Comprehensive analysis of autophagy associated genes and immune infiltrates in cervical cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38800011", "kind": "science-record", "revision": 3, "content_hash": "sha256:e652c782009299e5d08d4a5695ae1985df9b4f1a7d6fb633738fd5262717f0d6", "created_at": "2026-11-01T19:20:45Z", "updated_at": "2026-11-01T22:11:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive analysis of autophagy associated genes and immune infiltrates in cervical cancer.", "doi": "10.22038/IJBMS.2024.74431.16168", "pmid": "38800011", "authors": ["Shuzhen Li", "Kun Gao", "Desheng Yao"], "journal": "Iranian journal of basic medical sciences", "year": 2024, "abstract": "Objectives: Cervical cancer (CC) is the most common gynecological malignant tumor and the fourth leading cause of cancer-related death in women. The progression of CC is significantly affected by autophagy. Our objective was to use bioinformatics analysis to explore the expression, prognostic significance, and immune infiltration of autophagy-related genes in CC.\nMaterials and Methods: We identified a set of autophagy-related differentially expressed genes (ARDEGs) from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. ARDEGs were further validated by The Human Protein Atlas (HPA), GSE52903, and GSE39001 dataset. Hub genes were found by the STRING network and Cytoscape. We performed Gene Set Enrichment Analysis (GSEA), Gene ontology analysis (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and immune infiltration analysis to further understand the functions of the hub genes. Kaplan-Meier (K-M) and receiver operating characteristic (ROC) were used to check the hub genes.\nResults: A total of 10 up-regulated (CXCR4, BAX, SPHK1, EIF2AK2, TBK1, TNFSF10, ITGB4, CDKN2A, IL24, and BIRC5) and 19 down-regulated (PINK1, ATG16L2, ATG4D, IKBKE, MLST8, MAPK3, ERBB2, ULK3, TP53INP2, MTMR14, BNIP3, FOS, CCL2, FAS, CAPNS1, HSPB8, PTK6, FKBP1B , and DNAJB1) ARDEGs were identified. The ARDEGs were enriched in cell growth, apoptosis, human papillomavirus infection, and cytokine-mediated. Then, we found that low expression of MAPK3 was associated with poor prognosis in CC patients and was significantly enriched in immune pathways. In addition, the expression of MAPK3 was significantly positively correlated with the infiltration levels of macrophages, B cells, mast cell activation, and cancer-associated fibroblasts. Furthermore, MAPK3 was positively correlated with LGALS9, and negatively correlated with CTLA4 and CD40.\nConclusion: Our results show that MAPK3 can be used as a new prognostic biomarker to predict the prognosis of patients with CC.", "claims": [{"id": "claim-method", "statement": "We plotted the KM curve for ARDEGs(http://kmplot.com/ analysis) (27).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38800011", "locator": "sections[2] \"Materials and Methods\" paragraph 15", "quote": "We plotted the KM curve for ARDEGs(http://kmplot.com/ analysis) (27)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets included in this study can be downloaded from public repositories including the UCSC Xena database (http://genome.ucsc.edu), the TCGA Database (https://portal.gdc.cancer.gov/, and the GeneCards Database (https://www.genecards.org/ ).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38800011", "locator": "sections[7] \"Data Availability\" paragraph 2", "quote": "The datasets included in this study can be downloaded from public repositories including the UCSC Xena database (http://genome.ucsc.edu), the TCGA Database (https://portal.gdc.cancer.gov/, and the GeneCards Database (https://www.genecards.org/ )."}], "state": "complete"}, {"id": "claim-target-result", "statement": "MAPK3 can be used as a new prognostic biomarker to predict the prognosis of patients with cervical cancer.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38800011", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Our results show that MAPK3 can be used as a new prognostic biomarker to predict the prognosis of patients with CC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "MAPK3 can be used as a new prognostic biomarker to predict the prognosis of patients with cervical cancer.", "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:38800011"], "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:GSE39001"], "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:GSE39001"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38800011", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.22038/IJBMS.2024.74431.16168", "sha256": 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The ARDEGs were enriched in cell growth, apoptosis, human papillomavirus infection, and cytokin"], "order_basis": "paper_text_order:1416", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["uman Genome U133A Array platform, along with microarray gene expression profiling data from 21 CC pa", "rray [transcript (gene) version], along with microarray gene expression profiling data from 55 CC pa", "rray [transcript (gene) version], along with microarray gene expression profiling data from 19 CC pa", "identified using the GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array platform. T"], "order_basis": "paper_text_order:2969", "id": "assay:2"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["an proteomes (28). In our study, we utilized immunohistochemistry to validate the protein expression of MAPK3,"], "order_basis": "paper_text_order:7520", "id": "assay:3"}, {"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": ["We plotted the KM curve for ARDEGs(http://kmplot.com/ analysis) (27)."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}