Exploration of ANKRD27 as an immune-related prognostic factor in pan-cancer and hepatocellular carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39834932", "kind": "science-record", "revision": 4, "content_hash": "sha256:236426fa4b0f60597a4cc1094c1c687c61418610b842ff10e4384566b5460a6b", "created_at": "2026-11-01T20:30:08Z", "updated_at": "2026-11-01T22:56:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploration of ANKRD27 as an immune-related prognostic factor in pan-cancer and hepatocellular carcinoma.", "doi": "10.3389/fonc.2024.1511240", "pmid": "39834932", "authors": ["Ningzhe Shen", "Congcong Fan", "Haosun Ying", "Xinmiao Li", "Weizhi Zhang", "Jinglu Yu", "Jianjian Zheng", "Yifei Li"], "journal": "Frontiers in oncology", "year": 2024, "abstract": "Introduction: Ankyrin repeat domain 27 (ANKRD27) has been found to be associated with certain cancers. However, its clinical potential in pan-cancer remains unclear.\nMethods: Public datasets (TCGA and GTEx) were applied to analyze ANKRD27 expression in multiple cancer types and its correlations with immune scores, immune checkpoint genes, and immune modulatory genes. We also examined ANKRD27 expression in hepatocellular carcinoma (HCC) patients using TCGA and GSE14520 datasets. The upregulation of ANKRD27 was verified via qRT-PCR in vitro. Based on TCGA-HCC, external, and GSE14520 cohorts, the associations between ANKRD27 expression and survival outcome were explored via the Kaplan-Meier survival curve. The effects of ANKRD27 reduction on HCC cell growth, movement, and invasion were evaluated by CCK-8, Wound healing, and Transwell assays.\nResults: ANKRD27 exhibited aberrant expression in multiple cancers and was correlated with immune traits, including immune infiltration, immune checkpoint genes, and immune modulatory genes. Elevated expression of ANKRD27 was found in TCGA-HCC and GSE14520 cohorts and was confirmed in HCC cell lines. HCC patients with high ANKRD27 expression had poorer prognosis. In vitro, reducing ANKRD27 decreased the capability of proliferation, migration, and invasion in HCC cells. High ANKRD27 expression was associated with sensitivity to certain drugs.\nConclusion: ANKRD27 displays abnormal levels of expression in different cancer types and is linked to immune status in cancer. Furthermore, ANKRD27 may serve as a prognostic predictor for HCC.", "claims": [{"id": "claim-method", "statement": "The `coxph` function from the R package ‘survival’ was used in Cox regression analysis (16). The Kaplan-Meier survival curve was utilized to analyze the prognostic differences between HCC patients with high- and low- ANKRD27 expression. The Log-rank test was utilized for statistical assessment to attain significance in prognosis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39834932", "locator": "sections[4] \"Assessing the prognostic value across multiple cancer types\" paragraph 2", "quote": "The `coxph` function from the R package ‘survival’ was used in Cox regression analysis (16). The Kaplan-Meier survival curve was utilized to analyze the prognostic differences between HCC patients with high- and low- ANKRD27 expression. The Log-rank test was utilized for statistical assessment to attain significance in prognosis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39834932", "locator": "sections[29] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "HCC patients with high ANKRD27 expression had poorer prognosis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39834932", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "HCC patients with high ANKRD27 expression had poorer prognosis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "HCC patients with high ANKRD27 expression had poorer prognosis.", "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:39834932"], "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:GSE14520"], "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:GSE14520"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39834932", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2024.1511240", "sha256": "sha256:015313bc1f05fc4d14df7e9b46b05da838db0a9f5eef41a2821b75dadd837489", "bytes": 41204, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2024.1511240", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11744007", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE14520", "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=GSE14520", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14520", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . 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The Kaplan-Meier survival curve was utilized to analyze the prognostic differences between HCC patients with high- and low- ANKRD27 expression. The Log-rank test was utilized for statistical assessment to attain significance in prognosis."}}, {"id": "method-2", "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": "high", "quote": "Wilcoxon"}}, {"id": "method-3", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-4", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Log-rank"}}, {"id": "method-5", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO enrichment"}}, {"id": "method-6", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "chi-square"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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