← All .science files
pmid:33116763
Identifying the Mechanisms and Molecular Targets of Yizhiqingxin Formula on Alzheimer's Disease: Coupling Network Pharmacology with GEO Database.
Tingting Zhang · Linlin Pan · Yu Cao · Nanyang Liu · Wei Wei · Hao Li
Pharmacogenomics and personalized medicine · 2020 doi:10.2147/PGPM.S269726
Paper
complete
Experiment
complete
Data
partial
Analysis
complete
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 6 items
claims array · 1 item
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 4 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 161 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 44 items
[0] array · 5 items
[1] array · 5 items
[2] array · 4 items
[3] array · 4 items
[4] array · 4 items
[5] array · 4 items
[6] array · 4 items
[7] array · 4 items
[8] array · 5 items
[9] array · 4 items
[10] array · 4 items
[11] array · 4 items
[12] array · 4 items
[13] array · 4 items
[14] array · 4 items
[15] array · 4 items
[16] array · 4 items
[17] array · 4 items
[18] array · 4 items
[19] array · 4 items
[20] array · 4 items
[21] array · 4 items
[22] array · 5 items
[23] array · 4 items
[24] array · 4 items
[25] array · 4 items
[26] array · 4 items
[27] array · 4 items
[28] array · 4 items
[29] array · 4 items
[30] array · 4 items
[31] array · 4 items
[32] array · 4 items
[33] array · 4 items
[34] array · 4 items
[35] array · 4 items
[36] array · 4 items
[37] array · 4 items
[38] array · 4 items
[39] array · 4 items
[40] array · 4 items
[41] array · 4 items
[42] array · 4 items
[43] array · 4 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 111 items
[0] array · 7 items
[1] array · 7 items
[2] array · 7 items
[3] array · 7 items
[4] array · 7 items
[5] array · 7 items
[6] array · 7 items
[7] array · 7 items
[8] array · 7 items
[9] array · 7 items
[10] array · 7 items
[11] array · 7 items
[12] array · 7 items
[13] array · 7 items
[14] array · 7 items
[15] array · 7 items
[16] array · 7 items
[17] array · 7 items
[18] array · 7 items
[19] array · 7 items
[20] array · 7 items
[21] array · 7 items
[22] array · 7 items
[23] array · 7 items
[24] array · 7 items
[25] array · 7 items
[26] array · 7 items
[27] array · 7 items
[28] array · 7 items
[29] array · 7 items
[30] array · 7 items
[31] array · 7 items
[32] array · 7 items
[33] array · 7 items
[34] array · 7 items
[35] array · 7 items
[36] array · 7 items
[37] array · 7 items
[38] array · 7 items
[39] array · 7 items
[40] array · 7 items
[41] array · 7 items
[42] array · 7 items
[43] array · 7 items
[44] array · 7 items
[45] array · 7 items
[46] array · 7 items
[47] array · 7 items
[48] array · 7 items
[49] array · 7 items
[50] array · 7 items
[51] array · 7 items
[52] array · 7 items
[53] array · 7 items
[54] array · 7 items
[55] array · 7 items
[56] array · 7 items
[57] array · 7 items
[58] array · 7 items
[59] array · 7 items
[60] array · 7 items
[61] array · 7 items
[62] array · 7 items
[63] array · 7 items
[64] array · 7 items
[65] array · 7 items
[66] array · 7 items
[67] array · 7 items
[68] array · 7 items
[69] array · 7 items
[70] array · 7 items
[71] array · 7 items
[72] array · 7 items
[73] array · 7 items
[74] array · 7 items
[75] array · 7 items
[76] array · 7 items
[77] array · 7 items
[78] array · 7 items
[79] array · 7 items
[80] array · 7 items
[81] array · 7 items
[82] array · 7 items
[83] array · 7 items
[84] array · 7 items
[85] array · 7 items
[86] array · 7 items
[87] array · 7 items
[88] array · 7 items
[89] array · 7 items
[90] array · 7 items
[91] array · 7 items
[92] array · 7 items
[93] array · 7 items
[94] array · 7 items
[95] array · 7 items
[96] array · 7 items
[97] array · 7 items
[98] array · 7 items
[99] array · 7 items
[100] array · 7 items
[101] array · 7 items
[102] array · 7 items
[103] array · 7 items
[104] array · 7 items
[105] array · 7 items
[106] array · 7 items
[107] array · 7 items
[108] array · 7 items
[109] array · 7 items
[110] array · 7 items
gaps array · 2 items
analysis object · 4 fields
methods array · 2 items
[0] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 3 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 3 items
assets array · 4 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 6 items
assays array · 2 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 3 items
[1] object · 11 fields
required_operations array · 3 items
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33116763", "kind": "science-record", "revision": 8, "content_hash": "sha256:b26dae2764c01414daed0ac106d183f29c9aeef70050ae158e94cc8102ca4774", "created_at": "2026-11-01T15:41:14Z", "updated_at": "2026-11-01T22:02:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identifying the Mechanisms and Molecular Targets of Yizhiqingxin Formula on Alzheimer's Disease: Coupling Network Pharmacology with GEO Database.", "doi": "10.2147/PGPM.S269726", "pmid": "33116763", "authors": ["Tingting Zhang", "Linlin Pan", "Yu Cao", "Nanyang Liu", "Wei Wei", "Hao Li"], "journal": "Pharmacogenomics and personalized medicine", "year": 2020, "abstract": "BACKGROUND: Yizhiqingxin formula (YZQX) is a promising formula for the treatment of Alzheimer's disease (AD) with significant clinical effects. Here, we coupled a network pharmacology approach with the Gene Expression Omnibus (GEO) database to illustrate comprehensive mechanisms and screen for molecular targets of YZQX for AD treatment.\nMETHODS: First, active ingredients of YZQX were screened for the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database with the absorption, distribution, metabolism, and excretion (ADME) parameters. Subsequently, putative targets of active ingredients were predicted using the DrugBank database. AD-related targets were retrieved by analyzing published microarray data (accession number GSE5281). Protein-protein interaction (PPI) networks of YZQX putative targets and AD-related targets were constructed visually and merged to identify candidate targets for YZQX against AD using Cytoscape 3.7.2 software. We performed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to further clarify the biological functions of the candidate targets. The gene-pathway network was established to filter for key target genes.\nRESULTS: Forty-three active ingredients were identified, and 193 putative target genes were predicted. Seven hundred and ten targets related to AD were screened with |log2 FC| > 1 and P < 0.05. Based on the PPI network, 110 target genes of YZQX against AD were identified. Moreover, 32 related pathways including the PI3K-Akt signaling pathway, MAPK signaling pathway, ubiquitin-mediated proteolysis, apoptosis and the NF-kappa B signaling pathway were significantly enriched. In the gene-pathway network, MAPK1, AKT1, TP53, MDM2, EGFR, RELA, SRC, GRB2, CUL1, and MYC targets are putative core genes for YZQX in AD treatment.\nCONCLUSION: YZQX against AD may exert its neuroprotective effect via the PI3K-Akt signaling pathway, MAPK signaling pathway, and ubiquitin-mediated proteolysis. YZQX may be a promising drug that can be used in the treatment of AD.", "claims": [{"id": "claim-data-access", "statement": "Expression profiling data from GSE5281 were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/) based on the microarray platform GPL570 (Affymetrix Human Gene Expression Array), which contained 74 samples from healthy individuals and 87 AD samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33116763", "locator": "sections[5] \"Differentially Expressed Gene Search, Identification, and Analysis\" paragraph 2", "quote": "Expression profiling data from GSE5281 were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/) based on the microarray platform GPL570 (Affymetrix Human Gene Expression Array), which contained 74 samples from healthy individuals and 87 AD samples."}], "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:33116763"], "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:GSE5281"], "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:GSE5281"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33116763", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/PGPM.S269726", "sha256": "sha256:f8de69856455350bdfc849e2c15b1844415f57de9b1c33d52d22538abe0ff2e3", "bytes": 36245, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/PGPM.S269726", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7571582", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE5281", "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=GSE5281", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE5281", "version": null, "note": "Expression profiling data from GSE5281 were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/) based on the microarray platform GPL570 (Affymetrix Human Gene Expression Array), which contained 74 samples from healthy individuals and 87 AD samples.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Expression profiling data from GSE5281 were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/) based on the microarray platform GPL570 (Affymetrix Human Gene Expression Array), which contained 74 samples from healthy individuals and 87 AD samples.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM119615", "GSM119616", "GSM119617", "GSM119618", "GSM119619", "GSM119620", "GSM119621", "GSM119622", "GSM119623", "GSM119624", "GSM119625", "GSM119626", "GSM119627", "GSM119628", "GSM119629", "GSM119630", "GSM119631", "GSM119632", "GSM119633", "GSM119634", "GSM119635", "GSM119636", "GSM119637", "GSM119638", "GSM119639", "GSM119640", "GSM119641", "GSM119642", "GSM119643", "GSM119644", "GSM119645", "GSM119646", "GSM119647", "GSM119648", "GSM119649", "GSM119650", "GSM119651", "GSM119652", "GSM119653", "GSM119654", "GSM119655", "GSM119656", "GSM119657", "GSM119658", "GSM119659", "GSM119660", "GSM119661", "GSM119662", "GSM119663", "GSM119664", "GSM119665", "GSM119666", "GSM119667", "GSM119668", "GSM119669", "GSM119670", "GSM119671", "GSM119672", "GSM119673", "GSM119674", "GSM119675", "GSM119676", "GSM119677", "GSM119678", "GSM119679", "GSM119680", "GSM119681", "GSM119682", "GSM119683", "GSM119684", "GSM119685", "GSM119686", "GSM119687", "GSM119688", "GSM238763", "GSM238790", "GSM238791", "GSM238792", "GSM238793", "GSM238794", "GSM238795", "GSM238796", "GSM238797", "GSM238798", "GSM238799", "GSM238800", "GSM238801", "GSM238802", "GSM238803", "GSM238804", "GSM238805", "GSM238806", "GSM238807", "GSM238808", "GSM238809", "GSM238810", "GSM238811", "GSM238812", "GSM238813", "GSM238815", "GSM238816", "GSM238817", "GSM238818", "GSM238819", "GSM238820", "GSM238821", "GSM238822", "GSM238823", "GSM238824", "GSM238825", "GSM238826", "GSM238827", "GSM238834", "GSM238835", "GSM238837", "GSM238838", "GSM238839", "GSM238840", "GSM238841", "GSM238842", "GSM238843", "GSM238844", "GSM238845", "GSM238846", "GSM238847", "GSM238848", "GSM238851", "GSM238854", "GSM238855", "GSM238856", "GSM238857", "GSM238858", "GSM238860", "GSM238861", "GSM238862", "GSM238863", "GSM238864", "GSM238865", "GSM238867", "GSM238868", "GSM238870", "GSM238871", "GSM238872", "GSM238873", "GSM238874", "GSM238875", "GSM238877", "GSM238941", "GSM238942", "GSM238943", "GSM238944", "GSM238945", "GSM238946", "GSM238947", "GSM238948", "GSM238949", "GSM238951", "GSM238952", "GSM238953", "GSM238955", "GSM238963"], "sample_count": 161, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Alzheimer's disease and the normal aged brain (steph-affy-human-433773)", "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:33116763:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ca45d44c5da6a1bff4b4142e1d76108d87542b816c7503f772babbd566c6c0be", "bytes": 2148, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#t0001", "version": null, "note": "The Final Selected Ingredients in YZQX for Analysis", "structure": {"pmcid": "PMC7571582", "section_index": 10, "section_title": "Screening of Bioactive Ingredients and Putative Targets from YZQX", "row_count": 44, "column_count": 5}, "table": {"label": "Table 1", "caption": "The Final Selected Ingredients in YZQX for Analysis", "rows": [["Drug", "Molecular ID", "Molecular Name", "OB(%)", "DL"], ["Chuanxiong", "MOL001494", "Mandenol", "42", "0.19"], ["MOL002135", "Myricanone", "40.6", "0.51"], ["MOL002140", "Perlolyrine", "65.95", "0.27"], ["MOL002151", "Senkyunone", "47.66", "0.24"], ["MOL002157", "Wallichilide", "42.31", "0.71"], ["MOL000359", "Sitosterol", "36.91", "0.75"], ["MOL000433", "FA", "68.96", "0.71"], ["Huanglian", "MOL001454", "Berberine", "36.86", "0.78"], ["MOL013352", "Obacunone", "43.29", "0.77"], ["MOL002894", "Berberrubine", "35.74", "0.73"], ["MOL002897", "Epiberberine", "43.09", "0.78"], ["MOL002903", "(R)-Canadine", "55.37", "0.77"], ["MOL002904", "Berlambine", "36.68", "0.82"], ["MOL002907", "Corchoroside A_qt", "104.95", "0.78"], ["MOL000622", "Magnograndiolide", "63.71", "0.19"], ["MOL000762", "Palmidin A", "35.36", "0.65"], ["MOL000785", "Palmatine", "64.6", "0.65"], ["MOL000098", "Quercetin", "46.43", "0.28"], ["MOL001458", "Coptisine", "30.67", "0.86"], ["MOL002668", "Worenine", "45.83", "0.87"], ["MOL008647", "Moupinamide", "86.71", "0.26"], ["Renshen", "MOL002879", "Diop", "43.59", "0.39"], ["MOL000449", "Stigmasterol", "43.83", "0.76"], ["MOL000358", "Beta-sitosterol", "36.91", "0.75"], ["MOL003648", "Inermin", "65.83", "0.54"], ["MOL000422", "Kaempferol", "41.88", "0.24"], ["MOL004492", "Chrysanthemaxanthin", "38.72", "0.58"], ["MOL005308", "Aposiopolamine", "66.65", "0.22"], ["MOL005314", "Celabenzine", "101.88", "0.49"], ["MOL005317", "Deoxyharringtonine", "39.27", "0.81"], ["MOL005318", "Dianthramine", "40.45", "0.2"], ["MOL005320", "Arachidonate", "45.57", "0.2"], ["MOL005321", "Frutinone A", "65.9", "0.34"], ["MOL005344", "Ginsenoside rh2", "36.32", "0.56"], ["MOL005348", "Ginsenoside-Rh4_qt", "31.11", "0.78"], ["MOL005356", "Girinimbin", "61.22", "0.31"], ["MOL005357", "Gomisin B", "31.99", "0.83"], ["MOL005360", "Malkangunin", "57.71", "0.63"], ["MOL005376", "Panaxadiol", "33.09", "0.79"], ["MOL005384", "Suchilactone", "57.52", "0.56"], ["MOL005399", "Alexandrin_qt", "36.91", "0.75"], ["MOL005401", "Ginsenoside Rg5_qt", "39.56", "0.79"], ["MOL000787", "Fumarine", "59.26", "0.83"]], "row_count": 44, "column_count": 5, "numeric_cells": 129, "header_rows": 1, "locator": "section[10]/table-wrap[1]#t0001"}}, {"id": "asset:table:pmid:33116763:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fcd0caf43d3cb9420aff8a158ad73106fd9d1e39f07743656436b8260b408557", "bytes": 8018, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#t0002", "version": null, "note": "The Key Parameter Values of 110 Core Targets", "structure": {"pmcid": "PMC7571582", "section_index": 13, "section_title": "PPI Network Construction, Merging, and Analysis", "row_count": 111, "column_count": 7}, "table": {"label": "Table 2", "caption": "The Key Parameter Values of 110 Core Targets", "rows": [["Genes", "Betweenness", "Closeness", "Degree", "Eigenvector", "LAC", "Network"], ["NTRK1", "34,826.18", "0.664755", "1289", "0.116813", "53.29151", "277.6773"], ["CUL3", "21,198.02", "0.635588", "826", "0.114035", "56.47758", "229.5985"], ["APP", "10,243.13", "0.566848", "806", "0.055436", "28.96356", "72.53909"], ["HSP90AA1", "9460.703", "0.576881", "767", "0.067672", "43.58423", "114.5966"], ["EGFR", "9542.414", "0.570569", "744", "0.053291", "33.77992", "95.67655"], ["TP53", "19,385.39", "0.613891", "705", "0.093969", "51.64691", "187.0632"], ["ESR1", "15,416", "0.601847", "688", "0.088586", "47.31073", "153.2738"], ["XPO1", "9759.544", "0.57182", "687", "0.062664", "34.92015", "89.52947"], ["MCM2", "14,459.25", "0.613169", "651", "0.104016", "55.49354", "184.1087"], ["HSP90AB1", "7073.427", "0.567774", "640", "0.064062", "40.888", "93.63328"], ["FN1", "12,720.53", "0.607809", "635", "0.097986", "47.78167", "159.2176"], ["CDK2", "13,079.84", "0.59977", "622", "0.090112", "45.10315", "142.7661"], ["UBC", "12,601.12", "0.585626", "614", "0.071026", "43.33876", "131.519"], ["COPS5", "8276.179", "0.592951", "613", "0.094499", "54.41768", "148.6378"], ["CUL1", "8951.929", "0.593288", "564", "0.094188", "55.54103", "152.807"], ["CUL7", "9990.143", "0.599425", "552", "0.089742", "43.08069", "136.2477"], ["RNF2", "9862.539", "0.584641", "525", "0.074703", "37.84158", "110.2017"], ["CAND1", "6260.668", "0.582682", "508", "0.090651", "58.54333", "146.2511"], ["MYC", "5971.691", "0.55985", "503", "0.048495", "29.34222", "67.73357"], ["SIRT7", "6146.117", "0.569013", "496", "0.067372", "34.51938", "80.48613"], ["OBSL1", "6856.922", "0.584314", "489", "0.078196", "38.68543", "108.4209"], ["YWHAZ", "7172.03", "0.576243", "473", "0.075107", "50.46931", "118.5144"], ["NPM1", "8227.16", "0.588268", "469", "0.096871", "65.23567", "160.9559"], ["ITGA4", "7832.164", "0.586944", "466", "0.085024", "44.23226", "116.7656"], ["GRB2", "5536.105", "0.555674", "463", "0.051024", "35.73333", "73.91536"], ["VCP", "6197.81", "0.563479", "440", "0.061805", "40.44492", "85.07729"], ["CDC5L", "4925.157", "0.562264", "423", "0.060454", "40.74786", "86.73088"], ["EP300", "6009.564", "0.562567", "421", "0.052032", "41.77682", "97.50255"], ["VCAM1", "6003.134", "0.579444", "420", "0.079334", "39.46341", "97.94946"], ["CCDC8", "5004.908", "0.56654", "420", "0.065573", "33.0081", "72.19039"], ["FBXO6", "4267.925", "0.559549", "405", "0.058117", "27.9417", "57.70662"], ["HNRNPU", "5872.296", "0.574339", "400", "0.08583", "63", "138.3799"], ["BRCA1", "6517.061", "0.561054", "396", "0.049457", "31.98253", "75.49951"], ["SNW1", "6051.717", "0.561961", "396", "0.05577", "37.17672", "82.74052"], ["HSPA5", "5837.462", "0.565618", "396", "0.067442", "44.8642", "93.19859"], ["TRAF6", "6651.395", "0.555674", "392", "0.041215", "24.94762", "59.68665"], ["EED", "4392.456", "0.567465", "388", "0.070736", "42.96016", "93.1871"], ["HDAC1", "3202.844", "0.549526", "386", "0.043028", "39.17277", "74.42252"], ["HUWE1", "6899.481", "0.571507", "381", "0.067745", "39.42424", "95.38087"], ["EWSR1", "4716.752", "0.552729", "381", "0.05213", "32.06965", "61.19216"], ["HNRNPA1", "3161.637", "0.559549", "376", "0.070618", "55.08036", "99.03541"], ["RPA1", "4112.825", "0.555082", "374", "0.056751", "36.0566", "68.20034"], ["HSPA8", "4735.245", "0.560451", "354", "0.060211", "41.54425", "81.78843"], ["UBE2I", "4251.229", "0.548082", "353", "0.040825", "27.41304", "52.01266"], ["VHL", "4526.61", "0.553609", "353", "0.054592", "29.57971", "54.42804"], ["CUL2", "3517.477", "0.561054", "352", "0.068893", "40.7193", "76.78246"], ["RPA2", "3277.309", "0.550686", "352", "0.051589", "30.05181", "52.91248"], ["YWHAQ", "4217.219", "0.552729", "345", "0.052153", "33.845", "61.33131"], ["MDM2", "5224.652", "0.553316", "344", "0.048166", "30.26108", "59.62867"], ["PARK2", "5674.771", "0.559549", "342", "0.053931", "29.9417", "66.59044"], ["HIST1H3F", "2098.438", "0.556861", "339", "0.058623", "48.64055", "92.1532"], ["HIST1H3A", "2098.438", "0.556861", "339", "0.058623", "48.64055", "92.1532"], ["HIST1H3D", "2098.438", "0.556861", "339", "0.058623", "48.64055", "92.1532"], ["HIST1H3G", "2098.438", "0.556861", "339", "0.058623", "48.64055", "92.1532"], ["HIST1H3C", "2098.438", "0.556861", "339", "0.058623", "48.64055", "92.1532"], ["HIST1H3I", "2098.438", "0.556861", "339", "0.058623", "48.64055", "92.1532"], ["HIST1H3J", "2098.438", "0.556861", "339", "0.058623", "48.64055", "92.1532"], ["HIST1H3E", "2098.438", "0.556861", "339", "0.058623", "48.64055", "92.1532"], ["HIST1H3B", "2098.438", "0.556861", "339", "0.058623", "48.64055", "92.1532"], ["HIST1H3H", "2098.438", "0.556861", "339", "0.058623", "48.64055", "92.1532"], ["HDAC5", "4650.054", "0.565618", "332", "0.066067", "37.55328", "78.84761"], ["EEF1A1", "4669.956", "0.560753", "329", "0.070422", "47.2467", "84.56732"], ["HSPB1", "2002.872", "0.533777", "327", "0.037852", "28.41007", "38.56029"], ["CREBBP", "2243.336", "0.539018", "326", "0.034659", "36.86875", "62.29731"], ["CUL5", "2082.417", "0.551852", "323", "0.064059", "43.43655", "68.27214"], ["RPA3", "2151.833", "0.543796", "314", "0.04598", "29.25882", "45.84844"], ["U2AF2", "3871.685", "0.558052", "310", "0.05925", "43.12844", "86.10159"], ["IKBKG", "2045.93", "0.536799", "306", "0.035822", "27.27211", "40.40291"], ["YWHAG", "2690.41", "0.543512", "303", "0.045769", "34.15476", "53.60628"], ["PAN2", "3382.067", "0.554787", "302", "0.062376", "34.43333", "60.47694"], ["AR", "3134.942", "0.540415", "300", "0.031188", "27.61146", "48.51884"], ["SRC", "2442.609", "0.534598", "299", "0.025456", "25.61029", "43.73683"], ["SMURF1", "3391.445", "0.546646", "296", "0.045905", "24.20556", "41.60122"], ["YWHAE", "2110.936", "0.542382", "296", "0.050186", "38.06024", "54.26133"], ["IKBKE", "2788.819", "0.539855", "294", "0.03488", "18.56962", "31.93874"], ["CTNNB1", "4842.84", "0.547507", "291", "0.039217", "25.30939", "49.85884"], ["SUZ12", "3175.214", "0.548947", "290", "0.046405", "31.03627", "56.67218"], ["AKT1", "2149.736", "0.534598", "278", "0.028894", "23.78832", "34.81879"], ["FUS", "2869.735", "0.553022", "277", "0.061692", "43.76119", "71.4498"], ["ARRB2", "3047.877", "0.54837", "270", "0.052508", "29.98421", "50.1614"], ["MAPK1", "1661.102", "0.530249", "267", "0.027795", "25.20472", "36.14141"], ["HSPA4", "2869.613", "0.5421", "267", "0.041526", "28.74691", "45.89033"], ["RELA", "2373.639", "0.535421", "265", "0.030975", "26.1049", "40.14754"], ["STAU1", "2901.346", "0.551268", "265", "0.057269", "36.70408", "61.5319"], ["CUL4B", "1886.888", "0.542946", "258", "0.053202", "38.61078", "54.05284"], ["BMI1", "1681.993", "0.535146", "256", "0.033908", "23.49645", "33.33627"], ["SMAD2", "1860.082", "0.529442", "256", "0.025645", "20.41322", "29.0253"], ["COMMD3-BMI1", "1681.993", "0.535146", "256", "0.033908", "23.49645", "33.33627"], ["PARP1", "2103.137", "0.53874", "256", "0.046043", "36.66879", "50.39636"], ["SMAD3", "1986.411", "0.533231", "255", "0.027245", "25.03053", "38.00191"], ["YWHAB", "1680.029", "0.530519", "255", "0.031926", "26.15079", "35.30965"], ["TARDBP", "1933.812", "0.545788", "253", "0.061576", "49.70811", "74.31153"], ["RPS27A", "3022.78", "0.543512", "253", "0.051495", "37.50867", "55.10979"], ["CLTC", "2194.827", "0.536523", "250", "0.039743", "28.63265", "44.31083"], ["MYH9", "1763.332", "0.533504", "250", "0.03501", "29.61029", "45.29088"], ["TUBB", "2383.363", "0.544363", "249", "0.04812", "32.77457", "50.91263"], ["EZH2", "1941.901", "0.536799", "248", "0.040164", "30.76471", "43.82032"], ["JUN", "1296.69", "0.527834", "247", "0.023482", "25.16522", "34.51743"], ["FLNA", "2329.567", "0.537352", "247", "0.0397", "31.22819", "50.12443"], ["RB1", "1898.756", "0.53133", "246", "0.027173", "25.60769", "37.52534"], ["CDK1", "1528.586", "0.530789", "245", "0.033329", "26.04724", "35.02188"], ["HDAC2", "1782.979", "0.536523", "244", "0.038497", "36.54967", "54.55134"], ["UBL4A", "2439.333", "0.544079", "244", "0.054326", "40.25434", "56.65844"], ["CDC37", "1191.997", "0.525441", "244", "0.026047", "22.14019", "28.04657"], ["ACTB", "2757.472", "0.540975", "243", "0.041952", "29.14465", "44.85049"], ["RPL10", "1536.133", "0.537075", "243", "0.054545", "59.01935", "75.56065"], ["HNRNPK", "2495.745", "0.547219", "239", "0.057228", "43.24862", "65.25151"], ["XRCC6", "1638.875", "0.535421", "234", "0.04306", "30.7972", "41.1287"], ["PCNA", "1721.649", "0.531871", "234", "0.036312", "26.9771", "36.49264"], ["PRKDC", "2304.506", "0.540135", "233", "0.046236", "31.32298", "45.2468"]], "row_count": 111, "column_count": 7, "numeric_cells": 668, "header_rows": 1, "locator": "section[13]/table-wrap[1]#t0002"}}], "gaps": ["asset:data:geo:GSE5281 not downloaded", "asset:data:geo:GSE5281 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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"}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO enrichment"}}], "targets": [], "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE5281"], "resolved_accessions": ["GSE5281"], "statements": ["Expression profiling data from GSE5281 were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/) based on the microarray platform GPL570 (Affymetrix Human Gene Expression Array), which contained 74 samples from healthy individuals and 87 AD samples."], "basis": "The paper names GSE5281 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:33116763", "data:geo:GSE5281", "asset:table:pmid:33116763:1", "asset:table:pmid:33116763:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE5281"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:14:08Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": null}, "calls": 3, "usage": {"prompt_tokens": 20522, "completion_tokens": 590, "cached_tokens": 528}}, "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:33116763", "type": "paper", "label": "pmid:33116763"}, {"id": "source:pmid:33116763", "type": "manuscript", "label": "PMID 33116763 full text"}, {"id": "data:geo:GSE5281", "type": "dataset", "label": "GEO GSE5281"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33116763", "type": "paper", "label": "pmid:33116763"}, {"id": "source:pmid:33116763", "type": "manuscript", "label": "PMID 33116763 full text"}, {"id": "data:geo:GSE5281", "type": "dataset", "label": "GEO GSE5281"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33116763", "type": "extraction", "used": ["source:pmid:33116763"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE5281", "type": "accession_resolution", "used": ["data:geo:GSE5281"], "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:33116763", "parent_hash": "sha256:0e4626d175ffc54d3e3ab0022ec07f68e98b76a3d27de625b46d32430cbf2cd4", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE5281 licence not read", "asset:data:geo:GSE5281 not downloaded", "execution.not_run", "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": 0.99, "evidence": ["ing pathway, ubiquitin-mediated proteolysis, apoptosis and the NF-kappa B signaling pathway were si", "liferation, ubiquitin-proteasome system, and apoptosis.Figure 5Go analysis of core targets. (A) Bio", "ing pathway, ubiquitin-mediated proteolysis, apoptosis and NF-kappa B signaling pathway, and p53 si"], "order_basis": "paper_text_order:1704", "id": "assay:1"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}