Anoikis-related gene signatures in colorectal cancer: implications for cell differentiation, immune infiltration, and prognostic prediction.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38773226", "kind": "science-record", "revision": 4, "content_hash": "sha256:2ccea2e0bbb1f11e5d6d790ea2c0f8c2f335e5a5988bbbd4bb2b15845de56ed4", "created_at": "2026-11-01T19:20:43Z", "updated_at": "2026-11-01T22:11:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Anoikis-related gene signatures in colorectal cancer: implications for cell differentiation, immune infiltration, and prognostic prediction.", "doi": "10.1038/s41598-024-62370-y", "pmid": "38773226", "authors": ["Taohui Ding", "Zhao Shang", "Hu Zhao", "Renfeng Song", "Jianyong Xiong", "Chuan He", "Dan Liu", "Bo Yi"], "journal": "Scientific reports", "year": 2024, "abstract": "Colorectal cancer (CRC) is a malignant tumor originating from epithelial cells of the colon or rectum, and its invasion and metastasis could be regulated by anoikis. However, the key genes and pathways regulating anoikis in CRC are still unclear and require further research. The single cell transcriptome dataset GSE221575 of GEO database was downloaded and applied to cell subpopulation type identification, intercellular communication, pseudo time cell trajectory analysis, and receptor ligand expression analysis of CRC. Meanwhile, the RNA transcriptome dataset of TCGA, the GSE39582, GSE17536, and GSE17537 datasets of GEO were downloaded and merged into one bulk transcriptome dataset. The differentially expressed genes (DEGs) related to anoikis were extracted from these data sets, and key marker genes were obtained after feature selection. A clinical prognosis prediction model was constructed based on the marker genes and the predictive effect was analyzed. Subsequently, gene pathway analysis, immune infiltration analysis, immunosuppressive point analysis, drug sensitivity analysis, and immunotherapy efficacy based on the key marker genes were conducted for the model. In this study, we used single cell datasets to determine the anoikis activity of cells and analyzed the DEGs of cells based on the score to identify the genes involved in anoikis and extracted DEGs related to the disease from the transcriptome dataset. After dimensionality reduction selection, 7 marker genes were obtained, including TIMP1, VEGFA, MYC, MSLN, EPHA2, ABHD2, and CD24. The prognostic risk model scoring system built by these 7 genes, along with patient clinical data (age, tumor stage, grade), were incorporated to create a nomogram, which predicted the 1-, 3-, and 5-years survival of CRC with accuracy of 0.818, 0.821, and 0.824. By using the scoring system, the CRC samples were divided into high/low anoikis-related prognosis risk groups, there are significant differences in immune infiltration, distribution of immune checkpoints, sensitivity to chemotherapy drugs, and efficacy of immunotherapy between these two risk groups. Anoikis genes participate in the differentiation of colorectal cancer tumor cells, promote tumor development, and could predict the prognosis of colorectal cancer.", "claims": [{"id": "claim-method", "statement": "The least absolute shrinkage and selection operator (LASSO) analysis was performed on the prognosis-related genes to further select the characteristic genes and to develop a prognostic model.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38773226", "locator": "sections[9] \"Building and validation of a prognosis-prediction model\" paragraph 2", "quote": "The least absolute shrinkage and selection operator (LASSO) analysis was performed on the prognosis-related genes to further select the characteristic genes and to develop a prognostic model."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used in this study are available in TCGA (https://portal.gdc.cancer.gov/), GEO (https://www.ncbi.nlm.nih.gov/geo/), and TIDE databases (http://tide.dfci.harvard.edu/). IMvigor210 database was downloaded by the IMvigor210CoreBiologies R package (http://research-pub.gene.com/IMvigor210CoreBiologies/packageVersions/). The datas generated and analysed during the current study are available from the the article and supplementary information.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38773226", "locator": "sections[45] \"notes\" paragraph 1", "quote": "The datasets used in this study are available in TCGA (https://portal.gdc.cancer.gov/), GEO (https://www.ncbi.nlm.nih.gov/geo/), and TIDE databases (http://tide.dfci.harvard.edu/). IMvigor210 database was downloaded by the IMvigor210CoreBiologies R package (http://research-pub.gene.com/IMvigor210CoreBiologies/packageVersions/). The datas generated and analysed during the current study are available from the the article and supplementary information."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified seven anoikis-related prognostic marker genes and constructed a nomogram with 1-, 3-, and 5-year survival accuracies of 0.818, 0.821, and 0.824, respectively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38773226", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The prognostic risk model scoring system built by these 7 genes, along with patient clinical data (age, tumor stage, grade), were incorporated to create a nomogram, which predicted the 1-, 3-, and 5-years survival of CRC with accuracy of 0.818, 0.821, and 0.824."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study identified seven anoikis-related prognostic marker genes and constructed a nomogram with 1-, 3-, and 5-year survival accuracies of 0.818, 0.821, and 0.824, respectively.", "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:38773226"], "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. 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IMvigor210 database was downloaded by the IMvigor210CoreBiologies R package (http://research-pub.gene.com/IMvigor210CoreBiologies/packageVersions/). The datas generated and analysed during the current study are available from the the article and supplementary information.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in this study are available in TCGA (https://portal.gdc.cancer.gov/), GEO (https://www.ncbi.nlm.nih.gov/geo/), and TIDE databases (http://tide.dfci.harvard.edu/). IMvigor210 database was downloaded by the IMvigor210CoreBiologies R package (http://research-pub.gene.com/IMvigor210CoreBiologies/packageVersions/). 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Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics [Expression]", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE17536 not downloaded", "asset:data:geo:GSE17536 licence not read", "asset:data:geo:GSE17537 not downloaded", "asset:data:geo:GSE17537 licence not read", "asset:data:geo:GSE221575 not downloaded", "asset:data:geo:GSE221575 licence not read", "asset:data:geo:GSE39582 not downloaded", "asset:data:geo:GSE39582 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE39582", "GSE17536", "GSE17537", "GSE221575"], "resolved_accessions": ["GSE39582", "GSE17536", "GSE17537", "GSE221575"], "statements": ["The datasets used in this study are available in TCGA (https://portal.gdc.cancer.gov/), GEO (https://www.ncbi.nlm.nih.gov/geo/), and TIDE databases (http://tide.dfci.harvard.edu/). IMvigor210 database was downloaded by the IMvigor210CoreBiologies R package (http://research-pub.gene.com/IMvigor210CoreBiologies/packageVersions/). The datas generated and analysed during the current study are available from the the article and supplementary information."], "basis": "The paper names GSE39582, GSE17536, GSE17537, GSE221575 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:38773226", "data:geo:GSE17536"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE17536"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:19:05Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15292, "completion_tokens": 3217, "cached_tokens": 128}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:38773226", "type": "paper", "label": "pmid:38773226"}, {"id": "source:pmid:38773226", "type": "manuscript", "label": "PMID 38773226 full text"}, {"id": "data:geo:GSE17536", "type": "dataset", "label": "GEO GSE17536"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38773226", "type": "paper", "label": "pmid:38773226"}, {"id": "source:pmid:38773226", "type": "manuscript", "label": "PMID 38773226 full text"}, {"id": "data:geo:GSE17536", "type": "dataset", "label": "GEO GSE17536"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38773226", "type": "extraction", "used": ["source:pmid:38773226"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE17536", "type": "accession_resolution", "used": ["data:geo:GSE17536"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:38773226", "parent_hash": "sha256:f9cbb5e23efe2c450b6cbb56c70b2e8c065e9ea54d7a90c3c11e910077ef13ba", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE17536 licence not read", "asset:data:geo:GSE17536 not downloaded", "asset:data:geo:GSE17537 licence not read", "asset:data:geo:GSE17537 not downloaded", "asset:data:geo:GSE221575 licence not read", "asset:data:geo:GSE221575 not downloaded", "asset:data:geo:GSE39582 licence not read", "asset:data:geo:GSE39582 not downloaded", "execution.not_run", "method.group_comparison_wilcoxon", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "assays": [{"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Wilcoxon"], "order_basis": "analysis_only", "id": "assay:1"}]}