{ "sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35036134", "kind": "science-record", "revision": 5, "content_hash": "sha256:72157a942e231ccc2c6d35d0c7fddc99e357c2b7d9092437266945243912f900", "created_at": "2026-11-01T17:36:45Z", "updated_at": "2026-11-01T22:48:14Z", "generator": { "name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01" }, "paper": { "state": "complete", "title": "Identification of HMMR as a prognostic biomarker for patients with lung adenocarcinoma via integrated bioinformatics analysis.", "doi": "10.7717/peerj.12624", "pmid": "35036134", "authors": [ "Zhaodong Li", "Hongtian Fei", "Siyu Lei", "Fengtong Hao", "Lijie Yang", "Wanze Li", "Laney Zhang", "Rui Fei" ], "journal": "PeerJ", "year": 2021, "abstract": "BACKGROUND: Lung adenocarcinoma (LUAD) is the most prevalent tumor in lung carcinoma cases and threatens human life seriously worldwide. Here we attempt to identify a prognostic biomarker and potential therapeutic target for LUAD patients.\nMETHODS: Differentially expressed genes (DEGs) shared by GSE18842, GSE75037, GSE101929 and GSE19188 profiles were determined and used for protein-protein interaction analysis, enrichment analysis and clinical correlation analysis to search for the core gene, whose expression was further validated in multiple databases and LUAD cells (A549 and PC-9) by quantitative real-time PCR (qRT-PCR) and western blot analyses. Its prognostic value was estimated using the Kaplan-Meier method, meta-analysis and Cox regression analysis based on the Cancer Genome Atlas (TCGA) dataset and co-expression analysis was conducted using the Oncomine database. Gene Set Enrichment Analysis (GSEA) was performed to illuminate the potential functions of the core gene.\nRESULTS: A total of 115 shared DEGs were found, of which 24 DEGs were identified as candidate hub genes with potential functions associated with cell cycle and FOXM1 transcription factor network. Among these candidates, HMMR was identified as the core gene, which was highly expressed in LUAD as verified by multiple datasets and cell samples. Besides, high HMMR expression was found to independently predict poor survival in patients with LUAD. Co-expression analysis showed that HMMR was closely related to FOXM1 and was mainly involved in cell cycle as suggested by GSEA.\nCONCLUSION: HMMR might be served as an independent prognostic biomarker for LUAD patients, which needs further validation in subsequent studies.", "claims": [ { "id": "claim-method", "statement": "Its prognostic value was estimated using the Kaplan-Meier method, meta-analysis and Cox regression analysis based on the Cancer Genome Atlas (TCGA) dataset and co-expression analysis was conducted using the Oncomine database.", "kind": "methodological", "target": null, "evidence": [ { "asset": "source:pmid:35036134", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Its prognostic value was estimated using the Kaplan-Meier method, meta-analysis and Cox regression analysis based on the Cancer Genome Atlas (TCGA) dataset and co-expression analysis was conducted using the Oncomine database." } ], "state": "complete" } ], "gaps": [] }, "experiment": { "state": "complete", "objective": "", "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:35036134" ], "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:GSE101929" ], "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:GSE101929" ], "outputs": [ "the replicated result and its comparison" ], "instruments": [], "reagents": [] } ], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": [] }, "data": { "state": "partial", "assets": [ { "id": "source:pmid:35036134", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.12624", "sha256": "sha256:fed7512d3c424d35872ccc4be8d3580f6a08dcacde27620eab85af105f4b4e63", "bytes": 52218, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.12624", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": { "pmcid": "PMC8710063", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body" } }, { "id": "data:geo:GSE101929", "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=GSE101929", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE101929", "version": null, "note": "Multiple gene expression profiles retrieved from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/) were used for identification of DEGs and candidate core genes.", "structure": { "repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Multiple gene expression profiles retrieved from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/) were used for identification of DEGs and candidate core genes.", "access_statement_kind": "repository_route_statement", "sample_accessions": [ "GSM2718949", "GSM2718950", "GSM2718951", "GSM2718952", "GSM2718953", "GSM2718954", "GSM2718955", "GSM2718956", "GSM2718957", "GSM2718958", "GSM2718959", "GSM2718960", "GSM2718961", "GSM2718962", "GSM2718963", "GSM2718964", "GSM2718965", "GSM2718966", "GSM2718967", "GSM2718968", "GSM2718969", "GSM2718970", "GSM2718971", "GSM2718972", "GSM2718973", "GSM2718974", "GSM2718975", "GSM2718976", "GSM2718977", "GSM2718978", "GSM2718979", "GSM2718980", "GSM2718981", "GSM2718982", "GSM2718983", "GSM2718984", "GSM2718985", "GSM2718986", "GSM2718987", "GSM2718988", "GSM2718989", "GSM2718990", "GSM2718991", "GSM2718992", "GSM2718993", "GSM2718994", "GSM2718995", "GSM2718996", "GSM2718997", "GSM2718998", "GSM2718999", "GSM2719000", "GSM2719001", "GSM2719002", "GSM2719003", "GSM2719004", "GSM2719005", "GSM2719006", "GSM2719007", "GSM2719008", "GSM2719009", "GSM2719010", "GSM2719011", "GSM2719012", "GSM2719013", "GSM2719014" ], "sample_count": 66, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression data from African Americans and European Americans with non-small cell lung cancer", "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:GSE18842", "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=GSE18842", "sha256": null, "bytes": null, "access": 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"title": "Gene expression analysis of human lung cancer and control samples", "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:GSE19188", "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=GSE19188", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19188", "version": null, "note": "Multiple gene expression profiles retrieved from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/) were used for identification of DEGs and candidate core genes.", "structure": { "repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Multiple gene expression profiles retrieved from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/) were used for identification of DEGs and candidate core genes.", "access_statement_kind": "repository_route_statement", "sample_accessions": [ "GSM475656", "GSM475657", "GSM475658", "GSM475659", "GSM475660", "GSM475661", "GSM475662", "GSM475663", "GSM475664", "GSM475665", "GSM475666", "GSM475667", "GSM475668", "GSM475669", "GSM475670", "GSM475671", "GSM475672", "GSM475673", "GSM475674", "GSM475675", "GSM475676", "GSM475677", "GSM475678", "GSM475679", "GSM475680", "GSM475681", "GSM475682", "GSM475683", "GSM475684", "GSM475685", "GSM475686", "GSM475687", "GSM475688", "GSM475689", "GSM475690", "GSM475691", "GSM475692", "GSM475693", "GSM475694", "GSM475695", "GSM475696", "GSM475697", "GSM475698", "GSM475699", "GSM475700", "GSM475701", "GSM475702", "GSM475703", "GSM475704", "GSM475705", "GSM475706", "GSM475707", "GSM475708", "GSM475709", "GSM475710", "GSM475711", "GSM475712", "GSM475713", "GSM475714", "GSM475715", "GSM475716", "GSM475717", 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"GSM475795", "GSM475796", "GSM475797", "GSM475798", "GSM475799", "GSM475800", "GSM475801", "GSM475802", "GSM475803", "GSM475804", "GSM475805", "GSM475806", "GSM475807", "GSM475808", "GSM475809", "GSM475810", "GSM475811" ], "sample_count": 156, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data for early stage NSCLC", "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:GSE19804", "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=GSE19804", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19804", "version": null, "note": "Multiple gene expression profiles retrieved from the Gene Expression 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candidate core genes.", "structure": { "repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Multiple gene expression profiles retrieved from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/) were used for identification of DEGs and candidate core genes.", "access_statement_kind": "repository_route_statement", "sample_accessions": [ "GSM773540", "GSM773541", "GSM773542", "GSM773543", "GSM773544", "GSM773545", "GSM773546", "GSM773547", "GSM773548", "GSM773549", "GSM773550", "GSM773551", "GSM773552", "GSM773553", "GSM773554", "GSM773555", "GSM773556", "GSM773557", "GSM773558", "GSM773559", "GSM773560", "GSM773561", "GSM773562", "GSM773563", "GSM773564", "GSM773565", "GSM773566", "GSM773567", "GSM773568", "GSM773569", "GSM773570", "GSM773571", "GSM773572", "GSM773573", "GSM773574", "GSM773575", "GSM773576", "GSM773577", "GSM773578", "GSM773579", "GSM773580", "GSM773581", "GSM773582", "GSM773583", "GSM773584", "GSM773585", 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