Identification of core genes and clinical outcomes in tumors originated from endoderm (gastric cancer and lung carcinoma) via bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33761685", "kind": "science-record", "revision": 6, "content_hash": "sha256:9e999aa70a4268d7f95b94ef1ea1c7a84b47171931f6eb620e078841e1589c98", "created_at": "2026-11-01T15:41:30Z", "updated_at": "2026-11-01T21:24:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of core genes and clinical outcomes in tumors originated from endoderm (gastric cancer and lung carcinoma) via bioinformatics analysis.", "doi": "10.1097/MD.0000000000025154", "pmid": "33761685", "authors": ["Yewen Shi", "Dongmin Chang", "Wenhan Li", "FengYu Zhao", "Xiaoyong Ren", "Bin Hou"], "journal": "Medicine", "year": 2021, "abstract": "ABSTRACT: During last decade, bioinformatics analysis has provided an effective way to study the relationship between various genes and biological processes. In this study, we aimed to identify potential core candidate genes and underlying mechanisms of progression of lung and gastric carcinomas which both originated from endoderm. The expression profiles, GSE54129 (gastric carcinoma) and GSE27262 (lung carcinoma), were collected from GEO database. One hundred eleven patients with gastric carcinoma and 21 health people were included in this research. Meanwhile, there were 25 lung carcinoma patients. Then, 75 differentially expressed genes were selected via GEO2R online tool and Venn software, including 31 up-regulated genes and 44 down-regulated genes. Next, we used Database for Annotation, Visualization, and Integrated Discovery and Metascpe software to analyze Kyoto Encyclopedia of Gene and Genome pathway and gene ontology. Furthermore, Cytoscape software and MCODE App were performed to construct complex of these differentially expressed genes . Twenty core genes were identified, which mainly enriched in extracellular matrix-receptor interaction, focal adhesion, and PI3K-Akt pathway (P < .01). Finally, the significant difference of gene expression between cancer tissues and normal tissues in both lung and gastric carcinomas was examined by Gene Expression Profiling Interactive Analysis database. Twelve candidate genes with positive statistical significance (P < .01), COMP CTHRC1 COL1A1 SPP1 COL11A1 COL10A1 CXCL13 CLDN3 CLDN1 matrix metalloproteinases 7 ADAM12 PLAU, were picked out to further analysis. The Kaplan-Meier plotter website was applied to examine relationship among these genes and clinical outcomes. We found 4 genes (ADAM12, SPP1, COL1A1, COL11A1) were significantly associated with poor prognosis in both lung and gastric carcinoma patients (P < .05). In conclusion, these candidate genes may be potential therapeutic targets for cancer treatment.", "claims": [{"id": "claim-method", "statement": "Thus, we applied Kaplan–Meier-plotter website to estimate the effect of candidate genes on patients’ clinical outcomes based on GEO, EGA, and TCGA databases. The hazard ratio with 95% confidence intervals and log rank P value were calculated and showed on the plot.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33761685", "locator": "sections[8] \"Expression levels of hub genes and clinical outcomes analysis\" paragraph 2", "quote": "Thus, we applied Kaplan–Meier-plotter website to estimate the effect of candidate genes on patients’ clinical outcomes based on GEO, EGA, and TCGA databases. The hazard ratio with 95% confidence intervals and log rank P value were calculated and showed on the plot."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated during and/or analyzed during the current study are publicly available.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33761685", "locator": "sections[18] \"fn-group\" paragraph 1", "quote": "The datasets generated during and/or analyzed during the current study are publicly available."}], "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:33761685"], "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": {}, "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:33761685", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1097/MD.0000000000025154", "sha256": 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datasets, including 31 up-regulated genes and 44 down-regulated genes.", "structure": {"pmcid": "PMC10545272", "section_index": 10, "section_title": "Identification of core genes in tumors originated from endoderm", "row_count": 3, "column_count": 2}, "table": {"label": "Table 1", "caption": "All 75 differentially expressed genes (DEGs) were selected from 2 GSE datasets, including 31 up-regulated genes and 44 down-regulated genes.", "rows": [["DEGs", "Genes name"], ["Up-regulated", "ADAM12 PLAU MMP7 IGF2BP3 ANP32E CXCL13 COL1A1 CCL19 PCDH7 CST1 HOXA10 SPP1 GREM1 BUB1 COL3A1 CLDN3 HOXC10 COMP THBS2 WISP1 ESYT2 FDCSP SULF1 DOK5 ENC1 CLDN1 COL10A1 COL11A1 CTHRC1 COL1A2 PTPRB"], ["Down-regulated", "OTUD1 FRMD3 GATA6 MAL AHNAK KLF4 TMEM246 ABCA8 ACKR4 NEDD4L ASPA BMP2 ADRB2 FKBP1B KANK4 LAMA3 MIR6872 SEMA3B ADGRG6 NCKAP5 PLCB4 MYRF CLIC3 ADAMTS15 ADGRL3 CA2 ADTRP SSTR1 MYZAP PLLP HHIP PGC SOSTDC1 LRP4 RMST PIP5K1B SCNN1G KLK11 MAMDC2 BMP5 CLDN18 ABHD6 GKN2 HYAL1"]], "row_count": 3, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[10]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:33761685:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b203612078151b3180301fb9f16cf22969b5c3c8713e647c2c3680eb87b0e945", "bytes": 2447, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T2", "version": null, "note": "Different genes ontology in tumors originated from endoderm.", "structure": {"pmcid": "PMC10545272", "section_index": 11, "section_title": "DEGs ontology and KEGG pathway analysis in tumors originated from endoderm", "row_count": 24, "column_count": 6}, "table": {"label": "Table 2", "caption": "Different genes ontology in tumors originated from endoderm.", "rows": [["Expression", "Category", "Term", "Count", "P value", "FDR"], ["up-regulated", "GOTERM_BP_DIRECT", "GO:0030199–collagen fibril organization", "5", "9.1E-8", "1.14E-4"], ["", "GOTERM_BP_DIRECT", "GO:0007155∼cell adhesion", "5", "1.2E-4", "0.149489"], ["", "GOTERM_BP_DIRECT", "GO:0009954∼proximal/distal pattern formation", "3", "5.9E-4", "0.738304"], ["", "GOTERM_BP_DIRECT", "GO:0030326∼embryonic limb morphogenesis", "3", "1.0E-3", "1.233105"], ["", "GOTERM_BP_DIRECT", "GO:0071230∼cellular response to amino acid stimulus", "3", "2.0E-3", "2.464763"], ["", "GOTERM_CC_DIRECT", "GO:0005581∼collagen trimer", "6", "3.5E-8", "3.2E-5"], ["", "GOTERM_CC_DIRECT", "GO:0005615∼extracellular space", "10", "1.5E-5", "0.013266"], ["", "GOTERM_CC_DIRECT", "GO:0005578∼proteinaceous extracellular matrix", "5", "2.1E-4", "0.194531"], ["", "GOTERM_CC_DIRECT", "GO:0005584∼collagen type I trimer", "2", "3.4E-3", "3.032843"], ["", "GOTERM_MF_DIRECT", "GO:0005201∼extracellular matrix structural constituent", "4", "3.5E-5", "0.031544"], ["", "GOTERM_MF_DIRECT", "GO:0008201∼heparin binding", "4", "8.1E-4", "0.721484"], ["", "GOTERM_MF_DIRECT", "GO:0042802∼identical protein binding", "4", "1.6E-3", "1.446008"], ["", "GOTERM_MF_DIRECT", "GO:0048407∼platelet-derived growth factor binding", "2", "5.3E-3", "4.595293"], ["", "GOTERM_MF_DIRECT", "GO:0005509∼calcium ion binding", "5", "1.6E-2", "13.686396"], ["Down-regulated", "GOTERM_BP_DIRECT", "GO:0030509∼BMP signaling pathway", "3", "5.6E-3", "7.069993"], ["", "GOTERM_BP_DIRECT", "GO:2000065∼negative regulation of cortisol biosynthetic process", "2", "9.4E-3", "11.498954"], ["", "GOTERM_BP_DIRECT", "GO:0008285∼negative regulation of cell proliferation", "4", "1.3E-2", "15.820081"], ["", "GOTERM_BP_DIRECT", "GO:0043569∼negative regulation of insulin-like growth factor receptor signaling pathway", "2", "1.4E-2", "16.743886"], ["", "GOTERM_BP_DIRECT", "GO:0040007∼growth", "2", "3.9E-2", "40.514446"], ["", "GOTERM_CC_DIRECT", "GO:0005615∼extracellular space", "9", "9.2E-4", "0.886836"], ["", "GOTERM_CC_DIRECT", "GO:0070062∼extracellular exosome", "11", "3.6E-2", "29.452708"], ["", "GOTERM_MF_DIRECT", "GO:0070700∼BMP receptor binding", "2", "9.2E-4", "11.849758"], ["", "GOTERM_MF_DIRECT", "GO:0005160∼transforming growth factor beta receptor binding", "2", "3.6E-2", "44.045834"]], "row_count": 24, "column_count": 6, "numeric_cells": 92, "header_rows": 2, "locator": "section[11]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:33761685:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:721ae25352f299cfe4d5939f31ae5b5ae78797a44310b72151eb529c9f2d7d01", "bytes": 890, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[2]#T3", "version": null, "note": "KEGG pathway analysis of different genes.", "structure": {"pmcid": "PMC10545272", "section_index": 11, "section_title": "DEGs ontology and KEGG pathway analysis in tumors originated from endoderm", "row_count": 7, "column_count": 6}, "table": {"label": "Table 3", "caption": "KEGG pathway analysis of different genes.", "rows": [["Pathway ID", "Name", "Count", "%", "P value", "Genes"], ["hsa04512", "ECM–receptor interaction", "8", "0.1", "5.7E-8", "LAMA3, COMP, COL3A1, COL1A2, COL1A1, THBS2, COL11A1, SPP1"], ["hsa04510", "Focal adhesion", "8", "0.1", "2.0E-5", "LAMA3, COMP, COL3A1, COL1A2, COL1A1, THBS2, COL11A1, SPP1"], ["hsa05146", "Amoebiasis", "6", "01.", "7.6E-5", "PLCB4, LAMA3, COL3A1, COL1A2, COL1A1, COL11A1"], ["hsa04974", "Protein digestion and absorption", "5", "0.1", "4.2E-4", "COL3A1, COL1A2, COL1A1, COL11A1, COL10A1"], ["hsa04151", "PI3K-Akt signaling pathway", "8", "0.1", "4.4E-4", "LAMA3, COMP, COL3A1, COL1A2, COL1A1, THBS2, COL11A1, SPP1"], ["hsa04611", "Platelet activation", "5", "0.1", "2.0E-3", "PLCB4, COL3A1, COL1A2, COL1A1, COL11A1"]], "row_count": 7, "column_count": 6, "numeric_cells": 30, "header_rows": 1, "locator": "section[11]/table-wrap[2]#T3"}}, {"id": "asset:table:pmid:33761685:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4fc988b905f3c5e24e75b766bdaff892c21cf3a73127808ad6df6ab786398a55", "bytes": 546, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#T4", "version": null, "note": "KEGG pathway analysis of 20 selected genes.", "structure": {"pmcid": "PMC10545272", "section_index": 13, "section_title": "Reanalysis of 20 selected genes by KEGG pathway enrichment", "row_count": 4, "column_count": 6}, "table": {"label": "Table 4", "caption": "KEGG pathway analysis of 20 selected genes.", "rows": [["Pathway ID", "Name", "Count", "%", "P value", "Genes"], ["hsa04512", "ECM–receptor interaction", "6", "30", "5.0E-7", "COMP, COL1A2, COL1A1, COL11A1, THBS2, SPP1"], ["hsa04510", "Focal adhesion", "6", "30", "3.6E-5", "COMP, COL1A2, COL1A1, COL11A1, THBS2, SPP1"], ["hsa04151", "PI3K-Akt signaling pathway", "6", "30", "4.1E-4", 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.01)", "ADAM12 CLDN1 CLDN3 COL1A1 COL1A2 COL10A1 COL11A1 COMP CTHRC1 CXCL13 MMP7 PLAU SPP1 THBS2 WISP1"], ["Genes with statistical difference in lung cancers (P > .01)", "ACKR4 ADAM12 BMP2 CCL19 CLDN1 CLDN3 CLDN18 COL1A1 COL10A1 COL11A1 COMP CTHRC1 CXCL13 MMP7 PLAU SPP1 SSTR1"], ["Genes with statistical difference in 2 cancers (P < .01)", "COMP CTHRC1 COL1A1 SPP1 COL11A1 COL10A1 CXCL13 CLDN3 CLDN1 MMP7 ADAM12 PLAU"], ["Genes without statistical difference in 2 cancers (P > .01)", "COL1A2 BMP2 CCL19 ACKR4 SSTR1 CLDN18 THBS2 WISP1"]], "row_count": 5, "column_count": 2, "numeric_cells": 8, "header_rows": 1, "locator": "section[14]/table-wrap[1]#T5"}}, {"id": "asset:table:pmid:33761685:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3f7574d28498b0006b4b74d2c5c2b1c7b25d8971bf99a9a4ba2d8763c3d69e2e", "bytes": 682, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", 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