Identification of autophagy-related biomarker and analysis of immune infiltrates in oral carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35421271", "kind": "science-record", "revision": 5, "content_hash": "sha256:a7ae3b2c3cf8440a9ef72b9826e4ee419bcf6076d54c96d674b3651bf9800c5f", "created_at": "2026-11-01T18:14:14Z", "updated_at": "2026-11-01T22:48:50Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of autophagy-related biomarker and analysis of immune infiltrates in oral carcinoma.", "doi": "10.1002/jcla.24417", "pmid": "35421271", "authors": ["Honghai Fu", "Dianguo Zhao", "Legang Sun", "Yumei Huang", "Xiangrui Ma"], "journal": "Journal of clinical laboratory analysis", "year": 2022, "abstract": "BACKGROUND: Autophagy plays a vital role in the progression of the tumor. We aimed to investigate the expression, prognostic value, and immune infiltration of autophagy-related genes in oral carcinoma via bioinformatics analysis.\nMETHODS: The microarray datasets (GSE146483 and GSE23558) of oral carcinoma were downloaded from Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between normal and diseased groups were identified by the Limma package. The screened autophagy-related gene was further validated by the human protein atlas (HPA) database, TCGA database, and GSE78060 dataset.\nRESULTS: A total of 18 upregulated (top 10: EGFR, TNF, FADD, AURKA, E2F1, CHEK1, BRCA1, BIRC5, EIF2AK2, and CSF2) and 31 downregulated (top 10: MAP1LC3A, PARK2, AGT, IGF1, TP53INP1, CXCL12, IKBKB, SESN1, ULK2, and RRAGD) autophagy-related (DEGs) were identified, and FADD was found to be related to the prognosis of oral cancer patients. Gene set enrichment analysis indicated that FADD-associated genes were significantly enriched in immune-related pathways. Moreover, correlation analysis revealed that FADD expression was associated with immune infiltrates. Upregulation of FADD is associated with poor survival and immune infiltrates in oral cancer.\nCONCLUSION: We speculated that FADD is involved in the immune regulation of oral cancer, as well as autophagy.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes (DEGs) between normal and diseased groups were identified by Limma package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35421271", "locator": "sections[0] \"Abstract\" paragraph 6", "quote": "Differentially expressed genes (DEGs) between normal and diseased groups were identified by Limma package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data involved in the present study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35421271", "locator": "sections[25] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "All data involved in the present study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Upregulation of FADD is associated with poor survival and immune infiltrates in oral cancer.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35421271", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Upregulation of FADD is associated with poor survival and immune infiltrates in oral cancer."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Upregulation of FADD is associated with poor survival and immune infiltrates in oral 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:35421271"], "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:GSE146483"], "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:GSE146483"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35421271", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/jcla.24417", "sha256": "sha256:ac34da059b26ad6d990b295f7212e80f6c47d5bb2660694761f2a14a9a9c0404", "bytes": 33632, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/jcla.24417", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9102594", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE146483", "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=GSE146483", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE146483", "version": null, "note": "All data involved in the present study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data involved in the present study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4387009", "GSM4387010", "GSM4387011", "GSM4387012", "GSM4387013", "GSM4387014", "GSM4387015", "GSM4387016", "GSM4387017", "GSM4387018", "GSM4387019"], "sample_count": 11, "group_sizes": null, "group_sizes_basis": null, "platform": "17077", "taxon": "Homo sapiens", "title": "Development of gene expression signatures for oral cancer", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE23558", "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=GSE23558", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE23558", "version": null, "note": "All data involved in the present study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data involved in the present study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM577914", "GSM577915", "GSM577916", "GSM577917", "GSM577918", "GSM577919", "GSM577920", "GSM577921", "GSM577922", "GSM577923", "GSM577924", "GSM577925", "GSM577926", "GSM577927", "GSM577928", "GSM577929", "GSM577930", "GSM577931", "GSM577932", "GSM577933", "GSM577934", "GSM577935", "GSM577936", "GSM577937", "GSM577938", "GSM577939", "GSM577940", "GSM577941", "GSM577942", "GSM577943", "GSM577944", "GSM577945"], "sample_count": 32, "group_sizes": null, "group_sizes_basis": null, "platform": "6480", "taxon": "Homo sapiens", "title": "Gene Expression Profiling of Oral Squamous Cell Carcinoma", "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:GSE78060", "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=GSE78060", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE78060", "version": null, "note": "All data involved in the present study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data involved in the present study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2065795", "GSM2065796", "GSM2065797", "GSM2065798", "GSM2065799", "GSM2065800", "GSM2065801", "GSM2065802", "GSM2065803", "GSM2065804", "GSM2065805", "GSM2065806", "GSM2065807", "GSM2065808", "GSM2065809", "GSM2065810", "GSM2065811", "GSM2065812", "GSM2065813", "GSM2065814", "GSM2065815", "GSM2065816", "GSM2065817", "GSM2065818", "GSM2065819", "GSM2065820", "GSM2065821", "GSM2065822", "GSM2065823", "GSM2065824"], "sample_count": 30, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "A gene expression profiling to predict recurrence of advanced tongue squamous cell carcinoma (TSCC): Discovery and external validation", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE146483 not downloaded", "asset:data:geo:GSE146483 licence not read", "asset:data:geo:GSE23558 not downloaded", "asset:data:geo:GSE23558 licence not read", "asset:data:geo:GSE78060 not downloaded", "asset:data:geo:GSE78060 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differentially expressed genes (DEGs) between normal and diseased groups were identified by Limma package."}}], "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE146483", "GSE23558", "GSE78060"], "resolved_accessions": ["GSE146483", "GSE23558", "GSE78060"], "statements": ["All data involved in the present study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE146483, GSE23558, GSE78060 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:35421271", "data:geo:GSE146483"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE146483"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:42:00Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10381, "completion_tokens": 1926, "cached_tokens": 188}}, "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:35421271", "type": "paper", "label": "pmid:35421271"}, {"id": "source:pmid:35421271", "type": "manuscript", "label": "PMID 35421271 full text"}, {"id": "data:geo:GSE146483", "type": "dataset", "label": "GEO GSE146483"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35421271", "type": "paper", "label": "pmid:35421271"}, {"id": "source:pmid:35421271", "type": "manuscript", "label": "PMID 35421271 full text"}, {"id": "data:geo:GSE146483", "type": "dataset", "label": "GEO GSE146483"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35421271", "type": "extraction", "used": ["source:pmid:35421271"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE146483", "type": "accession_resolution", "used": ["data:geo:GSE146483"], "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:35421271", "parent_hash": "sha256:a0de6eb6a29d272cce1042e2e48eefd9019a5549d393dd9ba5d21262cb15e49f", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE146483 licence not read", "asset:data:geo:GSE146483 not downloaded", "asset:data:geo:GSE23558 licence not read", "asset:data:geo:GSE23558 not downloaded", "asset:data:geo:GSE78060 licence not read", "asset:data:geo:GSE78060 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ma via bioinformatics analysis. METHODS: The microarray datasets (GSE146483 and GSE23558) of oral ca"], "order_basis": "paper_text_order:298", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Differentially expressed genes (DEGs) between normal and diseased groups were identified by Limma package."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}