Immune-related gene-based model predicts the survival of colorectal carcinoma and reflected various biological statuses.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37920710", "kind": "science-record", "revision": 2, "content_hash": "sha256:baa825447a670b873fe1b00e55ad3458d1ae6a0debda5dcb87da51c84a2a9dff", "created_at": "2026-11-01T19:02:48Z", "updated_at": "2026-11-01T21:31:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Immune-related gene-based model predicts the survival of colorectal carcinoma and reflected various biological statuses.", "doi": "10.3389/fmolb.2023.1277933", "pmid": "37920710", "authors": ["Zhengchun Kang", "Bingchen Chen", "Xiuzhu Ma", "Feihu Yan", "Zhen Wang"], "journal": "Frontiers in molecular biosciences", "year": 2023, "abstract": "Bakcground: Prognosis of colorectal cancer (CRC) varies due to complex genetic-microenviromental interactions, and multiple gene-based prognostic models have been highlighted. Material and Method: In this work, the immune-related genes' expression-based model was developed and the scores of each sample were calculated. The correlation between the model and clinical information, immune infiltration, drug response and biological pathways were analyzed. Results: The high-score samples have a significantly longer survival (overall survival and progression-free survival) period than those with a low score, which was validated across seven datasets containing 1,325 samples (GSE17536 (N = 115), GSE17537 (N = 55), GSE33113 (N = 90), GSE37892 (N = 130), GSE38832 (N = 74), GSE39582 (N = 481), and TCGA (N = 380)). The score is significantly associated with clinical indicators, including age and stage, and further associated with PD-1/PD-L1 gene expression. Furthermore, high-score samples have significantly higher APC and a lower MUC5B mutation rate. The high-score samples show more immune infiltration (including CD4+ and CD8+ T cells, M1/M2 macrophages, and NK cells). Enriched pathway analyses showed that cancer-related pathways, including immune-related pathways, were significantly activated in high-score samples and that some drugs have significantly lower IC50 values than those with low score. Conclusion: The model developed based on immune-related genes is robust and reflected various statuses of CRC and may be a potential clinical indicator.", "claims": [{"id": "claim-method", "statement": "Differentially mutated genes between groups were evaluated using Fisher’s exact test (only non-synonymous mutation used), and significantly different (p <0.05) mutations were identified.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37920710", "locator": "sections[16] \"Genetic association\" paragraph 2", "quote": "Differentially mutated genes between groups were evaluated using Fisher’s exact test (only non-synonymous mutation used), and significantly different (p <0.05) mutations were identified."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37920710", "locator": "sections[23] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "High-score samples have a significantly higher APC mutation rate and a lower MUC5B mutation rate than low-score samples (p <0.05).", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "By comparing high-/low-score samples, it is found that the APC gene mutation rate of high-score samples is significantly higher than that of low-score samples, while MUC5B values are lower in high-score samples (p <0.05; Figure 4A)."}, "evidence": [{"asset": "source:pmid:37920710", "locator": "sections[6] \"Genetic signature of high-score samples\" paragraph 2", "quote": "By comparing high-/low-score samples, it is found that the APC gene mutation rate of high-score samples is significantly higher than that of low-score samples, while MUC5B values are lower in high-score samples (p <0.05; Figure 4A)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "High-score samples have a significantly higher APC mutation rate and a lower MUC5B mutation rate than low-score samples (p <0.05).", "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:37920710"], "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:GSE17536"], "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:GSE17536"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37920710", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fmolb.2023.1277933", "sha256": "sha256:136eb41e98d6408e888ce266ac590b84fe96608d51a2307c30c799ae70ad76b1", "bytes": 44726, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fmolb.2023.1277933", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10619740", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE17536", "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=GSE17536", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE17536", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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