Identification of mitophagy-related genes with diagnostic value in acute rejection following kidney transplantation using bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40596704", "kind": "science-record", "revision": 4, "content_hash": "sha256:7fa562111a765411ceeec51513ca9c916d701010e39cc6ee84656c7a40b96614", "created_at": "2026-11-01T20:30:41Z", "updated_at": "2026-11-01T22:56:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of mitophagy-related genes with diagnostic value in acute rejection following kidney transplantation using bioinformatics analysis.", "doi": "10.1038/s41598-025-09143-3", "pmid": "40596704", "authors": ["Jianan Ma", "Dawei Wu", "Xinyuan An", "Yongrui Zhang", "Haijian Wei"], "journal": "Scientific reports", "year": 2025, "abstract": "Acute rejection (AR) after kidney transplantation, is a common and serious complication that occurs when the recipient's immune system attacks the graft, and the specific genes and molecular mechanisms underlying the role of mitophagy are still unclear. This study integrated two transcriptomic datasets (GSE129166 and GSE25902) from the GEO database. Thirty differential mitophagy-related genes were identified by intersecting differentially expressed genes, module genes obtained through weighted gene co-expression network analysis and mitophagy-related genes. Functional enrichment analysis uncovered several biological processes and signaling pathways associated with these genes. Four candidate genes including CCND1, ZC3H15, RPL38, and ARPC4, were further identified through Random Forest and Support Vector Machine with recursive feature elimination. Internal, external datasets and a nomogram confirmed they could effectively predict AR. Moreover, these genes significantly correlated with the infiltration of multiple immune cells. Differential expressions of the four genes were also validated in patient's peripheral blood and AR mice. These four mitophagy-related genes may be novel biomarkers for predicting the occurrence and diagnosis of AR.", "claims": [{"id": "claim-method", "statement": "The DEGs between normal and AR specimens were processed with the “limma” package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40596704", "locator": "sections[4] \"Differentially expressed genes (DEGs) screening\" paragraph 2", "quote": "The DEGs between normal and AR specimens were processed with the “limma” package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analysed during this study are included in this published article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40596704", "locator": "sections[31] \"Data availability\" paragraph 2", "quote": "All data generated or analysed during this study are included in this published article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Four candidate genes including CCND1, ZC3H15, RPL38, and ARPC4, were further identified through Random Forest and Support Vector Machine with recursive feature elimination.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40596704", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Four candidate genes including CCND1, ZC3H15, RPL38, and ARPC4, were further identified through Random Forest and Support Vector Machine with recursive feature elimination."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Four candidate genes including CCND1, ZC3H15, RPL38, and ARPC4, were further identified through Random Forest and Support Vector Machine with recursive feature elimination.", "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:40596704"], "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:GSE129166"], "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:GSE129166"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40596704", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-025-09143-3", "sha256": "sha256:566042eb9aff4e00b196e4ea40e25e9e3b320499e2dd6114b74640c9d1d140e3", "bytes": 57141, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-025-09143-3", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12214719", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE129166", "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=GSE129166", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE129166", "version": null, "note": "All data generated or analysed during this study are included in this published article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analysed during this study are included in this published article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3701699", "GSM3701700", "GSM3701701", "GSM3701702", "GSM3701703", "GSM3701704", "GSM3701705", "GSM3701706", "GSM3701707", "GSM3701708", "GSM3701709", "GSM3701710", "GSM3701711", "GSM3701712", "GSM3701713", "GSM3701714", "GSM3701715", "GSM3701716", "GSM3701717", "GSM3701718", "GSM3701719", "GSM3701720", "GSM3701721", "GSM3701722", "GSM3701723", "GSM3701724", "GSM3701725", "GSM3701726", "GSM3701727", "GSM3701728", "GSM3701729", "GSM3701730", "GSM3701731", "GSM3701732", "GSM3701733", "GSM3701734", "GSM3701735", "GSM3701736", "GSM3701737", "GSM3701738", "GSM3701739", "GSM3701740", "GSM3701741", "GSM3701742", "GSM3701743", "GSM3701744", "GSM3701745", "GSM3701746", "GSM3701747", "GSM3701748", "GSM3701749", "GSM3701750", "GSM3701751", "GSM3701752", "GSM3701753", "GSM3701754", "GSM3701755", "GSM3701756", "GSM3701757", "GSM3701758", "GSM3701759", "GSM3701760", "GSM3701761", "GSM3701762", "GSM3701763", "GSM3701764", "GSM3701765", "GSM3701766", "GSM3701767", "GSM3701768", "GSM3701769", "GSM3701770", "GSM3701771", "GSM3701772", "GSM3701773", "GSM3701774", "GSM3701775", "GSM3701776", "GSM3701777", "GSM3701778", "GSM3701779", "GSM3701780", "GSM3701781", "GSM3701782", "GSM3701783", "GSM3701784", "GSM3701785", "GSM3701786", "GSM3701787", "GSM3701788", "GSM3701789", "GSM3701790", "GSM3701791", "GSM3701792", "GSM3701793", "GSM3701794", "GSM3701795", "GSM3701796", "GSM3701797", "GSM3701798", "GSM3701799", "GSM3701800", "GSM3701801", "GSM3701802", "GSM3701803", "GSM3701804", "GSM3701805", "GSM3701806", "GSM3701807", "GSM3701808", "GSM3701809", "GSM3701810", "GSM3701811", "GSM3701812", "GSM3701813", "GSM3701814", "GSM3701815", "GSM3701816", "GSM3701817", "GSM3701818", "GSM3701819", "GSM3701820", "GSM3701821", "GSM3701822", "GSM3701823", "GSM3701824", "GSM3701825", "GSM3701826", "GSM3701827", "GSM3701828", "GSM3701829", "GSM3701830", "GSM3701831", "GSM3701832", "GSM3701833", "GSM3701834", "GSM3701835", "GSM3701836", "GSM3701837", "GSM3701838", "GSM3701839", "GSM3701840", "GSM3701841", "GSM3701842", "GSM3701843", "GSM3701844", "GSM3701845", "GSM3701846", "GSM3701847", "GSM3701848", "GSM3701849", "GSM3701850", "GSM3701851", "GSM3701852", "GSM3701853", "GSM3701854", "GSM3701855", "GSM3701856", "GSM3701857", "GSM3701858", "GSM3701859", "GSM3701860", "GSM3701861", "GSM3701862", "GSM3701863", "GSM3701864", "GSM3701865", "GSM3701866", "GSM3701867", "GSM3701868", "GSM3701869", "GSM3701870", "GSM3701871", "GSM3701872", "GSM3701873", "GSM3701874", "GSM3701875", "GSM3701876", "GSM3701877", "GSM3701878", "GSM3701879", "GSM3701880", "GSM3701881", "GSM3701882", "GSM3701883", "GSM3701884", "GSM3701885", "GSM3701886", "GSM3701887", "GSM3701888", "GSM3701889", "GSM3701890", "GSM3701891", "GSM3701892", "GSM3701893", "GSM3701894", "GSM3701895", "GSM3701896", "GSM3701897", "GSM3701898", "GSM3701899", "GSM3701900", "GSM3701901", "GSM3701902", "GSM3701903", "GSM3701904", "GSM3701905", "GSM3701906", "GSM3701907", "GSM3701908", "GSM3701909", "GSM3701910"], "sample_count": 212, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression profiling in patients with a kidney transplantation", "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:GSE14328", "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=GSE14328", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14328", "version": null, "note": "All data generated or analysed during this study are included in this published article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analysed during this study are included in this published article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM357851", "GSM357859", "GSM357860", "GSM357861", "GSM357862", "GSM357863", "GSM358003", "GSM358004", "GSM358005", "GSM358006", "GSM358007", "GSM358008", "GSM358009", "GSM358015", "GSM358016", "GSM358017", "GSM358018", "GSM358020", "GSM358021", "GSM358258", "GSM358259", "GSM358265", "GSM358266", "GSM358268", "GSM358269", "GSM358281", "GSM358282", "GSM358286", "GSM358287", "GSM358288", "GSM358289", "GSM358290", "GSM358291", "GSM358292", "GSM358293", "GSM358294"], "sample_count": 36, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Three non-invasive protein biomarkers for solid-organ transplant rejection found through integrative genomics", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE1563", "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=GSE1563", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE1563", "version": null, "note": "All data generated or analysed during this study are included in this published article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analysed during this study are included in this published article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM26805", "GSM26806", "GSM26807", "GSM26808", "GSM26809", "GSM26810", "GSM26811", "GSM26812", "GSM26813", "GSM26814", "GSM26815", "GSM26816", "GSM26817", "GSM26818", "GSM26819", "GSM26820", "GSM26821", "GSM26822", "GSM26823", "GSM26824", "GSM26825", "GSM26826", "GSM26827", "GSM26828", "GSM26829", "GSM26830", "GSM26831", "GSM26832", "GSM26833", "GSM26834", "GSM26835", "GSM26836", "GSM26837", "GSM26838", "GSM26839", "GSM26840", "GSM26841", "GSM26842", "GSM26843", "GSM26844", "GSM26845", "GSM26846", "GSM26847", "GSM26848", "GSM26849", "GSM26850", "GSM26851", "GSM26852", "GSM26853", "GSM26854", "GSM26855", "GSM26856", "GSM26857", "GSM26858", "GSM26859", "GSM26860", "GSM26861", "GSM26862", "GSM26863", "GSM26864", "GSM26865", "GSM26866"], "sample_count": 62, "group_sizes": null, "group_sizes_basis": null, "platform": "8300", "taxon": "Homo sapiens", "title": "Kidney Transplant Rejection and Tissue Injury by Gene Profiling of Biopsies and Peripheral Blood Lymphocytes", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE25902", "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=GSE25902", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE25902", "version": null, "note": "All data generated or analysed during this study are included in this published article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analysed during this study are included in this published article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM635711", "GSM635712", "GSM635713", "GSM635714", "GSM635715", "GSM635716", "GSM635717", "GSM635718", "GSM635719", "GSM635720", "GSM635721", "GSM635722", "GSM635723", "GSM635724", "GSM635725", "GSM635726", "GSM635727", "GSM635728", "GSM635729", "GSM635730", "GSM635731", "GSM635732", "GSM635733", "GSM635734", "GSM635735", "GSM635736", "GSM635737", "GSM635738", "GSM635739", "GSM635740", "GSM635741", "GSM635742", "GSM635743", "GSM635744", "GSM635745", "GSM635746", "GSM635747", "GSM635748", "GSM635749", "GSM635750", "GSM635751", "GSM635752", "GSM635753", "GSM635754", "GSM635755", "GSM635756", "GSM635757", "GSM635758", "GSM635759", "GSM635760", "GSM635761", "GSM635762", "GSM635763", "GSM635764", "GSM635765", "GSM635766", "GSM635767", "GSM635768", "GSM635769", "GSM635770", "GSM635771", "GSM635772", "GSM635773", "GSM635774", "GSM635775", "GSM635776", "GSM635777", "GSM635778", "GSM635779", "GSM635780", "GSM635781", "GSM635782", "GSM635783", "GSM635784", "GSM635785", "GSM635786", "GSM635787", "GSM635788", "GSM635789", "GSM635790", "GSM635791", "GSM635792", "GSM635793", "GSM635794", "GSM635795", "GSM635796", "GSM635797", "GSM635798", "GSM635799", "GSM635800", "GSM635801", "GSM635802", "GSM635803", "GSM635804", "GSM635805", "GSM635806", "GSM635807", "GSM635808", "GSM635809", "GSM635810", "GSM635811", "GSM635812", "GSM635813", "GSM635814", "GSM635815", "GSM635816", "GSM635817", "GSM635818", "GSM635819", "GSM635820", "GSM635821", "GSM635822", "GSM635823", "GSM635824", "GSM635825", "GSM635826", "GSM635827", "GSM635828", "GSM635829", "GSM635830"], "sample_count": 120, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Innate and adaptive immune responses associate with progressive histological damage of renal allografts", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE129166 not downloaded", "asset:data:geo:GSE129166 licence not read", "asset:data:geo:GSE14328 not downloaded", "asset:data:geo:GSE14328 licence not read", "asset:data:geo:GSE1563 not downloaded", "asset:data:geo:GSE1563 licence not read", "asset:data:geo:GSE25902 not downloaded", "asset:data:geo:GSE25902 licence not read"]}, "analysis": {"state": "partial", "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": "The DEGs between normal and AR specimens were processed with the “limma” package."}}, {"id": "method-2", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-3", "family": "machine_learning", "specific": "random_forest", "label": "Machine learning", "dsl_operations": [], "missing_operations": ["machine_learning_random_forest"], "expressible": false, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "Random Forest"}}, {"id": "method-4", "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": "Support Vector Machine"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["GSE129166", "GSE25902", "GSE14328", "GSE1563"], "resolved_accessions": ["GSE129166", "GSE25902", "GSE14328", "GSE1563"], "statements": ["All data generated or analysed during this study are included in this published article."], "basis": "The paper names GSE129166, GSE25902, GSE14328, GSE1563 in Gene Expression Omnibus (GEO) 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:40596704", "data:geo:GSE129166"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE129166"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:55:45Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15451, "completion_tokens": 1771, "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:40596704", "type": "paper", "label": "pmid:40596704"}, {"id": "source:pmid:40596704", "type": "manuscript", "label": "PMID 40596704 full text"}, {"id": "data:geo:GSE129166", "type": "dataset", "label": "GEO GSE129166"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40596704", "type": "paper", "label": "pmid:40596704"}, {"id": "source:pmid:40596704", "type": "manuscript", "label": "PMID 40596704 full text"}, {"id": "data:geo:GSE129166", "type": "dataset", "label": "GEO GSE129166"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40596704", "type": "extraction", "used": ["source:pmid:40596704"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE129166", "type": "accession_resolution", "used": ["data:geo:GSE129166"], "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:40596704", "parent_hash": "sha256:67f23038111602f0c050397791f44c305e2b56982a0cd13941a2e64653f71c8e", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE129166 licence not read", "asset:data:geo:GSE129166 not downloaded", "asset:data:geo:GSE14328 licence not read", "asset:data:geo:GSE14328 not downloaded", "asset:data:geo:GSE1563 licence not read", "asset:data:geo:GSE1563 not downloaded", "asset:data:geo:GSE25902 licence not read", "asset:data:geo:GSE25902 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["NA (1µL) was mixed with ChamQ Universal SYBR qPCR Master Mix (Novizan, Cat# Q711-03) and subje", "Cat# Q711-03) and subjected to quantitative real-time PCR (qRT-PCR) on the Applied Biosystems StepOneP", "-PCR) on the Applied Biosystems StepOnePlus™ Real-Time PCR System Thermal Cycling Block. The mRNA level"], "order_basis": "paper_text_order:2225", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["enes Eight-week-old male Balb/c and C57BL/6J mice were bought from Charles River (Beijing, China).", "rst Hospital of Jilin University. The Balb/c mice were divided into groups as follows: the normal g", "to Balb/c recipients. Briefly, the recipient mice were anesthetized with isoflurane delivered throu", "utaneous injection to prevent infection. The mice were housed individually in separate cages, and b"], "order_basis": "paper_text_order:2753", "id": "assay:2"}, {"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 DEGs between normal and AR specimens were processed with the “limma” package."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}