Identification and analysis of key genes related to efferocytosis in colorectal cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39107816", "kind": "science-record", "revision": 3, "content_hash": "sha256:6ae0f04ce3c344246db720cfcbd42364eb926e66ea654441f7499969d0a747fa", "created_at": "2026-11-01T20:29:11Z", "updated_at": "2026-11-01T22:12:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and analysis of key genes related to efferocytosis in colorectal cancer.", "doi": "10.1186/s12920-024-01967-8", "pmid": "39107816", "authors": ["Shengliang Zhang", "Ying Jiang", "Lei Shi", "Tianning Wei", "Zhiwen Lai", "Xuan Feng", "Shiyuan Li", "Detao Tang"], "journal": "BMC medical genomics", "year": 2024, "abstract": "The impact of efferocytosis-related genes (ERGs) on the diagnosis of colorectal cancer (CRC) remains unclear. In this study, efferocytosis-associated biomarkers for the diagnosis of CRC were identified by integrating data from transcriptome sequencing and public databases. Finally, the expression of biomarkers was validated by real-time quantitative polymerase chain reaction (RT-qPCR). Our study may provide a reference for CRC diagnosis.\nBACKGROUND: It has been shown that some efferocytosis related genes (ERGs) are associated with the development of cancer. However, it is still uncertain how ERGs may influence the diagnosis of colorectal cancer (CRC).\nMETHODS: In our study, the CRC cohorts were gained from transcriptome sequencing and the gene expression omnibus (GEO) database (GSE71187). Efferocytosis related biomarkers with diagnostic utility for CRC were identified through combining differentially expressed analysis, machine learning algorithms, and receiver operating characteristic (ROC) analysis. Then, infiltration abundance of immune cells between CRC and control was evaluated. The regulatory networks (including mRNA-miRNA-lncRNA and miRNA/transcription factors (TF)-mRNA networks) were created. Finally, the expression of biomarkers was validated via real-time quantitative polymerase chain reaction (RT-qPCR).\nRESULTS: There were 3 biomarkers (ELMO3, P2RY12, and PDK4) related diagnosis for CRC patients gained. ELMO3 was highly expressed in CRC group, while P2RY12 and PDK4 was lowly expressed. Besides, the infiltrating abundance of 3 immune cells between CRC and control groups was significantly differential, namely activated CD4 memory T cells, macrophages M0, and resting mast cells. We then constructed a mRNA-miRNA-lncRNA network containing 3 mRNAs, 33 miRNAs, and 22 lncRNAs, and a miRNA/TF-mRNA network including 3 mRNAs, 33 miRNAs, and 7 TFs. Additionally, RT-qPCR results revealed that the expression trends of all biomarkers were consistent with the transcriptome sequencing data and GSE71187.\nCONCLUSION: Taken together, this study provides three efferocytosis related biomarkers (ELMO3, P2RY12, and PDK4) for diagnosis of CRC, providing a scientific reference for further studies of CRC.", "claims": [{"id": "claim-method", "statement": "Differences were analyzed via the Wilcoxon test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39107816", "locator": "sections[15] \"Statistical analysis\" paragraph 2", "quote": "Differences were analyzed via the Wilcoxon test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data is provided within the manuscript or supplementary information files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39107816", "locator": "sections[32] \"Data availability\" paragraph 2", "quote": "Data is provided within the manuscript or supplementary information files."}], "state": "complete"}, {"id": "claim-target-result", "statement": "There were 3 biomarkers (ELMO3, P2RY12, and PDK4) related diagnosis for CRC patients gained.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39107816", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "There were 3 biomarkers (ELMO3, P2RY12, and PDK4) related diagnosis for CRC patients gained."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "There were 3 biomarkers (ELMO3, P2RY12, and PDK4) related diagnosis for CRC patients gained.", "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:39107816"], "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:GSE71187"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE71187"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39107816", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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Our study may provide a reference for CRC", "time quantitative polymerase chain reaction (RT-qPCR). RESULTS: There were 3 biomarkers (ELMO3, P", "3 mRNAs, 33 miRNAs, and 7 TFs. Additionally, RT-qPCR results revealed that the expression trends", "e quantitative polymerase chain reaction (RT-qPCR). Our study may provide a reference for CRC"], "order_basis": "paper_text_order:422", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Differences were analyzed via the Wilcoxon test."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}