Prognostic values of a novel multi-mRNA signature for predicting relapse of cholangiocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32071556", "kind": "science-record", "revision": 8, "content_hash": "sha256:54005c953686bb96c92498ab740de2758178a09a174eaa2891357accea7cb2a1", "created_at": "2026-11-01T15:40:56Z", "updated_at": "2026-11-01T22:01:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognostic values of a novel multi-mRNA signature for predicting relapse of cholangiocarcinoma.", "doi": "10.7150/ijbs.38846", "pmid": "32071556", "authors": ["Han Guo", "Jie Cai", "Xuan Wang", "Bingrui Wang", "Fang Wang", "Xiang Li", "Xiaoye Qu", "Xianming Kong", "Yueqiu Gao", "Hailong Wu", "Xuehua Sun", "Qiang Xia", "Xiaoni Kong"], "journal": "International journal of biological sciences", "year": 2020, "abstract": "Cholangiocarcinoma (CCA) is an epithelial cancer and has high death and recurrence rates, current methods cannot satisfy the need for predicting cancer relapse effectively. So, we aimed at conducting a multi-mRNA signature to improve the relapse prediction of CCA. We analyzed mRNA expression profiling in large CCA cohorts from the Gene Expression Omnibus (GEO) database (GSE76297, GSE32879, GSE26566, GSE31370, and GSE45001) and The Cancer Genome Atlas (TCGA) database. The Least absolute shrinkage and selection operator (LASSO) regression model was used to establish a 7-mRNA-based signature that was significantly related to the recurrence-free survival (RFS) in two test series. Based on the 7-mRNA signature, the cohort TCGA patients could be divided into high-risk or low-risk subgroups with significantly different RFS [p < 0.001, hazard ratio (HR): 48.886, 95% confidence interval (CI): 6.226-3.837E+02]. Simultaneously, the prognostic value of the 7-mRNA signature was confirmed in clinical samples of Ren Ji hospital (p < 0.001, HR: 4.558, 95% CI: 1.829-11.357). Further analysis including multivariable and sub-group analyses revealed that the 7-mRNA signature was an independent prognostic value for recurrence of patients with CCA. In conclusion, our results might provide an efficient tool for relapse prediction and were beneficial to individualized management for CCA patients.", "claims": [{"id": "claim-data-access", "statement": "The gene expression data of CCAs were downloaded from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database. There were five appropriate CCA datasets from the GEO database (GSE76297, GSE32879, GSE26566, GSE31370, and GSE45001) met the following criteria: a). a total of more than 10 samples, including both tumor and non-tumor samples; b) annotated genes accounting for more than 90% of the total transcriptomes (n > 17000); and c) the number of differentially expressed genes (DEGs) more than 100.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32071556", "locator": "sections[3] \"Preparation of CCA datasets\" paragraph 2", "quote": "The gene expression data of CCAs were downloaded from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database. There were five appropriate CCA datasets from the GEO database (GSE76297, GSE32879, GSE26566, GSE31370, and GSE45001) met the following criteria: a). a total of more than 10 samples, including both tumor and non-tumor samples; b) annotated genes accounting for more than 90% of the total transcriptomes (n > 17000); and c) the number of differentially expressed genes (DEGs) more than 100."}], "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:32071556"], "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:GSE26566"], "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:GSE26566"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32071556", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7150/ijbs.38846", "sha256": "sha256:7f937413a2def852508d044ecf3414379c4955038bae6134ee4da3a83867cc69", "bytes": 40755, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7150/ijbs.38846", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7019144", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE26566", "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=GSE26566", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26566", "version": null, "note": "The gene expression data of CCAs were downloaded from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database. There were five appropriate CCA datasets from the GEO database (GSE76297, GSE32879, GSE26566, GSE31370, and GSE45001) met the following criteria: a). a total of more than 10 samples, including both tumor and non-tumor samples; b) annotated genes accounting for more than 90% of the total transcriptomes (n > 17000); and c) the number of differentially expressed genes (DEGs) more than 100.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression data of CCAs were downloaded from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database. 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There were five appropriate CCA datasets from the GEO database (GSE76297, GSE32879, GSE26566, GSE31370, and GSE45001) met the following criteria: a). a total of more than 10 samples, including both tumor and non-tumor samples; b) annotated genes accounting for more than 90% of the total transcriptomes (n > 17000); and c) the number of differentially expressed genes (DEGs) more than 100.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression data of CCAs were downloaded from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database. 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There were five appropriate CCA datasets from the GEO database (GSE76297, GSE32879, GSE26566, GSE31370, and GSE45001) met the following criteria: a). a total of more than 10 samples, including both tumor and non-tumor samples; b) annotated genes accounting for more than 90% of the total transcriptomes (n > 17000); and c) the number of differentially expressed genes (DEGs) more than 100.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression data of CCAs were downloaded from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database. There were five appropriate CCA datasets from the GEO database (GSE76297, GSE32879, GSE26566, GSE31370, and GSE45001) met the following criteria: a). a total of more than 10 samples, including both tumor and non-tumor samples; b) annotated genes accounting for more than 90% of the total transcriptomes (n > 17000); and c) the number of differentially expressed genes (DEGs) more than 100.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM813712", "GSM813713", "GSM813714", "GSM813715", "GSM813716", "GSM813717", "GSM813718", "GSM813719", "GSM813720", "GSM813721", "GSM813722", "GSM813723", "GSM813724", "GSM813725", "GSM813726", "GSM813727", "GSM813728", "GSM813729", "GSM813730", "GSM813731", "GSM813732", "GSM813733", "GSM813734", "GSM813735", "GSM813736", "GSM813737", "GSM813738", "GSM813739", "GSM813740", "GSM813741", "GSM813742", "GSM813743", "GSM813744", "GSM813745", "GSM813746", "GSM813747", "GSM813748"], "sample_count": 37, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Integrative Transcriptomic Profiling reveals Hepatic Stem-like Phenotype and Interplay of EMT and miR-200c in Intrahepatic Cholangiocarcinoma [mRNA]", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE76297", "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=GSE76297", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE76297", "version": null, "note": "The gene expression data of CCAs were downloaded from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database. There were five appropriate CCA datasets from the GEO database (GSE76297, GSE32879, GSE26566, GSE31370, and GSE45001) met the following criteria: a). a total of more than 10 samples, including both tumor and non-tumor samples; b) annotated genes accounting for more than 90% of the total transcriptomes (n > 17000); and c) the number of differentially expressed genes (DEGs) more than 100.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression data of CCAs were downloaded from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database. 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"family": "contingency_analysis", "specific": "fisher_exact", "label": "Categorical (contingency table) analysis", "dsl_operations": ["contingency_table", "chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "Fisher's exact"}}], "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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE76297", "GSE32879", "GSE26566", "GSE31370", "and GSE45001"], "resolved_accessions": ["GSE76297", "GSE32879", "GSE26566", "GSE31370"], "statements": ["The gene expression data of CCAs were downloaded from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database. There were five appropriate CCA datasets from the GEO database (GSE76297, GSE32879, GSE26566, GSE31370, and GSE45001) met the following criteria: a). a total of more than 10 samples, including both tumor and non-tumor samples; b) annotated genes accounting for more than 90% of the total transcriptomes (n > 17000); and c) the number of differentially expressed genes (DEGs) more than 100."], "basis": "The paper names GSE76297, GSE32879, GSE26566, GSE31370 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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