO:0032103, GO:0010810, GO:0045785, GO:0048732, GO:0051783, GO:0001701, GO:0010811, GO:0060249, GO:0033044, GO:0031589, GO:0045807, GO:0097529, GO:0045861, GO:0030595, GO:0070482, GO:0048871, GO:0051346, GO:0036293, GO:0001666, GO:0002576, GO:0001894, GO:0002685, GO:0002688, GO:0045862, GO:0060627, GO:0071453, GO:0001954, GO:0042692, GO:0007219, GO:0001952, GO:0050920, GO:0030100, GO:0060326, GO:0050678, GO:0051098, GO:0002687, GO:0061138, GO:0016049, GO:0045927", "hsa04668, hsa05323, hsa04510, hsa04933"]], "row_count": 9, "column_count": 8, "numeric_cells": 32, "header_rows": 1, "locator": "section[13]/table-wrap[1]#Tab3"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", 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The adjusted P-values (adj P-value) were adopted to avoid the occurrence of false-positive results. Using the Benjamini-Hochberg method [22] via the multtest package in R, the FDR (that is, adjusted p-value) < 0.05 and |log2fold-change (FC)| > 1 were used as the cut-off criteria, as previously reported [7–11]. The three gene expression profiles above were downloaded from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/) [18] for identification of DEGs."}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO enrichment"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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