Differential expression of long non-coding RNA and mRNA in children with Henoch-Schönlein purpura nephritis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30651843", "kind": "science-record", "revision": 8, "content_hash": "sha256:6cada2525edb672135b260df1d41288102b7355bdc802c62b4438942791f7c62", "created_at": "2026-11-01T15:40:40Z", "updated_at": "2026-11-01T22:43:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Differential expression of long non-coding RNA and mRNA in children with Henoch-Schönlein purpura nephritis.", "doi": "10.3892/etm.2018.7038", "pmid": "30651843", "authors": ["Shuang Pang", "Jing Lv", "Shengzhi Wang", "Guanqi Yang", "Xiaohuan Ding", "Jun Zhang"], "journal": "Experimental and therapeutic medicine", "year": 2019, "abstract": "Long non-coding RNAs (lncRNAs) serve an essential role in regulating immunological functions. However, their impact on Henoch-Schönlein purpura nephritis (HSPN), has remained elusive. The present study determined the expression of lncRNAs and mRNAs in the peripheral blood of 6 children with HSPN and recruited 4 healthy children for comparative study. High-throughput sequencing revealed outstanding differences in lncRNA and mRNA expression, which were verified through reverse transcription-quantitative polymerase chain reaction. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were used to investigate the associated biological functions and possible mechanisms of lncRNAs and mRNAs in HSPN. A total of 820 differentially expressed lncRNAs between the two groups were identified, of which 34 were upregulated and 786 were downregulated. Simultaneously, a total of 3,557 mRNAs were also identified to be differentially expressed, of which 1,232 were upregulated and 2,325 were downregulated. The results revealed that the expression of lncRNAs including ENST00000378432, ENST00000571370, uc001kfc.1 and uc010qna.2 was decreased in HSPN patients compared with that in healthy controls. These lncRNAs were associated with the p53 signaling pathway and apoptosis-associated genes (AKT2, tumor protein 53, phosphatase and tensin homolog and FAS). Further studies of those lncRNAs will be performed to elucidate their functions in apoptosis. Complete raw data files were deposited in the Gene Expression Omnibus (GEO) at National Center for Biotechnology information under the GEO accession no. GSE102114 (www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102114).", "claims": [{"id": "claim-method", "statement": "Fisher's exact test was used for GO analysis and KEGG pathway analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30651843", "locator": "sections[9] \"Statistical analysis\" paragraph 2", "quote": "Fisher's exact test was used for GO analysis and KEGG pathway analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and analyzed during the present study are available from the Gene Expression Omnibus (GSE102114; www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102114).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30651843", "locator": "sections[21] \"Availability of data and materials\" paragraph 2", "quote": "The datasets generated and analyzed during the present study are available from the Gene Expression Omnibus (GSE102114; www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102114)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:30651843"], "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:GSE102114"], "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:GSE102114"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30651843", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/etm.2018.7038", "sha256": "sha256:eadf3a18edc4bc39dbb730ca78736f59070286de2df3bc7b188a5e339c78805f", "bytes": 40050, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3892/etm.2018.7038", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6307475", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE102114", "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=GSE102114", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE102114", "version": null, "note": "The datasets generated and analyzed during the present study are available from the Gene Expression Omnibus (GSE102114; www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102114).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and analyzed during the present study are available from the Gene Expression Omnibus (GSE102114; www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102114).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2724040", "GSM2724041", "GSM2724042", "GSM2724043", "GSM2724044", "GSM2724045", "GSM2724046", "GSM2724047", "GSM2724048", "GSM2724049"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "Differential expression of long non‑coding RNA and mRNA in children with Henoch‑Schönlein purpura nephritis", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30651843:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:674365a725daca86381346c3e7bdbbffaf72b8b6b6669dc986136c6fde12f846", "bytes": 571, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#tI-etm-0-0-7038", "version": null, "note": "Clinical characteristics of 6 HSPN cases.", "structure": {"pmcid": "PMC6307475", "section_index": 4, "section_title": "Patients and sample collection", "row_count": 8, "column_count": 7}, "table": {"label": "Table I.", "caption": "Clinical characteristics of 6 HSPN cases.", "rows": [["Patient ID", "S64", "S87", "S105", "S111", "S173", "S303"], ["Age (years)", "14", "13", "10", "14", "11", "11"], ["Sex", "F", "F", "M", "M", "M", "M"], ["Purpura", "+", "+", "+", "+", "+", "+"], ["Abdominal pain", "−", "+", "−", "−", "−", "+"], ["Arthralgia", "−", "+", "+", "−", "+", "+"], ["Period between the onset of HSPN", "12", "10", "34", "16", "60", "20"], ["and initiation of therapy (months)"]], "row_count": 8, "column_count": 7, "numeric_cells": 18, "header_rows": 1, "locator": "section[4]/table-wrap[1]#tI-etm-0-0-7038"}}, {"id": "asset:table:pmid:30651843:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:cf7467bad1e532c91f08a28e3b54fc7652e58a43ced9b6efe2ded14c793517b2", "bytes": 944, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#tII-etm-0-0-7038", "version": null, "note": "Primers used for reverse transcription-quantitative polymerase chain reaction.", "structure": {"pmcid": "PMC6307475", "section_index": 8, "section_title": "RT-qPCR validation", "row_count": 22, "column_count": 3}, "table": {"label": "Table II.", "caption": "Primers used for reverse transcription-quantitative polymerase chain reaction.", "rows": [["Gene name/direction", "Sequence (5′ to 3′)", "Product length (bp)"], ["ENSG00000267121", "", ""], ["F", "GAGGAAGACCCTGGAAGGAG", "203"], ["R", "GTCCCAAGCTTCAGTCATCC", ""], ["ENSG00000252310", "", ""], ["F", "GGTCCGAGTGTTGTGGGTTA", "50"], ["R", "GGGGGAGACAATGTTAAATCAA", ""], ["uc001kfc.1", "", ""], ["F", "AAAATTAGCCAGGCATGGTG", "209"], ["R", "TCTCTCACGGCTCTTGTGTG", ""], ["uc010qna.2", "", ""], ["F", "GGGTCTTCCTCATGGCACTA", "202"], ["R", "CAGGCCTTCCAAGTTCTGAG", ""], ["ENST00000378432", "", ""], ["F", "CCTTTTCTCCATGGCATTTG", "202"], ["R", "TCCTGCATTCATTCATTCCA", ""], ["ENST00000571370", "", ""], ["F", "GGTTGTTTCATTCCGCAGTT", "204"], ["R", "TTTCTGGGACGATGAAAAGG", ""], ["ACTB", "", ""], ["F", "GGCCTCCAAGGAGTAAGACC", "73"], ["R", "AGGGGAGATTCAGTGTGGTG", ""]], "row_count": 22, "column_count": 3, "numeric_cells": 14, "header_rows": 1, "locator": "section[8]/table-wrap[1]#tII-etm-0-0-7038"}}, {"id": "asset:table:pmid:30651843:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:dca9ce26e2a85023c151fcaa54a71e84b06017a5458be38eca0c0929705ba41c", "bytes": 639, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#tIII-etm-0-0-7038", "version": null, "note": "Baseline demographic and clinical data of subjects.", "structure": {"pmcid": "PMC6307475", "section_index": 12, "section_title": "Subject characteristics", "row_count": 6, "column_count": 4}, "table": {"label": "Table III.", "caption": "Baseline demographic and clinical data of subjects.", "rows": [["Parameter", "HSPN group (n=6)", "HC group (n=4)", "Normal range"], ["Sex (male/female), n", "4:2", "1:3", ""], ["Age (years, mean ± SD)", "12.17±1.72", "11.25±2.99", ""], ["Serum IgA (g/l, mean ± SD)", "3.00±1.21", "1.39±0.55", "0.63–1.79"], ["Urine red blood cell count (p/µl, mean ± SD)", "387.48±590.34", "3.60±8.10", "0-25.00"], ["24-h urine protein quantity (g/24 h, mean ± SD)", "0.280±0.150", "0.050±0.007", "0–0.150"]], "row_count": 6, "column_count": 4, "numeric_cells": 16, "header_rows": 1, "locator": "section[12]/table-wrap[1]#tIII-etm-0-0-7038"}}, {"id": "asset:table:pmid:30651843:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:549d244354adb8e10f5c1d11587e5ed180cee63741dd0693f746f70649485bf8", "bytes": 1855, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#tIV-etm-0-0-7038", "version": null, "note": "Top 25 aberrantly expressed lncRNAs according to the FC values between the two groups.", "structure": {"pmcid": "PMC6307475", "section_index": 13, "section_title": "Differentially expressed lncRNAs", "row_count": 28, "column_count": 5}, "table": {"label": "Table IV.", "caption": "Top 25 aberrantly expressed lncRNAs according to the FC values between the two groups.", "rows": [["lncRNA ID", "FC value", "P-value", "Class", "Database"], ["Upregulated", "", "", "", ""], ["ENSG00000202354", "736.95", "0.030", "Intergenic", "Ensembl"], ["ENSG00000252310", "487.59", "0.007", "Intergenic", "Ensembl"], ["Downregulated", "", "", "", ""], ["ENSG00000259001", "−12971.66", "0.036", "Bidirectional", "Ensembl"], ["HLA-B", "−182.99", "0.039", "Sense", "UCSC_knowngene"], ["ENSG00000257621", "−65.40", "0.012", "Intronic", "Ensembl"], ["ENSG00000262380", "−44.54", "0.010", "Sense", "Ensembl"], ["BC047651", "−42.38", "0.010", "Sense", "UCSC_knowngene"], ["ENSG00000267121", "−42.31", "0.002", "Intergenic", "Ensembl"], ["ENSG00000230105", "−42.22", "0.025", "Intergenic", "Ensembl"], ["DQ598910", "−41.06", "0.002", "Sense", "UCSC_knowngene"], ["ENSG00000236535", "−39.99", "0.020", "Sense", "Ensembl"], ["ENSG00000262879", "−38.70", "0.007", "Intergenic", "Ensembl"], ["BC044596", "−38.50", "0.034", "Sense", "UCSC_knowngene"], ["ENSG00000231485", "−36.49", "0.041", "Intergenic", "Ensembl"], ["ENSG00000260060", "−26.54", "0.045", "Intergenic", "Ensembl"], ["ENSG00000232593", "−26.14", "0.031", "Intergenic", "Ensembl"], ["ENSG00000246016", "−24.65", "0.018", "Intergenic", "Ensembl"], ["MGC72080", "−24.52", "0.021", "Intergenic", "UCSC_knowngene"], ["XLOC_012288", "−23.80", "0.036", "Intergenic", "TCONS"], ["ENSG00000247556", "−21.99", "0.018", "Intergenic", "Ensembl"], ["ENSG00000267672", "−21.24", "0.002", "Sense", "Ensembl"], ["ENSG00000227195", "−19.36", "0.035", "Intergenic", "Ensembl"], ["AX747098", "−19.05", "0.018", "Sense", "UCSC_knowngene"], ["AK098491", "−18.85", "0.007", "Sense", "UCSC_knowngene"], ["ENSG00000253430", "−18.81", "0.003", "Sense", "Ensembl"]], "row_count": 28, "column_count": 5, "numeric_cells": 74, "header_rows": 1, "locator": "section[13]/table-wrap[1]#tIV-etm-0-0-7038"}}, {"id": "asset:table:pmid:30651843:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:022eb3263f63d911dee53dbfaf6fce3d63bc2ba8d0dc21b898a40c75e61daa88", "bytes": 2214, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#tV-etm-0-0-7038", "version": null, "note": "Top 25 differentially expressed mRNAs according to the FC values between the two groups.", "structure": {"pmcid": "PMC6307475", "section_index": 14, "section_title": "Differentially expressed mRNAs", "row_count": 28, "column_count": 5}, "table": {"label": "Table V.", "caption": "Top 25 differentially expressed mRNAs according to the FC values between the two groups.", "rows": [["Gene name", "Ensembl ID", "FC value", "P-value", "Chromosome"], ["Upregulated"], ["RPL17-C18orf32", "ENSG00000215472", "17.16", "0.026", "chr18:47008027-47018906"], ["MNDA", "ENSG00000163563", "16.94", "<0.001", "chr1:158801106-158819296"], ["IFIT1", "ENSG00000185745", "15.09", "0.001", "chr10:90973325-91174314"], ["Downregulated"], ["ZNF431", "ENSG00000196705", "−33.88", "<0.001", "chr19:21324826-21373034"], ["APOBR", "ENSG00000184730", "−29.51", "0.001", "chr16:28467692-28510291"], ["CROCC", "ENSG00000058453", "−29.46", "0.002", "chr1:17066767-17299474"], ["CTD-2583A14.10", "ENSG00000268750", "−28.25", "0.002", "chr19:58281022-58427978"], ["PAGR1", "ENSG00000263136", "−27.74", "0.001", "chr16:29262828-30215631"], ["KLRD1", "ENSG00000134539", "−25.48", "<0.001", "chr12:10378656-10469850"], ["SYMPK", "ENSG00000125755", "−21.33", "<0.001", "chr19:46318667-46366548"], ["SCT", "ENSG00000070031", "−21.32", "0.018", "chr11:626430-627143"], ["CEP250", "ENSG00000126001", "−20.73", "<0.001", "chr20:34042984-34099804"], ["ZNF674", "ENSG00000251192", "−20.15", "<0.001", "chrX:46357161-46404892"], ["GIGYF1", "ENSG00000146830", "−19.36", "<0.001", "chr7:100277129-100287071"], ["ZNF814", "ENSG00000204514", "−18.82", "<0.001", "chr19:58281022-58427978"], ["CEBPZ-AS1", "ENSG00000218739", "−18.02", "<0.001", "chr2:37394962-37551951"], ["RABEP2", "ENSG00000177548", "−17.18", "<0.001", "chr16:28889725-28950667"], ["SMARCA4", "ENSG00000127616", "−17.17", "<0.001", "chr19:11071597-11176071"], ["CRIP1", "ENSG00000257341", "−16.97", "0.004", "chr14:105952653-105965912"], ["SULT1A3", "ENSG00000261052", "−16.30", "0.002", "chr16:29262828-30215631"], ["TMEM180", "ENSG00000138111", "−15.97", "<0.001", "chr10:104221148-104236802"], ["CCDC88B", "ENSG00000168071", "−15.71", "<0.001", "chr11:64107694-64125006"], ["TCHP", "ENSG00000139437", "−15.38", "<0.001", "chr12:110338068-110434194"], ["CHCHD6", "ENSG00000159685", "−15.37", "0.003", "chr3:126423062-126679249"], ["BAIAP2", "ENSG00000175866", "−15.31", "<0.001", "chr17:79008947-79156964"]], "row_count": 28, "column_count": 5, "numeric_cells": 108, "header_rows": 1, "locator": "section[14]/table-wrap[1]#tV-etm-0-0-7038"}}], "gaps": ["asset:data:geo:GSE102114 not downloaded", "asset:data:geo:GSE102114 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "contingency_analysis", "specific": "fisher_exact", "label": "Categorical (contingency table) analysis", "dsl_operations": ["contingency_table", "chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Fisher's exact test was used for GO analysis and KEGG pathway analysis."}}, {"id": "method-2", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Student's t-test"}}, {"id": "method-3", "family": "group_comparison", "specific": "mann_whitney", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Mann-Whitney"}}], "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": ["contingency_table", "chi_square_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: fisher_exact."}, "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": ["GSE102114"], "resolved_accessions": ["GSE102114"], "statements": ["The datasets generated and analyzed during the present study are available from the Gene Expression Omnibus (GSE102114; www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102114)."], "basis": "The paper names GSE102114 in Gene Expression Omnibus (GEO) at National Center for Biotechnology information and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["contingency_table", "chi_square_test"], "assets": ["source:pmid:30651843", "data:geo:GSE102114", "asset:table:pmid:30651843:1", "asset:table:pmid:30651843:2", "asset:table:pmid:30651843:3", "asset:table:pmid:30651843:4", "asset:table:pmid:30651843:5"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE102114"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:13:22Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 32164, "completion_tokens": 1259, "cached_tokens": 656}}, "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:30651843", "type": "paper", "label": "pmid:30651843"}, {"id": "source:pmid:30651843", "type": "manuscript", "label": "PMID 30651843 full text"}, {"id": "data:geo:GSE102114", "type": "dataset", "label": "GEO GSE102114"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30651843", "type": "paper", "label": "pmid:30651843"}, {"id": "source:pmid:30651843", "type": "manuscript", "label": "PMID 30651843 full text"}, {"id": "data:geo:GSE102114", "type": "dataset", "label": "GEO GSE102114"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30651843", "type": "extraction", "used": ["source:pmid:30651843"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE102114", "type": "accession_resolution", "used": ["data:geo:GSE102114"], "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:30651843", "parent_hash": "sha256:f0147e1c05634c5867a4ace0a78ff8a5180d88fc6e89c69d534b0e939604e0e4", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE102114 licence not read", "asset:data:geo:GSE102114 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": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ssociated with the p53 signaling pathway and apoptosis-associated genes (AKT2, tumor protein 53, ph", "be performed to elucidate their functions in apoptosis. Complete raw data files were deposited in t"], "order_basis": "paper_text_order:1345", "id": "assay:1"}, {"role": "analysis", "definition_id": "contingency_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["contingency_table", "chi_square_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Fisher's exact test was used for GO analysis and KEGG pathway analysis."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}