Identification of Serum miRNAs as Effective Diagnostic Biomarkers for Distinguishing Primary Central Nervous System Lymphoma from Glioma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35497882", "kind": "science-record", "revision": 5, "content_hash": "sha256:666431d429fe55f21dcf636f3e90205fa5a51205068da697a56d5a487d56ed8c", "created_at": "2026-11-01T18:14:22Z", "updated_at": "2026-11-01T22:48:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Serum miRNAs as Effective Diagnostic Biomarkers for Distinguishing Primary Central Nervous System Lymphoma from Glioma.", "doi": "10.1155/2022/5052609", "pmid": "35497882", "authors": ["Pei-Pei Si", "Xiao-Hui Zhou", "Zhen-Zhen Qu"], "journal": "Journal of immunology research", "year": 2022, "abstract": "Invasive surgical cerebrum biopsy results in delayed treatment for the definitive diagnosis of primary central nervous system lymphoma (PCNSL). The existent research was aimed at confirming the underlying diagnostic miRNAs of distinguishing PCNSL from glioma. A publicly available miRNA expression profiles (GSE139031) from adult PCNSL as well as glioma specimens were provided by GEO datasets. Differentially expressed miRNAs (DEMs) were filtered between 42 PCNSL patients and 170 glioma patients. Candidate miRNAs were identified through SVM-RFE analysis and LASSO model. ROC assays were operated to determine the diagnostic value of serum miRNAs in distinguishing PCNSL from glioma. StarBase v2.0 was applied to screen the targeting genes of miRNAs, and KEGG analysis was applied using the targeting genes of miRNAs. In this study, we identified 12 dysregulated miRNAs between PCNSL and glioma samples. The ten critical miRNAs (miR-6820-3p, miR-6803-3p, miR-30a-3p, miR-4751, miR-3918, miR-146a-3p, miR-548am-3p, miR-371a-3p, miR-487a-3p, and miR-4756-5p) between these two algorithms were ultimately identified. The results of KEGG revealed that the targeting genes of hsa-miR-3918 were primarily related to MAPK signal pathway, PI3K-Akt signal pathway, and human papillomavirus infection. Overall, bioinformatics analysis revealed that ten miRNAs are potential biomarker for distinguishing PCNSL from glioma.", "claims": [{"id": "claim-method", "statement": "The limma package of R (http://www.bioconductor.org/) was applied to count the P value and FDR, separately. The DEMs were filtered out on the basis of adjusted P value < 0.05 as well as ∣ logFC | ≥1.2.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35497882", "locator": "sections[4] \"2.2. Identification of DEMs\" paragraph 2", "quote": "The limma package of R (http://www.bioconductor.org/) was applied to count the P value and FDR, separately. The DEMs were filtered out on the basis of adjusted P value < 0.05 as well as ∣ logFC | ≥1.2."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are available from the corresponding author upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35497882", "locator": "sections[17] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of this study are available from the corresponding author upon request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Overall, bioinformatics analysis revealed that ten miRNAs are potential biomarker for distinguishing PCNSL from glioma.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "The DEMs were filtered out on the basis of adjusted P value < 0.05 as well as ∣ logFC | ≥1.2."}, "evidence": [{"asset": "source:pmid:35497882", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Overall, bioinformatics analysis revealed that ten miRNAs are potential biomarker for distinguishing PCNSL from glioma."}, {"asset": "source:pmid:35497882", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A publicly available miRNA expression profiles (GSE139031) from adult PCNSL as well as glioma specimens were provided by GEO datasets."}, {"asset": "source:pmid:35497882", "locator": "sections[4] \"2.2. Identification of DEMs\" paragraph 2", "quote": "The DEMs were filtered out on the basis of adjusted P value < 0.05 as well as ∣ logFC | ≥1.2."}, {"asset": "source:pmid:35497882", "locator": "sections[11] \"3.2. Identification of the Diagnostic miRNAs\" paragraph 2", "quote": "The DEMs were decreased with LASSO regression algorithm, leading to the confirmation of 10 miRNAs as diagnostic biomarkers for distinguishing PCNSL from glioma (Figure 2(a))."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Overall, bioinformatics analysis revealed that ten miRNAs are potential biomarker for distinguishing PCNSL from glioma.", "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:35497882"], "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:GSE139031"], "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": {"fdr_threshold": "th adjusted P value and FDR filtering, LASSO regres"}, "inputs": ["data:geo:GSE139031"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35497882", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/5052609", "sha256": "sha256:d4f0a2784cfbe0e7755b07b6a2da14175e42bae9a0b5c79b7b52b462e08511d0", "bytes": 13744, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/5052609", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9045974", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE139031", "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=GSE139031", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE139031", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4127086", "GSM4127087", "GSM4127088", "GSM4127089", "GSM4127090", "GSM4127091", "GSM4127092", "GSM4127093", "GSM4127094", "GSM4127095", "GSM4127096", "GSM4127097", "GSM4127098", "GSM4127099", "GSM4127100", "GSM4127101", "GSM4127102", "GSM4127103", "GSM4127104", "GSM4127105", "GSM4127106", "GSM4127107", "GSM4127108", "GSM4127109", "GSM4127110", "GSM4127111", "GSM4127112", "GSM4127113", "GSM4127114", "GSM4127115", "GSM4127116", "GSM4127117", "GSM4127118", "GSM4127119", "GSM4127120", "GSM4127121", "GSM4127122", "GSM4127123", "GSM4127124", "GSM4127125", "GSM4127126", "GSM4127127", "GSM4127128", "GSM4127129", "GSM4127130", "GSM4127131", "GSM4127132", "GSM4127133", "GSM4127134", "GSM4127135", "GSM4127136", "GSM4127137", "GSM4127138", "GSM4127139", "GSM4127140", "GSM4127141", "GSM4127142", "GSM4127143", "GSM4127144", "GSM4127145", "GSM4127146", "GSM4127147", "GSM4127148", "GSM4127149", "GSM4127150", "GSM4127151", "GSM4127152", "GSM4127153", "GSM4127154", "GSM4127155", "GSM4127156", "GSM4127157", "GSM4127158", "GSM4127159", "GSM4127160", "GSM4127161", "GSM4127162", "GSM4127163", "GSM4127164", "GSM4127165", "GSM4127166", "GSM4127167", "GSM4127168", "GSM4127169", "GSM4127170", "GSM4127171", "GSM4127172", "GSM4127173", "GSM4127174", "GSM4127175", "GSM4127176", "GSM4127177", "GSM4127178", "GSM4127179", "GSM4127180", "GSM4127181", "GSM4127182", "GSM4127183", "GSM4127184", "GSM4127185", "GSM4127186", "GSM4127187", "GSM4127188", "GSM4127189", "GSM4127190", "GSM4127191", "GSM4127192", "GSM4127193", "GSM4127194", "GSM4127195", "GSM4127196", "GSM4127197", "GSM4127198", "GSM4127199", "GSM4127200", "GSM4127201", "GSM4127202", "GSM4127203", "GSM4127204", "GSM4127205", "GSM4127206", "GSM4127207", "GSM4127208", "GSM4127209", "GSM4127210", "GSM4127211", "GSM4127212", "GSM4127213", "GSM4127214", "GSM4127215", "GSM4127216", "GSM4127217", "GSM4127218", "GSM4127219", "GSM4127220", "GSM4127221", "GSM4127222", "GSM4127223", "GSM4127224", "GSM4127225", "GSM4127226", "GSM4127227", "GSM4127228", "GSM4127229", "GSM4127230", "GSM4127231", "GSM4127232", "GSM4127233", "GSM4127234", "GSM4127235", "GSM4127236", "GSM4127237", "GSM4127238", "GSM4127239", "GSM4127240", "GSM4127241", "GSM4127242", "GSM4127243", "GSM4127244", "GSM4127245", "GSM4127246", "GSM4127247", "GSM4127248", "GSM4127249", "GSM4127250", "GSM4127251", "GSM4127252", "GSM4127253", "GSM4127254", "GSM4127255", "GSM4127256", "GSM4127257", "GSM4127258", "GSM4127259", "GSM4127260", "GSM4127261", "GSM4127262", "GSM4127263", "GSM4127264", "GSM4127265", "GSM4127266", "GSM4127267", "GSM4127268", "GSM4127269", "GSM4127270", "GSM4127271", "GSM4127272", "GSM4127273", "GSM4127274", "GSM4127275", "GSM4127276", "GSM4127277", "GSM4127278", "GSM4127279", "GSM4127280", "GSM4127281", "GSM4127282", "GSM4127283", "GSM4127284", "GSM4127285", "GSM4127286", "GSM4127287", "GSM4127288", "GSM4127289", "GSM4127290", "GSM4127291", "GSM4127292", "GSM4127293", "GSM4127294", "GSM4127295", "GSM4127296", "GSM4127297", "GSM4127298", "GSM4127299", "GSM4127300", "GSM4127301", "GSM4127302", "GSM4127303", "GSM4127304", "GSM4127305", "GSM4127306", "GSM4127307", "GSM4127308", "GSM4127309", "GSM4127310", "GSM4127311", "GSM4127312", "GSM4127313", "GSM4127314", "GSM4127315", "GSM4127316", "GSM4127317", "GSM4127318", "GSM4127319", "GSM4127320", "GSM4127321", "GSM4127322", "GSM4127323", "GSM4127324", "GSM4127325", "GSM4127326", "GSM4127327", "GSM4127328", "GSM4127329", "GSM4127330", "GSM4127331", "GSM4127332", "GSM4127333", "GSM4127334", "GSM4127335", "GSM4127336", "GSM4127337", "GSM4127338", "GSM4127339", "GSM4127340", "GSM4127341", "GSM4127342", "GSM4127343", "GSM4127344", "GSM4127345", "GSM4127346", "GSM4127347", "GSM4127348", "GSM4127349", "GSM4127350", "GSM4127351", "GSM4127352", "GSM4127353", "GSM4127354", "GSM4127355", "GSM4127356", "GSM4127357", "GSM4127358", "GSM4127359", "GSM4127360", "GSM4127361", "GSM4127362", "GSM4127363", "GSM4127364", "GSM4127365", "GSM4127366", "GSM4127367", "GSM4127368", "GSM4127369", "GSM4127370", "GSM4127371", "GSM4127372", "GSM4127373", "GSM4127374", "GSM4127375", "GSM4127376", "GSM4127377", "GSM4127378", "GSM4127379", "GSM4127380", "GSM4127381", "GSM4127382", "GSM4127383", "GSM4127384", "GSM4127385", "GSM4127386", "GSM4127387", "GSM4127388", "GSM4127389", "GSM4127390", "GSM4127391", "GSM4127392", "GSM4127393", "GSM4127394", "GSM4127395", "GSM4127396", "GSM4127397", "GSM4127398", "GSM4127399", "GSM4127400", "GSM4127401", "GSM4127402", "GSM4127403", "GSM4127404", "GSM4127405", "GSM4127406", "GSM4127407", "GSM4127408", "GSM4127409", "GSM4127410", "GSM4127411", "GSM4127412", "GSM4127413", "GSM4127414", "GSM4127415", "GSM4127416", "GSM4127417", "GSM4127418", "GSM4127419", "GSM4127420", "GSM4127421", "GSM4127422", "GSM4127423", "GSM4127424", "GSM4127425", "GSM4127426", "GSM4127427", "GSM4127428", "GSM4127429", "GSM4127430", "GSM4127431", "GSM4127432", "GSM4127433", "GSM4127434", "GSM4127435", "GSM4127436", "GSM4127437", "GSM4127438", "GSM4127439", "GSM4127440", "GSM4127441", "GSM4127442", "GSM4127443", "GSM4127444", "GSM4127445", "GSM4127446", "GSM4127447", "GSM4127448", "GSM4127449", "GSM4127450", "GSM4127451", "GSM4127452", "GSM4127453", "GSM4127454", "GSM4127455", "GSM4127456", "GSM4127457", "GSM4127458", "GSM4127459", "GSM4127460", "GSM4127461", "GSM4127462", "GSM4127463", "GSM4127464", "GSM4127465", "GSM4127466", "GSM4127467", "GSM4127468", "GSM4127469", "GSM4127470", "GSM4127471", "GSM4127472", "GSM4127473", "GSM4127474", "GSM4127475", "GSM4127476", "GSM4127477", "GSM4127478", "GSM4127479", "GSM4127480", "GSM4127481", "GSM4127482", "GSM4127483", "GSM4127484", "GSM4127485", "GSM4127486", "GSM4127487", "GSM4127488", "GSM4127489", "GSM4127490", "GSM4127491", "GSM4127492", "GSM4127493", "GSM4127494", "GSM4127495", "GSM4127496", "GSM4127497", "GSM4127498", "GSM4127499", "GSM4127500", "GSM4127501", "GSM4127502", "GSM4127503", "GSM4127504", "GSM4127505", "GSM4127506", "GSM4127507", "GSM4127508", "GSM4127509", "GSM4127510", "GSM4127511", "GSM4127512", "GSM4127513", "GSM4127514", "GSM4127515", "GSM4127516", "GSM4127517", "GSM4127518", "GSM4127519", "GSM4127520", "GSM4127521", "GSM4127522", "GSM4127523", "GSM4127524", "GSM4127525", "GSM4127526", "GSM4127527", "GSM4127528", "GSM4127529", "GSM4127530", "GSM4127531", "GSM4127532", "GSM4127533", "GSM4127534", "GSM4127535", "GSM4127536", "GSM4127537", "GSM4127538", "GSM4127539", "GSM4127540", "GSM4127541", "GSM4127542", "GSM4127543", "GSM4127544", "GSM4127545", "GSM4127546", "GSM4127547", "GSM4127548", "GSM4127549", "GSM4127550", "GSM4127551", "GSM4127552", "GSM4127553", "GSM4127554", "GSM4127555", "GSM4127556", "GSM4127557", "GSM4127558", "GSM4127559", "GSM4127560", "GSM4127561", "GSM4127562", "GSM4127563", "GSM4127564", "GSM4127565", "GSM4127566", "GSM4127567", "GSM4127568", "GSM4127569", "GSM4127570", "GSM4127571", "GSM4127572", "GSM4127573", "GSM4127574", "GSM4127575", "GSM4127576", "GSM4127577", "GSM4127578", "GSM4127579", "GSM4127580", "GSM4127581", "GSM4127582", "GSM4127583", "GSM4127584", "GSM4127585", "GSM4127586", "GSM4127587", "GSM4127588", "GSM4127589", "GSM4127590", "GSM4127591", "GSM4127592", "GSM4127593", "GSM4127594", "GSM4127595", "GSM4127596", "GSM4127597", "GSM4127598", "GSM4127599", "GSM4127600", "GSM4127601", "GSM4127602", "GSM4127603", "GSM4127604", "GSM4127605", "GSM4127606", "GSM4127607", "GSM4127608", "GSM4127609", "GSM4127610", "GSM4127611", "GSM4127612", "GSM4127613", "GSM4127614", "GSM4127615", "GSM4127616", "GSM4127617", "GSM4127618", "GSM4127619", "GSM4127620", "GSM4127621", "GSM4127622", "GSM4127623", "GSM4127624", "GSM4127625", "GSM4127626", "GSM4127627", "GSM4127628", "GSM4127629", "GSM4127630", "GSM4127631", "GSM4127632", "GSM4127633", "GSM4127634", "GSM4127635", "GSM4127636", "GSM4127637", "GSM4127638", "GSM4127639", "GSM4127640", "GSM4127641", "GSM4127642", "GSM4127643", "GSM4127644", "GSM4127645", "GSM4127646", "GSM4127647", "GSM4127648", "GSM4127649", "GSM4127650", "GSM4127651", "GSM4127652", "GSM4127653", "GSM4127654", "GSM4127655", "GSM4127656", "GSM4127657", "GSM4127658", "GSM4127659", "GSM4127660", "GSM4127661", "GSM4127662", "GSM4127663", "GSM4127664", "GSM4127665"], "sample_count": 580, "group_sizes": null, "group_sizes_basis": null, "platform": "21263", "taxon": "Homo sapiens", "title": "Assessment of the Diagnostic Utility of Serum MicroRNA Classification in Patients with Diffuse Glioma", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE139031 not downloaded", "asset:data:geo:GSE139031 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": {"fdr_threshold": "th adjusted P value and FDR filtering, LASSO regres"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The limma package of R (http://www.bioconductor.org/) was applied to count the P value and FDR, separately. The DEMs were filtered out on the basis of adjusted P value < 0.05 as well as ∣ logFC | ≥1.2."}}, {"id": "method-2", "family": "machine_learning", "specific": "support_vector_machine", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "SVM"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "cross_validate", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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": ["GSE139031"], "resolved_accessions": ["GSE139031"], "statements": ["The data used to support the findings of this study are available from the corresponding author upon request."], "basis": "The paper names GSE139031 in GEO datasets 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:35497882", "data:geo:GSE139031"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE139031"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:44:22Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 5754, "completion_tokens": 1746, "cached_tokens": 128}}, "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:35497882", "type": "paper", "label": "pmid:35497882"}, {"id": "source:pmid:35497882", "type": "manuscript", "label": "PMID 35497882 full text"}, {"id": "data:geo:GSE139031", "type": "dataset", "label": "GEO GSE139031"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35497882", "type": "paper", "label": "pmid:35497882"}, {"id": "source:pmid:35497882", "type": "manuscript", "label": "PMID 35497882 full text"}, {"id": "data:geo:GSE139031", "type": "dataset", "label": "GEO GSE139031"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35497882", "type": "extraction", "used": ["source:pmid:35497882"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE139031", "type": "accession_resolution", "used": ["data:geo:GSE139031"], "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:35497882", "parent_hash": "sha256:9d22239e263a203845b978bee6526ca51aaa5edc800f726a423bd7302987a0ea", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE139031 licence not read", "asset:data:geo:GSE139031 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["The limma package of R (http://www.bioconductor.org/) was applied to count the P value and FDR, separately. The DEMs were filtered out on the basis of adjusted P value < 0.05 as well as ∣ logFC | ≥1.2."], "order_basis": "analysis_only", "id": "assay:1"}]}