Integrated transcriptomics explored the cancer-promoting genes CDKN3 in esophageal squamous cell cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34044866", "kind": "science-record", "revision": 7, "content_hash": "sha256:17c263cbbcd13e53050861c9b57f5ceb73f9191689803d7c66c478d57a157546", "created_at": "2026-11-01T15:41:37Z", "updated_at": "2026-11-01T22:03:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated transcriptomics explored the cancer-promoting genes CDKN3 in esophageal squamous cell cancer.", "doi": "10.1186/s13019-021-01534-7", "pmid": "34044866", "authors": ["Wanpeng Wang", "Kai Liao", "Hao Chun Guo", "Suqin Zhou", "Ran Yu", "Yanyan Liu", "Yan Pan", "Juan Pu"], "journal": "Journal of cardiothoracic surgery", "year": 2021, "abstract": "BACKGROUND AND OBJECTIVES: Each individual studies is limited to multi-factors and potentially lead to a significant difference of results among them. The present study aim to explore the critical genes related to the development of Esophageal squamous cell carcinoma (ESCC) by integrated transcriptomics and to investigate the clinical significance by experimental validation.\nMETHODS: Datasets of protein-coding genes expression which involved in ESCC were downloaded from Gene Expression Omnibus (GEO) database. The \"Robustrankaggreg\" package in language was used for data integration, and the different expression genes (DEGs) were identified based the cut-off criteria as follows: adjust p-value < 0.05, |fold change (FC)| ≥ 1.5; The protein expression of seed gene in 184 cases of primary ESCC tissues and 50 tumor adjacent normal tissues (at least 5 cm away from the tumor, and defind as the controls) were detected by immunohistochemistry; The relationship between the expression level of seed genes and clinical parameter were analyze. Enumeration data were represented by frequency or percentage (%) and were tested by x2 test. The P value of less than 0.05 was considered statistically significant.\nRESULTS: A total of 244 DEGs were identified by comparing gene expression patterns between ESCC patients and the controls based on integrating dataset of GSE77861, GSE77861, GSE100942, GSE26886, GSE17351, GSE38129, GSE33426, GSE20347 and GSE23400; The Cyclin-dependent kinase inhibitor 3 (CDKN3) were identified the top 1 seed gene of top cluster by use of protein-protein Interaction network and plug-in Molecular Complex Detection; The level of CDKN3 mRNA was significantly increased in ESCC patients compared to controls; The positive expression rate of CDKN3 protein in ESCC tissue samples was 32 and 61.4% in control, respectively. The correlations between the expression level of CDKN3 and lymph node metastasis or clinical staging of ESCC patients are statistically significant.\nCONCLUSION: Integrated transcriptomics is an efficient approach to system biology. By this procedure, our study improved the understanding of the transcriptome status of ESCC.", "claims": [{"id": "claim-method", "statement": "Enumeration data were represented by frequency or percentage (%) and were tested by x2 test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34044866", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Enumeration data were represented by frequency or percentage (%) and were tested by x2 test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34044866", "locator": "sections[23] \"notes\" paragraph 1", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "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:34044866"], "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:GSE100942"], "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:GSE100942"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34044866", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s13019-021-01534-7", "sha256": "sha256:9917ce03aa8f9d98242190ef015dd745fadf8ec716c3d6169b1934c2319b836e", "bytes": 16699, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s13019-021-01534-7", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8161916", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE100942", "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=GSE100942", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE100942", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2696912", "GSM2696913", "GSM2696914", "GSM2696915", "GSM2696916", "GSM2696917", "GSM2696918", "GSM2696919", "GSM2696920", "GSM2696921"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from human Esophageal squamous cell carcinoma (ESCC)", "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:GSE17351", "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=GSE17351", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE17351", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM433786", "GSM433787", "GSM433788", "GSM433789", "GSM433790", "GSM433791", "GSM433792", "GSM433793", "GSM433794", "GSM433795"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from esophageal squamous cell carcinoma (ESCC)", "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:GSE26886", "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=GSE26886", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26886", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM661721", "GSM661722", "GSM661723", "GSM661724", "GSM661725", "GSM661726", "GSM661727", "GSM661728", "GSM661729", "GSM661730", "GSM661731", "GSM661732", "GSM661733", "GSM661734", "GSM661735", "GSM661736", "GSM661737", "GSM661738", "GSM661739", "GSM661740", "GSM661741", "GSM661742", "GSM661743", "GSM661744", "GSM661745", "GSM661746", "GSM661747", "GSM661748", "GSM661749", "GSM661750", "GSM661751", "GSM661752", "GSM661753", "GSM661754", "GSM661755", "GSM661756", "GSM661757", "GSM661758", "GSM661759", "GSM661760", "GSM661761", "GSM661762", "GSM661763", "GSM661764", "GSM661765", "GSM661766", "GSM661767", "GSM661768", "GSM661769", "GSM661770", "GSM661771", "GSM661772", "GSM661773", "GSM661774", "GSM661775", "GSM661776", "GSM661777", "GSM661778", "GSM661779", "GSM661780", "GSM661781", "GSM661782", "GSM661783", "GSM661784", "GSM661785", "GSM661786", "GSM661787", "GSM661788", "GSM661789"], "sample_count": 69, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression profiling of Barrett's esophagus, adenocarcinoma, esophageal squamous epithelium and squamous cell carcinoma", "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:GSE33426", "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=GSE33426", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE33426", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM718600", "GSM718601", "GSM718604", "GSM718605", "GSM718608", "GSM718609", "GSM718612", "GSM718613", "GSM718619", "GSM718620", "GSM718623", "GSM718624", "GSM718627", "GSM718628", "GSM718631", "GSM718632", "GSM718635", "GSM718636", "GSM826782", "GSM826783", "GSM826784", "GSM826785", "GSM826786", "GSM826787", "GSM826788", "GSM826789", "GSM826790", "GSM826791", "GSM826792", "GSM826793", "GSM826794", "GSM826795", "GSM826796", "GSM826797", "GSM826798", "GSM826799", "GSM826800", "GSM826801", "GSM826802", "GSM826803", "GSM826804", "GSM826805", "GSM826806", "GSM826807", "GSM826808", "GSM826809", "GSM826810", "GSM826811", "GSM826812", "GSM826813", "GSM826814", "GSM826815", "GSM826816", "GSM826817", "GSM826818", "GSM826819", "GSM826820", "GSM826821", "GSM826822", "GSM826823", "GSM826824", "GSM826825", "GSM826826", "GSM826827", "GSM826828", "GSM826829", "GSM826830", "GSM826831", "GSM826832", "GSM826833", "GSM826834"], "sample_count": 71, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Three-Dimensional Tumor Profiling Reveals Minimal mRNA  Heterogeneity in Esophageal Squamous Cell Carcinoma", "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:GSE38129", "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=GSE38129", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE38129", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM935144", "GSM935145", "GSM935146", "GSM935147", "GSM935148", "GSM935149", "GSM935150", "GSM935151", "GSM935152", "GSM935153", "GSM935154", "GSM935155", "GSM935156", "GSM935157", "GSM935158", "GSM935159", "GSM935160", "GSM935161", "GSM935162", "GSM935163", "GSM935164", "GSM935165", "GSM935166", "GSM935167", "GSM935168", "GSM935169", "GSM935170", "GSM935171", "GSM935172", "GSM935173", "GSM935174", "GSM935175", "GSM935176", "GSM935177", "GSM935178", "GSM935179", "GSM935180", "GSM935181", "GSM935182", "GSM935183", "GSM935184", "GSM935185", "GSM935186", "GSM935187", "GSM935188", "GSM935189", "GSM935190", "GSM935191", "GSM935192", "GSM935193", "GSM935194", "GSM935195", "GSM935196", "GSM935197", "GSM935198", "GSM935199", "GSM935200", "GSM935201", "GSM935202", "GSM935203"], "sample_count": 60, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "A pilot study of integrative genomics analysis of genes with biallelic loss and its relation to the expression of mRNA and micro-RNA in esophageal squamous cell 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:GSE77861", "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=GSE77861", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE77861", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2061761", "GSM2061762", "GSM2061763", "GSM2061764", "GSM2061765", "GSM2061766", "GSM2061767", "GSM2061768", "GSM2061769", "GSM2061770", "GSM2061771", "GSM2061772", "GSM2061773", "GSM2061774"], "sample_count": 14, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "African American esophageal squamous cell carcinoma expression profile reveals loss of detox networks", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:34044866:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:22289951e4dc5aa68e238fd461fcc3dda2866683b792401444cfde2dd72db09f", "bytes": 520, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "The datasets of ESCC protein-coding genes expression included the present study", "structure": {"pmcid": "PMC8161916", "section_index": 3, "section_title": "Data source", "row_count": 5, "column_count": 10}, "table": {"label": "Table 1", "caption": "The datasets of ESCC protein-coding genes expression included the present study", "rows": [["GSE", "77,861", "100,942", "26,886", "17,351", "38,129", "33,426", "29,001", "20,347", "23,400"], ["Platform", "GPL570", "GPL571", "GPL96/97"], ["Number of probe (n)", "54,675", "22,277", "44,928"], ["ESCC (n)", "7", "5", "9", "5", "30", "59", "21", "17", "53"], ["Con (n)", "7", "5", "19", "5", "30", "12", "24", "17", "53"]], "row_count": 5, "column_count": 10, "numeric_cells": 33, "header_rows": 1, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:34044866:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:651339b68c9d8324246cfd4dfbfd9cd34642d8e46d8f078d51ece981cec7385b", "bytes": 924, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#Tab2", "version": null, "note": "The relationship between the expression level of CDKN3 and clinical significance", "structure": {"pmcid": "PMC8161916", "section_index": 15, "section_title": "Correlation between between CDKN3 and ESCC patients", "row_count": 26, "column_count": 6}, "table": {"label": "Table 2", "caption": "The relationship between the expression level of CDKN3 and clinical significance", "rows": [["Items", "N", "CDKN3 protein", "x2", "P"], ["Positive", "Negative"], ["Gender"], ["Male", "157", "94", "63", "1.071", "0.301"], ["Female", "27", "19", "8"], ["Age"], ["≤ 60 years", "91", "52", "39", "0.788", "0.375"], [">60 years", "93", "56", "32"], ["Location"], ["Neck/upper thoracic", "56", "34", "22", "0.017", "0.898"], ["Mid/lower thoracic", "128", "79", "49"], ["Grade"], ["G1/G2", "125", "75", "50", "0.328", "0.567"], ["G3", "59", "38", "21"], ["T"], ["T1/T2", "79", "48", "31", "0.025", "0.874"], ["T3/T4", "105", "65", "40"], ["N"], ["N0", "79", "38", "41", "10.352", "0.001"], ["N1", "105", "75", "30"], ["M"], ["M0", "175", "107", "69", "1.479", "0.224"], ["M1", "9", "8", "2"], ["Stage"], ["I + II", "106", "57", "49", "6.158", "0.013"], ["III + IV", "78", "56", "22"]], "row_count": 26, "column_count": 6, "numeric_cells": 66, "header_rows": 2, "locator": "section[15]/table-wrap[1]#Tab2"}}], "gaps": ["asset:data:geo:GSE100942 not downloaded", "asset:data:geo:GSE100942 licence not read", "asset:data:geo:GSE17351 not downloaded", "asset:data:geo:GSE17351 licence not read", "asset:data:geo:GSE26886 not downloaded", "asset:data:geo:GSE26886 licence not read", "asset:data:geo:GSE33426 not downloaded", "asset:data:geo:GSE33426 licence not read", "asset:data:geo:GSE38129 not downloaded", "asset:data:geo:GSE38129 licence not read", "asset:data:geo:GSE77861 not downloaded", "asset:data:geo:GSE77861 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Enumeration data were represented by frequency or percentage (%) and were tested by x2 test."}}, {"id": "method-2", "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"}}, {"id": "method-3", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein Interaction"}}], "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": ["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: chi_square."}, "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": ["GSE77861", "GSE100942", "GSE26886", "GSE17351", "GSE38129", "GSE33426", "GSE20347 and GSE23400"], "resolved_accessions": ["GSE77861", "GSE100942", "GSE26886", "GSE17351", "GSE38129", "GSE33426"], "statements": ["The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE77861, GSE100942, GSE26886, GSE17351, GSE38129, GSE33426 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": ["chi_square_test"], "assets": ["source:pmid:34044866", "data:geo:GSE100942", "asset:table:pmid:34044866:1", "asset:table:pmid:34044866:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE100942"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:30:28Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 13930, "completion_tokens": 2579, "cached_tokens": 784}}, "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:34044866", "type": "paper", "label": "pmid:34044866"}, {"id": "source:pmid:34044866", "type": "manuscript", "label": "PMID 34044866 full text"}, {"id": "data:geo:GSE100942", "type": "dataset", "label": "GEO GSE100942"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34044866", "type": "paper", "label": "pmid:34044866"}, {"id": "source:pmid:34044866", "type": "manuscript", "label": "PMID 34044866 full text"}, {"id": "data:geo:GSE100942", "type": "dataset", "label": "GEO GSE100942"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34044866", "type": "extraction", "used": ["source:pmid:34044866"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE100942", "type": "accession_resolution", "used": ["data:geo:GSE100942"], "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:34044866", "parent_hash": "sha256:59e7154390560f8641c4f3be9a4378090e8397f5e04edd2f5173a69d9881a648", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE100942 licence not read", "asset:data:geo:GSE100942 not downloaded", "asset:data:geo:GSE17351 licence not read", "asset:data:geo:GSE17351 not downloaded", "asset:data:geo:GSE26886 licence not read", "asset:data:geo:GSE26886 not downloaded", "asset:data:geo:GSE33426 licence not read", "asset:data:geo:GSE33426 not downloaded", "asset:data:geo:GSE38129 licence not read", "asset:data:geo:GSE38129 not downloaded", "asset:data:geo:GSE77861 licence not read", "asset:data:geo:GSE77861 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": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["and defind as the controls) were detected by immunohistochemistry; The relationship between the expression lev"], "order_basis": "paper_text_order:986", "id": "assay:1"}, {"role": "analysis", "definition_id": "contingency_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["chi_square_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Enumeration data were represented by frequency or percentage (%) and were tested by x2 test."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}