{"document":"journal-rps/record","document_version":"1.2","document_notes":{"1.1":"Added the canonical source the journal holds and the execution evidence another application produced. The sections that were already here say what they said in 1.0.","1.2":"Added the scope of a re-execution verdict: what the run re-executed, what it did not, and how much of the registered work answered. A verdict on a check of the paper's printed figures and a verdict on a re-run protocol are now stated apart. No earlier section changed."},"generated_at":"2026-11-09T19:40:31+00:00","publisher":"Journal of Open Source Science","what_this_is":"The journal's record for one paper, as one file. It holds the paper as it was read, the readings made of it, the registered plan, the runs, the result and the ledger behind it. A reading is a reading, a run is a run, and a verdict is not an editorial decision. The runs section records Journal executions. The execution_evidence section holds analyses performed by Automated Assays, with their source versions and results.","record":{"id":"818dabf4-6127-4996-82db-3637083ad242","title":"Identification of HMMR as a prognostic biomarker for patients with lung adenocarcinoma via integrated bioinformatics analysis.","state":"submitted","article_type":"original_research","relationship_kind":"original","revision":0,"version":1,"synthetic":false,"doi":"10.7717/peerj.12624","authors":["Zhaodong Li","Hongtian Fei","Siyu Lei","Fengtong Hao","Lijie Yang","Wanze Li","Laney Zhang","Rui Fei"],"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.","package_hash":"8fb1d6204a4c014e9c90be7e502545fe52bd168752c9b9e8ed937afa47a1dbc5","plan_hash":null,"plan_version":null,"first_receipt_at":"2026-11-04T07:03:24+00:00","decided_at":null,"days_open":5,"intake":{"method":"sci_import","source_name":"PeerJ","source_identifier":"pmid:35036134","source_url":null,"corpus_record_id":"pmid:35036134","recorded_by":"Journal Editor","ingested_at":"2026-11-04T07:03:24+00:00"},"lineage":{"relationship":"original","parent":null,"descendants":[]}},"source_text":{"held":false,"kind":"abstract","what_the_kind_means":"only the abstract was read","characters":null,"sha256":null,"intact":null,"note":"The hash is of the text as it arrived. 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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. 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\"access_route\": \"GEO accession URL\",\n     \"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.\",\n     \"access_statement_kind\": \"repository_route_statement\",\n     \"sample_accessions\": [\n      \"GSM1941120\",\n      \"GSM1941121\",\n      \"GSM1941122\",\n      \"GSM1941123\",\n      \"GSM1941124\",\n      \"GSM1941125\",\n      \"GSM1941126\",\n      \"GSM1941127\",\n      \"GSM1941128\",\n      \"GSM1941129\",\n      \"GSM1941130\",\n      \"GSM1941131\",\n      \"GSM1941132\",\n      \"GSM1941133\",\n      \"GSM1941134\",\n      \"GSM1941135\",\n      \"GSM1941136\",\n      \"GSM1941137\",\n      \"GSM1941138\",\n      \"GSM1941139\",\n      \"GSM1941140\",\n      \"GSM1941141\",\n      \"GSM1941142\",\n      \"GSM1941143\",\n      \"GSM1941144\",\n      \"GSM1941145\",\n      \"GSM1941146\",\n      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},\n   {\n    \"id\": \"agent:minimax-reader\",\n    \"type\": \"software\",\n    \"label\": \"MiniMax literature reader\"\n   }\n  ],\n  \"source_run_id\": \"reading-sci-2026-11-01\",\n  \"dsl_catalogue_fingerprint\": \"343fb30756ba6ec3\",\n  \"capability_table_fingerprint\": \"2cb3e42f047d2ecf\",\n  \"snapshot_id\": \"ba34b49490d9bfaf\"\n },\n \"lineage\": {\n  \"parent_id\": \"pmid:35036134\",\n  \"parent_hash\": \"sha256:ab3ca215faa3771cc00ffa070bfb6487070c4a004ccc2e38b66f6b87fcbe752b\",\n  \"fork_of\": null,\n  \"generation\": 4\n },\n \"gaps\": [\n  \"asset:data:geo:GSE101929 licence not read\",\n  \"asset:data:geo:GSE101929 not downloaded\",\n  \"asset:data:geo:GSE18842 licence not read\",\n  \"asset:data:geo:GSE18842 not downloaded\",\n  \"asset:data:geo:GSE19188 licence not read\",\n  \"asset:data:geo:GSE19188 not downloaded\",\n  \"asset:data:geo:GSE19804 licence not read\",\n  \"asset:data:geo:GSE19804 not downloaded\",\n  \"asset:data:geo:GSE31210 licence not read\",\n  \"asset:data:geo:GSE31210 not downloaded\",\n  \"asset:data:geo:GSE50081 licence not read\",\n  \"asset:data:geo:GSE50081 not downloaded\",\n  \"asset:data:geo:GSE68465 licence not read\",\n  \"asset:data:geo:GSE68465 not downloaded\",\n  \"asset:data:geo:GSE75037 licence not read\",\n  \"asset:data:geo:GSE75037 not downloaded\",\n  \"execution.not_run\",\n  \"review.human_critique\",\n  \"review.independent_reader\",\n  \"review.machine_critique\"\n ],\n \"assays\": [\n  {\n   \"role\": \"data_generation\",\n   \"definition_id\": \"cell_culture\",\n   \"definition_version\": \"99e1195c7d6f\",\n   \"definition_digest\": null,\n   \"required_operations\": [],\n   \"support_state\": \"partial\",\n   \"source_hashes\": {\n    \"assay_lexicon\": \"99e1195c7d6f\"\n   },\n   \"confidence\": 0.99,\n   \"evidence\": [\n    \"idated in multiple databases and LUAD cells (A549 and PC-9) by quantitative real-time PCR (qRT\",\n    \"Materials and Methods Cell culture HBE, A549 and PC-9 cells were cultured according to pr\"\n   ],\n   \"order_basis\": \"paper_text_order:658\",\n   \"id\": \"assay:1\"\n  },\n  {\n   \"role\": \"data_generation\",\n   \"definition_id\": \"qpcr\",\n   \"definition_version\": \"99e1195c7d6f\",\n   \"definition_digest\": null,\n   \"required_operations\": [],\n   \"support_state\": \"partial\",\n   \"source_hashes\": {\n    \"assay_lexicon\": \"99e1195c7d6f\"\n   },\n   \"confidence\": 0.93,\n   \"evidence\": [\n    \"d LUAD cells (A549 and PC-9) by quantitative real-time PCR (qRT-PCR) and western blot analyses. Its pro\"\n   ],\n   \"order_basis\": \"paper_text_order:689\",\n   \"id\": \"assay:2\"\n  },\n  {\n   \"role\": \"data_generation\",\n   \"definition_id\": \"western_blot\",\n   \"definition_version\": \"99e1195c7d6f\",\n   \"definition_digest\": null,\n   \"required_operations\": [],\n   \"support_state\": \"partial\",\n   \"source_hashes\": {\n    \"assay_lexicon\": \"99e1195c7d6f\"\n   },\n   \"confidence\": 0.93,\n   \"evidence\": [\n    \"by quantitative real-time PCR (qRT-PCR) and western blot analyses. Its prognostic value was estimated\"\n   ],\n   \"order_basis\": \"paper_text_order:718\",\n   \"id\": \"assay:3\"\n  },\n  {\n   \"role\": \"analysis\",\n   \"definition_id\": \"survival_analysis\",\n   \"definition_version\": \"f2132e96ae6c7a4e\",\n   \"definition_digest\": null,\n   \"required_operations\": [\n    \"survival_km\"\n   ],\n   \"support_state\": \"supported\",\n   \"source_hashes\": {\n    \"dsl_catalogue\": \"f2132e96ae6c7a4e\"\n   },\n   \"confidence\": 1.0,\n   \"evidence\": [\n    \"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.\"\n   ],\n   \"order_basis\": \"consumes_earlier_output\",\n   \"id\": \"assay:4\"\n  }\n ]\n}\n","document":{"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 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