Elementary screening of lymph node metastatic-related genes in gastric cancer based on the co-expression network of messenger RNA, microRNA and long non-coding RNA.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29489999", "kind": "science-record", "revision": 5, "content_hash": "sha256:10264d2ade7bc0fe43a7d405e8f3f8feb0c64671a944495a0c95b8331a7013f1", "created_at": "2026-11-01T15:40:32Z", "updated_at": "2026-11-01T21:21:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Elementary screening of lymph node metastatic-related genes in gastric cancer based on the co-expression network of messenger RNA, microRNA and long non-coding RNA.", "doi": "10.1590/1414-431x20176685", "pmid": "29489999", "authors": ["Zhonghua Song", "Wenhua Zhao", "Danfeng Cao", "Jinqing Zhang", "Shouhua Chen"], "journal": "Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologica", "year": 2018, "abstract": "Gastric cancer (GC) is the fifth most common cancer and the third leading cause of cancer-related deaths worldwide. The high mortality might be attributed to delay in detection and is closely related to lymph node metastasis. Therefore, it is of great importance to explore the mechanism of lymph node metastasis and find strategies to block GC metastasis. Messenger RNA (mRNA), microRNA (miRNA) and long non-coding RNA (lncRNA) expression data and clinical data were downloaded from The Cancer Genome Atlas (TCGA) database. A total of 908 differentially expressed factors with variance >0.5 including 542 genes, 42 miRNA, and 324 lncRNA were screened using significant analysis microarray algorithm, and interaction networks were constructed using these differentially expressed factors. Furthermore, we conducted functional modules analysis in the network, and found that yellow and turquoise modules could separate samples efficiently. The groups classified in the yellow and turquoise modules had a significant difference in survival time, which was verified in another independent GC mRNA dataset (GSE62254). The results suggested that differentially expressed factors in the yellow and turquoise modules may participate in lymph node metastasis of GC and could be applied as potential biomarkers or therapeutic targets for GC.", "claims": [{"id": "claim-method", "statement": "Significant analysis microarray (SAM) (20) is an algorithm used to screen the differentially expressed genes (DEGs). Samples of gastric cancer were selected from the TCGA database (http://cancergenome.nih.gov/), in which mRNAs data and miRNAs data were profiled from the Illumina platform.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29489999", "locator": "sections[5] \"Identification of differentially expressed genes and functional enrichment analysis\" paragraph 2", "quote": "Significant analysis microarray (SAM) (20) is an algorithm used to screen the differentially expressed genes (DEGs)."}, {"asset": "source:pmid:29489999", "locator": "sections[3] \"Data sources\" paragraph 2", "quote": "Samples of gastric cancer were selected from the TCGA database (http://cancergenome.nih.gov/), in which mRNAs data and miRNAs data were profiled from the Illumina platform."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Samples of gastric cancer were selected from the TCGA database (http://cancergenome.nih.gov/), in which mRNAs data and miRNAs data were profiled from the Illumina platform. The lncRNAs data were annotated from mRNA transcriptomic database through matching to the HGNC database. In total, 396 samples with mRNA-miRNA-lncRNA paired samples were obtained, and 356 samples remained after removing 40 samples with unclear status in lymph node metastasis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29489999", "locator": "sections[3] \"Data sources\" paragraph 2", "quote": "Samples of gastric cancer were selected from the TCGA database (http://cancergenome.nih.gov/), in which mRNAs data and miRNAs data were profiled from the Illumina platform. The lncRNAs data were annotated from mRNA transcriptomic database through matching to the HGNC database. In total, 396 samples with mRNA-miRNA-lncRNA paired samples were obtained, and 356 samples remained after removing 40 samples with unclear status in lymph node metastasis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The results suggested that differentially expressed factors in the yellow and turquoise modules may participate in lymph node metastasis of GC and could be applied as potential biomarkers or therapeutic targets for GC.", "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:29489999"], "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:GSE62254"], "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:GSE62254"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29489999", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1590/1414-431x20176685", "sha256": "sha256:b1d7eb5efb9719a01bbed35b796eb512cba1b3d6b03072f00b45ac450057f4fd", "bytes": 30416, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1590/1414-431x20176685", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5856436", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE62254", "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=GSE62254", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62254", "version": null, "note": "Samples of gastric cancer were selected from the TCGA database (http://cancergenome.nih.gov/), in which mRNAs data and miRNAs data were profiled from the Illumina platform. 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analysis microarray (SAM) (20) is an algorithm used to screen the differentially expressed genes (DEGs). 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