FAM83D is associated with gender, AJCC stage, overall survival and disease-free survival in hepatocellular carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30910840", "kind": "science-record", "revision": 8, "content_hash": "sha256:33a5fd756cbc3d162db40ac3a0a0d01c6a8cac8158adba26750a7e5d8c90fd69", "created_at": "2026-11-01T15:40:43Z", "updated_at": "2026-11-01T22:43:52Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "FAM83D is associated with gender, AJCC stage, overall survival and disease-free survival in hepatocellular carcinoma.", "doi": "10.1042/BSR20181640", "pmid": "30910840", "authors": ["Xuling Liu", "Hong Gao", "Jie Zhang", "Dongying Xue"], "journal": "Bioscience reports", "year": 2019, "abstract": "Prognostic significance of family with sequence similarity 83, member D (FAM83D) in hepatocellular carcinoma (HCC) patients has not been well-investigated using Gene Expression Omnibus (GEO) series and TCGA database, we compared FAM83D expression levels between tumor and adjacent tissues, and correlated FAM83D in tumors with outcomes and clinico-pathological features in HCC patients. Validated in GSE33006, GSE45436, GSE84402 and TCGA, FAM83D was significantly overexpressed in tumor tissues than that in adjacent tissues (all P<0.01). FAM83D up-regulation was significantly associated with worse overall survival (OS) and disease-free survival (DFS) in HCC patients (Log rank P=0.00583 and P=4.178E-04, respectively). Cox analysis revealed that FAM83D high expression was significantly associated with OS in HCC patients [hazard ratio (HR) = 1.44, 95% confidence interval (CI) = 1.005-2.063, P=0.047]. Additionally, patients deceased or recurred/progressed had significantly higher FAM83D mRNA levels than those living or disease-free (P=0.0011 and P=0.0238, respectively). FAM83D high expression group had significantly more male patients and advanced American Joint Committee on Cancer (AJCC) stage cases (P=0.048 and P=0.047, respectively). FAM83D mRNA were significantly overexpressed in male (P=0.0193). Compared with patients with AJCC stage I, those with AJCC stage II and stage III-IV had significantly higher FAM83D mRNA levels (P = 0.0346 and P=0.0045, respectively). In conclusion, overexpressed in tumors, FAM83D is associated with gender, AJCC stage, tumor recurrence and survival in HCC.", "claims": [{"id": "claim-method", "statement": "The gene expression data were processed using the RMA algorithm. Differences between the individual groups were analyzed using Student’s t-test, χ2 test or Ridit analysis. The Kaplan–Meier method was used to compare OS and RFS between different groups, and the log-rank test was used to estimate the difference in survivals. Factors associated with the OS in HCC patients were assessed both by Cox univariate and multivariate analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30910840", "locator": "sections[3] \"Source of data\" paragraph 2", "quote": "The gene expression data were processed using the RMA algorithm."}, {"asset": "source:pmid:30910840", "locator": "sections[5] \"Statistical analysis\" paragraph 2", "quote": "Differences between the individual groups were analyzed using Student’s t-test, χ2 test or Ridit analysis."}, {"asset": "source:pmid:30910840", "locator": "sections[5] \"Statistical analysis\" paragraph 2", "quote": "The Kaplan–Meier method was used to compare OS and RFS between different groups, and the log-rank test was used to estimate the difference in survivals."}, {"asset": "source:pmid:30910840", "locator": "sections[5] \"Statistical analysis\" paragraph 2", "quote": "Factors associated with the OS in HCC patients were assessed both by Cox univariate and multivariate analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Gene expression profiles for HCC including GSE33006, GSE45436 and GSE84402 were obtained from Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/). Tumor and adjacent samples in GSE33006 [17], GSE45436 and GSE84402 [18] were processed on Affymetrix Human Genome U133 Plus 2.0 Array.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30910840", "locator": "sections[3] \"Source of data\" paragraph 2", "quote": "Gene expression profiles for HCC including GSE33006, GSE45436 and GSE84402 were obtained from Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/). Tumor and adjacent samples in GSE33006 [17], GSE45436 and GSE84402 [18] were processed on Affymetrix Human Genome U133 Plus 2.0 Array."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:30910840"], "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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false}}, {"id": "asset:table:pmid:30910840:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:31b2107ecc6767799894f56af3d33968795ed83bf647f597b283e05a804e6f14", "bytes": 804, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#T2", "version": null, "note": "Cox regression analysis of risk factors associated with OS in HCC patients", "structure": {"pmcid": "PMC6504662", "section_index": 8, "section_title": "Associations between FAM83D and outcomes in HCC patients", "row_count": 13, "column_count": 5}, "table": {"label": "Table 2", "caption": "Cox regression analysis of risk factors associated with OS in HCC patients", "rows": [["Variables", "Univariate", "Multivariate"], ["", "HR (95% CI)", "P-value", "HR (95% CI)", "P-value"], ["FAM83D, log2"], ["Low", "1.0", "Reference", "1.0", "Reference"], ["High", "1.624 (1.145–2.304)", "0.007", 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patients", "structure": {"pmcid": "PMC6504662", "section_index": 8, "section_title": "Associations between FAM83D and outcomes in HCC patients", "row_count": 13, "column_count": 5}, "table": {"label": "Table 3", "caption": "Cox regression analysis of risk factors associated with DFS in HCC patients", "rows": [["Variables", "Univariate", "Multivariate"], ["", "HR (95% CI)", "P-value", "HR (95% CI)", "P-value"], ["FAM83D, log2"], ["Low", "1.0", "Reference", "", ""], ["High", "1.362 (1.01–1.835)", "0.043", "", ""], ["AJCC stage"], ["I", "1.0", "Reference", "1.0", "Reference"], ["II", "2.819 (1.961–4.052)", "<0.001", "2.293 (1.527–3.445)", "<0.001"], ["III–IV", "1.982 (1.069–3.678)", "0.03", "", ""], ["Vascular invasion"], ["None", "1.0", "Reference", "1.0", "Reference"], ["Micro", "2.042 (1.022–4.079)", "0.043", "", ""], ["Macro", "2.2 (1.502–3.221)", "<0.001", "1.555 (1.022–2.367)", "0.039"]], "row_count": 13, "column_count": 5, "numeric_cells": 22, "header_rows": 2, "locator": "section[8]/table-wrap[2]#T3"}}, {"id": "asset:table:pmid:30910840:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a13551c5a50932960ef7c03fc08265b3d8150895d605f3f96f3ed3fbd96850b8", "bytes": 1582, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#T1", "version": null, "note": "Characteristics of HCC patients between FAM83D high and FAM83D low groups", "structure": {"pmcid": "PMC6504662", "section_index": 9, "section_title": "Associations between FAM83D and clinico-pathological features in HCC patients", "row_count": 30, "column_count": 4}, "table": {"label": "Table 1", "caption": "Characteristics of HCC patients between FAM83D high and FAM83D low groups", "rows": [["Variables", "FAM83D expression level", "P-value"], ["", "Low (n=184)", "High (n=183)", ""], ["Gender, male (%)", "116 (63.0)", "133 (72.7)", "0.048"], ["Age, median (IQR), years", "61 (17)", "61 (19)", "0.257"], ["BMI, median (IQR), kg/m2", "23.9 (7.31)", "23.8 (7.31)", "0.372"], ["Race, n (%)", "", "", "0.116"], ["Asian", "75 (40.8)", "84 (45.9)", ""], ["White", "96 (52.2)", "83 (45.4)", ""], ["Black or African American", "5 (2.7)", "12 (6.6)", ""], ["Family history of cancer, n (%)", "61 (33.2)", "50 (27.3)", "0.224"], ["Neoplasm histologic grade, n (%)", "", "", ""], ["G1–2", "122 (66.3)", "105 (57.4)", "0.065"], ["G3–4", "59 (32.1)", "76 (41.5)", ""], ["AJCC stage, n (%)", "", "", "0.047"], ["I", "96 (52.2)", "75 (41.0)", ""], ["II", "37 (20.1)", "46 (25.1)", ""], ["III", "34 (18.5)", "51 (27.9)", ""], ["IV", "3 (1.6)", "1 (0.5)", ""], ["Vascular invasion, n (%)", "", "", "0.958"], ["Macro", "9 (4.9)", "8 (4.4)", ""], ["Micro", "46 (25.0)", "44 (24.0)", ""], ["None", "108 (58.7)", "96 (52.5)", ""], ["Child-pugh classification, n (%)", "", "", "0.574"], ["A", "115 (62.5)", "103 (56.3)", ""], ["B", "10 (5.4)", "11 (6.0)", ""], ["C", "1 (0.5)", 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Differences between the individual groups were analyzed using Student’s t-test, χ2 test or Ridit analysis. The Kaplan–Meier method was used to compare OS and RFS between different groups, and the log-rank test was used to estimate the difference in survivals. Factors associated with the OS in HCC patients were assessed both by Cox univariate and multivariate analysis."}}, {"id": "method-2", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {"hazard_ratio": "S in HCC patients (both HR > 1"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-3", "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": "χ2"}}], "targets": [], "gaps": []}, "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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE33006", "GSE45436", "GSE84402"], "resolved_accessions": ["GSE33006", "GSE45436", "GSE84402"], "statements": ["Gene expression profiles for HCC including GSE33006, GSE45436 and GSE84402 were obtained from Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/). Tumor and adjacent samples in GSE33006 [17], GSE45436 and GSE84402 [18] were processed on Affymetrix Human Genome U133 Plus 2.0 Array."], "basis": "The paper names GSE33006, GSE45436, GSE84402 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["logrank_test"], "assets": ["source:pmid:30910840", "data:geo:GSE33006", "asset:table:pmid:30910840:1", "asset:table:pmid:30910840:2", "asset:table:pmid:30910840:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE33006"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:14:17Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 20448, "completion_tokens": 2026, "cached_tokens": 792}}, "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:30910840", "type": "paper", "label": "pmid:30910840"}, {"id": "source:pmid:30910840", "type": "manuscript", "label": "PMID 30910840 full text"}, {"id": "data:geo:GSE33006", "type": "dataset", "label": "GEO GSE33006"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30910840", "type": "paper", "label": "pmid:30910840"}, {"id": "source:pmid:30910840", "type": "manuscript", "label": "PMID 30910840 full text"}, {"id": "data:geo:GSE33006", "type": "dataset", "label": "GEO GSE33006"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30910840", "type": "extraction", "used": ["source:pmid:30910840"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE33006", "type": "accession_resolution", "used": ["data:geo:GSE33006"], "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:30910840", "parent_hash": "sha256:9e12d68a893dba9f898fd9deeed0bc3f441b3a2a0cc7487d226e886280febaac", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE33006 licence not read", "asset:data:geo:GSE33006 not downloaded", "asset:data:geo:GSE45436 licence not read", "asset:data:geo:GSE45436 not downloaded", "asset:data:geo:GSE84402 licence not read", "asset:data:geo:GSE84402 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The gene expression data were processed using the RMA algorithm. Differences between the individual groups were analyzed using Student’s t-test, χ2 test or Ridit analysis. The Kaplan–Meier method was used to compare OS and RFS between different groups, and the log-rank test was used to estimate the difference in survivals. Factors associated with the OS in HCC patients were assessed both by Cox univariate and multivariate analysis."], "order_basis": "analysis_only", "id": "assay:1"}]}