The prognostic value of TPM1-4 in hepatocellular carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34850589", "kind": "science-record", "revision": 3, "content_hash": "sha256:cb7ffbc8595567a5bad645cc9cfd82ca4e675b4cb8b83ccb61b892f9ac956316", "created_at": "2026-11-01T17:36:32Z", "updated_at": "2026-11-01T21:26:42Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The prognostic value of TPM1-4 in hepatocellular carcinoma.", "doi": "10.1002/cam4.4453", "pmid": "34850589", "authors": ["Zhihui Tian", "Jian Zhao", "Yusheng Wang"], "journal": "Cancer medicine", "year": 2022, "abstract": "BACKGROUND: Despite advances in multiple disciplinary diagnoses and treatments, the prognosis of hepatocellular carcinoma (HCC) remains poor. Some evidence has identified that the aberrant expression of tropomyosins (TPMs) is involved with some cancers development. However, prognostic values of TPMs in HCC have not been thoroughly investigated.\nMETHODS: Original TPM1-4 mRNA expression of TCGA HCC data and GTEx was downloaded from UCSC XENA. Oncomine database and GSE46408 were used for verification. Clinical stages and survival analysis of TPM1-4 in HCC were performed by GEPIA2. cBioPortal was utilized to assess TPM1-4 gene alteration in HCC. TIMER2.0 was used for investigating the relevance of TPM1-4 to tumor-infiltrating immune cells in HCC. Additionally, we constructed a TPM1-4 prognostic model to explore the value of TPM1-4 for prognostic evaluation in HCC. LinkedOmics was applied to elucidate TPM3 co-expression networks in HCC.\nRESULTS: This present study showed that TPM1-4 was upregulated in all HCC tissues, and TPM3 overexpression was correlated with poor survival outcomes in patients with HCC. Besides, TPM3 amplification was the main altered type in TPM1-4 genetic alteration, which affected the prognosis of HCC patients. The risk model revealed that TPM1, TPM2, and TPM3 were applied to risk assessment of HCC prognosis, among which TPM3 expression was significantly higher in the high-risk group than that in the low-risk group. Univariate and multivariate cox regression analyses indicated that TPM3 may be an independent prognostic factor of HCC prognosis. In addition, TPM3 co-expression genes mainly participated in the cell cycle by maintaining microtubule cytoskeleton in HCC progression. TPM1-4 was associated with some tumor-infiltrating immune cells in HCC.\nCONCLUSION: Our study detected that the expression level of TPM1-4 was all remarkably elevated in HCC, suggesting that TPM1-4 may serve an important role in HCC development. High TPM3 expression was found to be correlated with poor overall survival, and TPM3 may be an independent prognostic factor for HCC.", "claims": [{"id": "claim-method", "statement": "Univariate and multivariate Cox regression analyses were performed to identify the prognostic value of TPM1–4 in HCC.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34850589", "locator": "sections[6] \"Construction of TPM prognostic model\" paragraph 2", "quote": "Univariate and multivariate Cox regression analyses were performed to identify the prognostic value of TPM1–4 in HCC."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data sets analyzed during the present study are available from online repositories: UCSC XENA, Oncomine database, GSE46408, GEPIA2, cBioportal, TIMER2.0 and LinkedOmics.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34850589", "locator": "sections[22] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The data sets analyzed during the present study are available from online repositories: UCSC XENA, Oncomine database, GSE46408, GEPIA2, cBioportal, TIMER2.0 and LinkedOmics."}], "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:34850589"], "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:GSE46408"], "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:GSE46408"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34850589", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/cam4.4453", "sha256": "sha256:6a97919412c1b71b9fd90adc09789ff5c8d674dd500766428eae6f6d9041006d", "bytes": 41788, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/cam4.4453", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8729055", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE46408", "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=GSE46408", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE46408", "version": null, "note": "The data sets analyzed during the present study are available from online repositories: UCSC XENA, Oncomine database, GSE46408, GEPIA2, cBioportal, TIMER2.0 and LinkedOmics.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data sets analyzed during the present study are available from online repositories: UCSC XENA, Oncomine database, GSE46408, GEPIA2, cBioportal, TIMER2.0 and LinkedOmics.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1129834", "GSM1129835", "GSM1129836", "GSM1129837", "GSM1129838", "GSM1129839", "GSM1129840", "GSM1129841", "GSM1129842", "GSM1129843", "GSM1129844", "GSM1129845"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "4133", "taxon": "Homo sapiens", "title": "Analysis of genes overexpressed in hepatocellular carcinoma", "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:GSE46408 not downloaded", "asset:data:geo:GSE46408 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "Univariate and multivariate Cox regression analyses were performed to identify the prognostic value of TPM1–4 in HCC."}}], "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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