Identification of candidate biomarkers associated with apoptosis in melanosis coli: GNG5, LPAR3, MAPK8, and PSMC6.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30559147", "kind": "science-record", "revision": 8, "content_hash": "sha256:ef373bfaf791cdc45db62f463ad106b08db31a040083f9836273bea5ec873217", "created_at": "2026-11-01T15:40:39Z", "updated_at": "2026-11-01T22:00:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of candidate biomarkers associated with apoptosis in melanosis coli: GNG5, LPAR3, MAPK8, and PSMC6.", "doi": "10.1042/BSR20181369", "pmid": "30559147", "authors": ["Xiaohang Hua", "Jiangang Chen", "Lingli Wu"], "journal": "Bioscience reports", "year": 2019, "abstract": "Purpose: Melanosis coli (MC) is a disorder of pigmentation of the wall of the colon, often identified at the time of colonoscopy. The aim of the present study is to identify candidate biomarkers for MC. Methods: The transcriptome data for MC (GSE78933) with five MC tissues and five corresponding normal tissues is obtained from the NCBI Gene Expression Omnibus (GEO) database. R/Bioconductor package limma was used to screen differently expressed genes (DEGs). ClueGO of cytoscape was applied for Gene Ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Based on STRING V10 database, protein-protein interaction (PPI) network was constructed. The pathological tissue and normal tissue from 23 MC patients and 23 controls were collected, respectively. The relative expression of hub nodes was detected by qRT-PCR and Western blot. For regulating the expression of these genes, overexpression vector was constructed or siRNA transfection was used. Finally, apoptosis was detected by flow cytometry. Results: Total 1342 DEGs were screened, including 786 up-regulated and 556 down-regulated genes. These genes were mainly enriched in stimulatory C-type lectin receptor signaling pathway, polysaccharide biosynthetic process, intracellular, and oxidative phosphorylation. PPI network was then constructed with 426 DEGs and 895 interactions. Thereinto, G-protein subunit γ 5 (GNG5), lysophosphatidic acid receptor 3 (LPAR3), mitogen-activated protein kinase 8 (MAPK8), NHP2L1, proteasome 26S subunit, ATPase 6 (PSMC6), and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit β (PIK3CB) were hub nodes with higher degree. RT-PCR and Western blot results showed that GNG5, LPAR3, MAPK8, and PSMC6 were differently expressed with significance. The expression of these screened genes is also related with cell apoptosis. Conclusion: GNG5, LPAR3, MAPK8, and PSMC6 might be candidate biomarkers associated with apoptosis in MC.", "claims": [{"id": "claim-method", "statement": "t test was used to compare the mean between two groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30559147", "locator": "sections[11] \"Statistical analysis\" paragraph 2", "quote": "t test was used to compare the mean between two groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The expression profile of MC was acquired from Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo) database of NCBI (GEO accession: GSE78933) with the platform of [HTA-2_0] Affymetrix Human Transcriptome Array 2.0 [transcript (gene) version]. The profile included five colonic mucosa samples in MC groups and five colonic mucosa samples in MC groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30559147", "locator": "sections[3] \"Acquisition and preprocessing of data\" paragraph 2", "quote": "The expression profile of MC was acquired from Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo) database of NCBI (GEO accession: GSE78933) with the platform of [HTA-2_0] Affymetrix Human Transcriptome Array 2.0 [transcript (gene) version]. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE78933"], "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:GSE78933"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30559147", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1042/BSR20181369", "sha256": "sha256:eea34288c4db2b60ef3389af0132439d409a94b7c8cab5cfee3c1e31959a144e", "bytes": 24635, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1042/BSR20181369", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6340944", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE78933", "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=GSE78933", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE78933", "version": null, "note": "The expression profile of MC was acquired from Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo) database of NCBI (GEO accession: GSE78933) with the platform of [HTA-2_0] Affymetrix Human Transcriptome Array 2.0 [transcript (gene) version]. 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Finally, apoptosis was detected by flow cytometry. Results: Tot", "ese screened genes is also related with cell apoptosis. Conclusion: GNG5, LPAR3, MAPK8, and PSMC6 m", "ight be candidate biomarkers associated with apoptosis in MC."], "order_basis": "paper_text_order:10", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ion of hub nodes was detected by qRT-PCR and Western blot. For regulating the expression of these gene", "ere hub nodes with higher degree. RT-PCR and Western blot results showed that GNG5, LPAR3, MAPK8, and"], "order_basis": "paper_text_order:931", "id": "assay:2"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["erexpression vector was constructed or siRNA transfection was used. Finally, apoptosis was detected by", "es, overexpression vector was constructed or siRNA transfection was used. Finally, apoptosis wa"], "order_basis": "paper_text_order:1032", "id": "assay:3"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["was used. Finally, apoptosis was detected by flow cytometry. Results: Total 1342 DEGs were screened, inc"], "order_basis": "paper_text_order:1096", "id": "assay:4"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["cell line (FHC) was purchased from ATCC and cultured in DMEM with 10% FBS. The cells were incubated"], "order_basis": "paper_text_order:2137", "id": "assay:5"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["limma"], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}