Identification of the function of FOSB in cholangiocarcinoma using bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38192979", "kind": "science-record", "revision": 4, "content_hash": "sha256:11cf060afed7a99de6a73fb21dcdff3bcbcb329cb1035c3ac6da38ae1317ba6f", "created_at": "2026-11-01T19:20:06Z", "updated_at": "2026-11-01T22:53:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of the function of FOSB in cholangiocarcinoma using bioinformatics analysis.", "doi": "10.21037/tcr-23-829", "pmid": "38192979", "authors": ["Yihang Zhao", "Hong Tang", "Yaxian Kuai", "Jianhua Xu", "Bin Sun", "Yang Li"], "journal": "Translational cancer research", "year": 2023, "abstract": "Background: Exploring the potential mechanism of cholangiocarcinoma (CCA) metabolic reprogramming is significant for guiding clinical treatment. However, related research and exploration are still lacking. Therefore, we aimed to identify a reliable metabolism-related gene or biomarker of CCA using bioinformatics analysis.\nMethods: The GSE26566, GSE45001, and GSE132305 datasets were obtained from the Gene Expression Omnibus (GEO) database. Differently expressed genes (DEGs) between CCA tissues and adjacent tissues were screened out. The key gene was identified through enrichment and functional analysis, and its immune and clinical correlation was investigated utilizing the Tumor Immune Evaluation Resource (TIMER2.0), the Tumor-Immune System Interactions Database (TISIDB), the Gene Expression Profiling Interactive Analysis (GEPIA2), and the Kaplan-Meier Plotter. Finally, immunohistochemistry (IHC) was performed to validate the results.\nResults: By analysis, the expression of FBJ murine osteosarcoma viral oncogene homolog B (FOSB) was significantly downregulated in CCA tissues when compared with adjacent tissues. Moreover, the expression levels of FOSB positively correlated with tumor-infiltrating immune cells in most tumors, and patients with high FOSB expression tended to have a better prognosis. The FOSB and SIRT3/HIF1A axes have similar expression trends and metabolic functions in CCA cells, and the correlation between of them was preliminarily explored by IHC experiments.\nConclusions: The expression levels of FOSB are closely related to the prognosis of CCA patients, which may be a predictive indicator for prognosis and immunotherapy.", "claims": [{"id": "claim-method", "statement": "The data were normalized using the limma package of RStudio (Posit; Boston, MA, USA) and differently expressed genes (DEGs) were obtained between CCA and adjacent tissues [|log fold change (FC)| >1, P value <0.05, and the base of |logFC| was 2]. Kaplan-Meier Plotter and Gene Expression Profiling Interactive Analysis (GEPIA2) website were used to plot the survival analysis map of tumors (28,29).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38192979", "locator": "sections[5] \"Datasets downloading and differential analysis\" paragraph 2", "quote": "The data were normalized using the limma package of RStudio (Posit; Boston, MA, USA) and differently expressed genes (DEGs) were obtained between CCA and adjacent tissues [|log fold change (FC)| >1, P value <0.05, and the base of |logFC| was 2]."}, {"asset": "source:pmid:38192979", "locator": "sections[8] \"Survival analysis\" paragraph 2", "quote": "Kaplan-Meier Plotter and Gene Expression Profiling Interactive Analysis (GEPIA2) website were used to plot the survival analysis map of tumors (28,29)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data Sharing Statement: Available at https://tcr.amegroups.com/article/view/10.21037/tcr-23-829/dss", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38192979", "locator": "sections[24] \"fn-group\" paragraph 1", "quote": "Data Sharing Statement: Available at https://tcr.amegroups.com/article/view/10.21037/tcr-23-829/dss"}], "state": "complete"}, {"id": "claim-target-result", "statement": "FOSB expression is closely related to prognosis in cholangiocarcinoma patients and may be a predictive indicator for prognosis and immunotherapy.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38192979", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "The expression levels of FOSB are closely related to the prognosis of CCA patients, which may be a predictive indicator for prognosis and immunotherapy."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "FOSB expression is closely related to prognosis in cholangiocarcinoma patients and may be a predictive indicator for prognosis and immunotherapy.", "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:38192979"], "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:GSE132305"], "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:GSE132305"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38192979", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tcr-23-829", "sha256": 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Kaplan-Meier Plotter and Gene Expression Profiling Interactive Analysis (GEPIA2) website were used to plot the survival analysis map of tumors (28,29)."}}, {"id": "method-2", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {"fold_change": "adjacent tissues [|log fold change (FC)| >1, P value <0"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "limma"}}], "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": ["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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Finally, immunohistochemistry (IHC) was performed to validate the results.", "eier Plotter. Finally, immunohistochemistry (IHC) was performed to validate the results. Resu", "etween of them was preliminarily explored by IHC experiments. Conclusions: The expression lev"], "order_basis": "paper_text_order:929", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Results: By analysis, the expression of FBJ murine osteosarcoma viral oncogene homolog B (FOSB)", "represents negative correlation). FOSB, FBJ murine osteosarcoma viral oncogene homolog B."], "order_basis": "paper_text_order:1040", "id": "assay:2"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The data were normalized using the limma package of RStudio (Posit; Boston, MA, USA) and differently expressed genes (DEGs) were obtained between CCA and adjacent tissues [|log fold change (FC)| >1, P value <0.05, and the base of |logFC| was 2]. Kaplan-Meier Plotter and Gene Expression Profiling Interactive Analysis (GEPIA2) website were used to plot the survival analysis map of tumors (28,29)."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}