Integrated identification of key genes and pathways in Alzheimer's disease via comprehensive bioinformatical analyses.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31346329", "kind": "science-record", "revision": 7, "content_hash": "sha256:3943d3ec311b108d60af5360bd401432aa3fdcd30db3a9b01727f8ec6ef59bc7", "created_at": "2026-11-01T15:40:47Z", "updated_at": "2026-11-01T22:00:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated identification of key genes and pathways in Alzheimer's disease via comprehensive bioinformatical analyses.", "doi": "10.1186/s41065-019-0101-0", "pmid": "31346329", "authors": ["Tingting Yan", "Feng Ding", "Yan Zhao"], "journal": "Hereditas", "year": 2019, "abstract": "BACKGROUND: Alzheimer's disease (AD) is known to be caused by multiple factors, meanwhile the pathogenic mechanism and development of AD associate closely with genetic factors. Existing understanding of the molecular mechanisms underlying AD remains incomplete.\nMETHODS: Gene expression data (GSE48350) derived from post-modern brain was extracted from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were derived from hippocampus and entorhinal cortex regions between AD patients and healthy controls and detected via Morpheus. Functional enrichment analyses, including Gene Ontology (GO) and pathway analyses of DEGs, were performed via Cytoscape and followed by the construction of protein-protein interaction (PPI) network. Hub proteins were screened using the criteria: nodes degree≥10 (for hippocampus tissues) and ≥ 8 (for entorhinal cortex tissues). Molecular Complex Detection (MCODE) was used to filtrate the important clusters. University of California Santa Cruz (UCSC) and the database of RNA-binding protein specificities (RBPDB) were employed to identify the RNA-binding proteins of the long non-coding RNA (lncRNA).\nRESULTS: 251 & 74 genes were identified as DEGs, which consisted of 56 & 16 up-regulated genes and 195 & 58 down-regulated genes in hippocampus and entorhinal cortex, respectively. Biological analyses demonstrated that the biological processes and pathways related to memory, transmembrane transport, synaptic transmission, neuron survival, drug metabolism, ion homeostasis and signal transduction were enriched in these genes. 11 genes were identified as hub genes in hippocampus and entorhinal cortex, and 3 hub genes were identified as the novel candidates involved in the pathology of AD. Furthermore, 3 lncRNAs were filtrated, whose binding proteins were closely associated with AD.\nCONCLUSIONS: Through GO enrichment analyses, pathway analyses and PPI analyses, we showed a comprehensive interpretation of the pathogenesis of AD at a systematic biology level, and 3 novel candidate genes and 3 lncRNAs were identified as novel and potential candidates participating in the pathology of AD. The results of this study could supply integrated insights for understanding the pathogenic mechanism underlying AD and potential novel therapeutic targets.", "claims": [{"id": "claim-data-access", "statement": "All data generated or analyzed during this study are included in this published article [and its supplementary information files].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31346329", "locator": "sections[21] \"Availability of data and materials\" paragraph 2", "quote": "All data generated or analyzed during this study are included in this published article [and its supplementary information files]."}], "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:31346329"], "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:GSE48350"], "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:GSE48350"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31346329", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s41065-019-0101-0", "sha256": "sha256:046264978612ca0bf0b866e2211d37cb9fdee6d1e34a344bb933a50d7b08cf43", "bytes": 55445, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s41065-019-0101-0", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6636172", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE48350", "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=GSE48350", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE48350", "version": null, "note": "All data generated or analyzed during this study are included in this published article [and its supplementary information files].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in this published article [and its supplementary information files].", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1176196", "GSM1176197", "GSM1176198", "GSM1176199", "GSM1176200", "GSM1176201", "GSM1176202", "GSM1176203", "GSM1176204", "GSM1176205", "GSM1176206", "GSM1176207", "GSM1176208", "GSM1176209", "GSM1176210", "GSM1176211", "GSM1176212", "GSM1176213", "GSM1176214", "GSM1176215", "GSM1176216", "GSM1176217", "GSM1176218", "GSM1176219", "GSM1176220", "GSM1176221", "GSM1176222", "GSM1176223", "GSM1176224", "GSM1176225", "GSM1176226", "GSM1176227", "GSM1176228", "GSM1176229", "GSM1176230", "GSM1176231", "GSM1176232", "GSM1176233", "GSM1176234", "GSM1176235", "GSM1176236", "GSM1176237", "GSM1176238", "GSM1176239", "GSM1176240", "GSM1176241", "GSM1176242", "GSM1176243", "GSM1176244", "GSM1176245", "GSM1176246", "GSM1176247", "GSM1176248", "GSM1176249", "GSM1176250", "GSM1176251", "GSM1176252", "GSM1176253", "GSM1176254", "GSM1176255", "GSM1176256", "GSM1176257", "GSM1176258", "GSM1176259", "GSM1176260", "GSM1176261", "GSM1176262", "GSM1176263", "GSM1176264", "GSM1176265", "GSM1176266", "GSM1176267", "GSM1176268", "GSM1176269", "GSM1176270", "GSM1176271", "GSM1176272", "GSM1176273", "GSM1176274", "GSM1176275", "GSM300166", "GSM300167", "GSM300168", "GSM300169", "GSM300170", "GSM300171", "GSM300172", "GSM300173", "GSM300174", "GSM300175", "GSM300176", "GSM300177", "GSM300178", "GSM300179", "GSM300180", "GSM300181", "GSM300182", "GSM300183", "GSM300185", "GSM300186", "GSM300187", "GSM300188", "GSM300189", "GSM300190", "GSM300191", "GSM300192", "GSM300193", "GSM300194", "GSM300195", "GSM300196", "GSM300197", "GSM300198", "GSM300199", "GSM300200", "GSM300201", "GSM300202", "GSM300203", "GSM300204", "GSM300205", "GSM300206", "GSM300207", "GSM300208", "GSM300209", "GSM300210", "GSM300211", "GSM300212", "GSM300213", "GSM300214", "GSM300215", "GSM300216", "GSM300217", "GSM300218", "GSM300219", "GSM300220", "GSM300221", "GSM300222", "GSM300223", "GSM300224", "GSM300225", "GSM300226", "GSM300227", "GSM300228", "GSM300229", "GSM300230", "GSM300231", "GSM300232", "GSM300233", "GSM300234", "GSM300235", "GSM300236", "GSM300237", "GSM300238", "GSM300239", "GSM300240", "GSM300241", "GSM300242", "GSM300243", "GSM300244", "GSM300245", "GSM300246", "GSM300247", "GSM300248", "GSM300249", "GSM300250", "GSM300251", "GSM300252", "GSM300253", "GSM300254", "GSM300255", "GSM300256", "GSM300258", "GSM300259", "GSM300260", "GSM300261", "GSM300262", "GSM300263", "GSM300264", "GSM300265", "GSM300266", "GSM300267", "GSM300268", "GSM300269", "GSM300270", "GSM300271", "GSM300272", "GSM300273", "GSM300274", "GSM300275", "GSM300276", "GSM300277", "GSM300278", "GSM300279", "GSM300280", "GSM300281", "GSM300282", "GSM300283", "GSM300284", "GSM300285", "GSM300286", "GSM300287", "GSM300288", "GSM300289", "GSM300290", "GSM300291", "GSM300292", "GSM300293", "GSM300294", "GSM300295", "GSM300296", "GSM300297", "GSM300298", "GSM300299", "GSM300300", "GSM300301", "GSM300302", "GSM300303", "GSM300304", "GSM300305", "GSM300306", "GSM300307", "GSM300308", "GSM300309", "GSM300310", "GSM300311", "GSM300312", "GSM300313", "GSM300314", "GSM300315", "GSM300316", "GSM300317", "GSM300318", "GSM300319", "GSM300320", "GSM300321", "GSM300322", "GSM300323", "GSM300324", "GSM300325", "GSM300326", "GSM300327", "GSM300328", "GSM300329", "GSM300330", "GSM300331", "GSM300332", "GSM300333", "GSM300335", "GSM300338", "GSM300339", "GSM300340", "GSM300341", "GSM318840", "GSM350078"], "sample_count": 253, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Alzheimer's Disease Dataset", "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:31346329:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:882908f674665857dfb6cef12268c1f8db9eb52a3f30868b8f4ff45cf986dd65", "bytes": 2638, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "DEGs were identified from the dataset", "structure": {"pmcid": "PMC6636172", "section_index": 3, "section_title": "Identification of DEGs", "row_count": 5, "column_count": 2}, "table": {"label": "Table 1", "caption": "DEGs were identified from the dataset", "rows": [["", "Gene symbol"], ["Up-regulated genes (hippocampus tissues)", "ANKIB1 SLC25A46 ZNF621 XIST C1orf87 MAP 3 K19 CD163 LTF AGBL2 PZP TAC1 IGFBP7-AS1 SLC27A6 C1orf192 CD44 SYNE2 FAM216B ABCA6 SPATA18 CCDC11 FAM81B SERPINI2 CRLF1 WDR49 TNFRSF11B DNAAF3 CDK19 RASSF9 FREM3 ANKFN1 ZBBX ART3 CAPS SLC7A11 PIH1D3 WWTR1 CCDC81 EFCAB1 TEX26 EFEMP1 DNAH6 SLC19A3 C21orf62 TDGF1 /// TDGF1P3 MORN5 STON2 CP DYNC2H1 ECM2 WDR96 CXorf30 FANCB CDC14A LEPR /// LEPROT FHL5 ARHGEF7"], ["Down-regulated genes (hippocampus tissues)", "NWD2 ADAD2 BSN AMPH SLC26A10 NRP1 CYP2A7P1 EBP PCLO ETNK1 SLC24A3 KIT KCNJ6 DDX50 CD300C DIRAS3 RAB3C TTC5 KCNG3 KALRN SCNN1G ACSL4 MICAL2 MAP 7D2 CALY SOX1 C16orf74 DNASE1L2 NEFH ANK1 COL2A1 LOC100132891 RCOR3 GABRG2 SPDEF ACHE RDH10 TRAF3IP1 CNR1 TMEM35 PDPN F12 KCNC1 OBSCN STC2 EXOSC3 ACTRT3 RHCG DGAT2 SLC35G1 CAMK1 KCNK10 DCAF15 METTL10 GLS2 FHL2 MICB MCHR1 PPM1E TP53I11 KCMF1 CELF4 SCG2 SCN2B VAPA CARTPT NRP2 CDC42 MIR22 /// MIR22HG BRSK2 SPANXA1 /// SPANXA2 /// SPANXB1 /// SPANXC ATP1A3 SLC2A3 PLK2 HOMER2 GFOD1 NCDN GLRX PCOLCE2 MATN1 NFKBID LAMP5 LY86-AS1 RPL27A /// SNORA45A SYN2 KCNA1 KCNJ5 GSDMB SLC6A3 CADPS ATP8A2 SRGAP3 NUP93 TMEM155 QRICH1 IL4I1 DHRS2 AFF2 KISS1R STRIP2 TRPV2 SGPP2 OPRK1 SLC22A8 SSTR2 SLC1A6 C14orf180 RIMKLA KLK7 RET NKX2–5 ACTN1 SPAG11A LEPREL2 IGFBPL1 FABP3 MAGEL2 PPP1R17 IL12RB1 SYT2 SNORD114–3 AFF3 PCDH20 LRRFIP1 LINC00622 L3MBTL1 PYCRL TBC1D26 /// ZNF286A ATF7IP2 PWP2 CACNA1A KCNJ4 TRHDE SUSD4 UBASH3B SIAH1 PTH2R SDK1 CCNJL KCNQ5 TMEM61 PML NRIP3 METTL7B LINC00282 WIPF3 CLSTN2 GREM2 LOC389906 IFRD1 MRAP2 CENPVP1 /// CENPVP2 KCNIP2 KDM6B CTSG KMT2D CPNE4 PGM5 CARD14 CST7 SPOCD1 HINT3 NR4A3 CENPW VEGFA PCDH8 PKIB DNAJB5 ARC GRP CKS2 PTGS1 ARHGAP36 A1BG RTF1 AQP3 TSPAN18 TH CHGB CITED1 CALB1 CRABP1 MIR7-3HG PDYN FNDC9 SCGN WFIKKN2 BDNF RAE1 INHBA EGR4 FOSB LAMB3 EGR2 MPO NPAS4"], ["Up-regulated genes (entorhinal cortex tissues)", "ANKIB1 TAC1 SLC25A46 XIST ZNF621 C1orf192 SPATA13 PKP2 CDK19 A2ML1 CX3CR1 C1orf87 RAPGEF5 CD24 ID2 /// ID2B DST"], ["Down-regulated genes (entorhinal cortex tissues)", "RIT2 SLC17A6 POPDC3 RPLP2P1 /// RPLP2P1 NEFH CKS2 LRRFIP1 CYP27C1 CABP1 SCGB3A1 LY86-AS1 VASH2 QPCT CENPF MPP7 TWIST2 COL4A1 TCERG1L RGS2 HSPB3 ANKRD34C OTP KDELR3 TPSAB1 BRE-AS1 CARTPT SECTM1 XIRP1 IL1RL1 GPR68 MMP10 TPSB2 DUSP2 RSPO2 PTGS2 RTF1 IL7R GPR3 FOSL1 LINC00622 IL11 DHRS2 FOSB CBLN1 SAA1 /// SAA2 C2CD4A SPOCD1 TGFBI HDC HS3ST2 LINC00960 ATP1B4 RAE1 PMCH LAMB3 OXT INHBA AVP"]], "row_count": 5, "column_count": 2, "numeric_cells": 4, "header_rows": 1, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:31346329:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:730ef63bea321c731dc9b21f8952532f19a8a67049bfc5e7805b7073b055cabc", "bytes": 896, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#Tab2", "version": null, "note": "Pathway enrichment in Module 1", "structure": {"pmcid": "PMC6636172", "section_index": 6, "section_title": "PPI network analyses and module analyses", "row_count": 7, "column_count": 6}, "table": {"label": "Table 2", "caption": "Pathway enrichment in Module 1", "rows": [["#Pathway ID", "Pathway description", "Observed gene count", "False discovery rate", "Matching proteins in your network (ids)", "Matching proteins in your network (labels)"], ["5131", "Shigellosis", "2", "0.0131", "ENSP00000314458, ENSP00000398632", "CD44,CDC42"], ["4640", "Hematopoietic cell lineage", "2", "0.0146", "ENSP00000288135, ENSP00000398632", "CD44,KIT"], ["4014", "Ras signaling pathway", "2", "0.0323", "ENSP00000288135, ENSP00000314458", "CDC42,KIT"], ["4015", "Rap1 signaling pathway", "2", "0.0323", "ENSP00000288135, ENSP00000314458", "CDC42,KIT"], ["4144", "Endocytosis", "2", "0.0323", "ENSP00000288135, ENSP00000314458", "CDC42,KIT"], ["5205", "Proteoglycans in cancer", "2", "0.0323", "ENSP00000314458, ENSP00000398632", "CD44,CDC42"]], "row_count": 7, "column_count": 6, "numeric_cells": 30, "header_rows": 1, "locator": "section[6]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:31346329:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c0a5d03f0fe28a6c901239427098ecdafae8825e715e041c728bb5c861f9298d", "bytes": 599, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[2]#Tab3", "version": null, "note": "Pathway enrichment in Module 2", "structure": {"pmcid": "PMC6636172", "section_index": 6, "section_title": "PPI network analyses and module analyses", "row_count": 3, "column_count": 6}, "table": {"label": "Table 3", "caption": "Pathway enrichment in Module 2", "rows": [["#Pathway ID", "Pathway description", "Observed gene count", "False discovery rate", "Matching proteins in Your network (ids)", "Matching Proteins In your Network (labels)"], ["4080", "Neuroactive ligand- receptor interaction", "4", "0.00166", "ENSP00000234371, ENSP00000265572, ENSP00000350198, ENSP00000358511", "CNR1, KISS1R, OPRK1, SSTR2"], ["5030", "Cocaine addiction", "2", "0.0359", "ENSP00000370571, ENSP00000414303", "BDNF,TH"]], "row_count": 3, "column_count": 6, "numeric_cells": 8, "header_rows": 1, "locator": "section[6]/table-wrap[2]#Tab3"}}, {"id": "asset:table:pmid:31346329:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8ba44ff4929966e365ccc31596f39f4dd1602e6379f5c36ff074ebf746e74c62", "bytes": 981, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[3]#Tab4", "version": null, "note": "Pathway enrichment in Module 3", "structure": {"pmcid": "PMC6636172", "section_index": 6, "section_title": "PPI network analyses and module analyses", "row_count": 5, "column_count": 6}, "table": {"label": "Table 4", "caption": "Pathway enrichment in Module 3", "rows": [["#Pathway ID", "Pathway description", "Observed gene count", "False discovery rate", "Matching proteins in Your network (ids)", "Matching Proteins In your Network (labels)"], ["R-HSA:416476", "G alpha (q) signaling events", "5", "3.80E-09", "ENSP00000321106, ENSP00000324270, ENSP00000332225, ENSP00000369647, ENSP00000434045", "AVP,GPR68, OXTR, PMCH, TAC1"], ["R-HSA:373076", "Class A/1 (Rhodopsin-like receptors)", "5", "1.49E-08", "ENSP00000321106, ENSP00000324270, ENSP00000332225, ENSP00000369647, ENSP00000434045", "AVP,GPR68, OXTR, PMCH, TAC1"], ["R-HSA:375276", "Peptide ligand-binding receptors", "4", "2.80E-07", "ENSP00000321106, ENSP00000324270, ENSP00000332225, ENSP00000369647", "AVP,OXTR, PMCH, TAC1"], ["R-HSA:388479", "Vasopressin-like receptors", "2", "5.84E-06", "ENSP00000324270, ENSP00000369647", "AVP,OXTR"]], "row_count": 5, "column_count": 6, "numeric_cells": 19, "header_rows": 1, "locator": "section[6]/table-wrap[3]#Tab4"}}, {"id": "asset:table:pmid:31346329:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6bfe3c78f00bc5421f247b7859ccf4d67cb29f760070b01dc67f3e958b8c735b", "bytes": 1340, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#Tab5", "version": null, "note": "Information of RNA-binding proteins of lncRNAs", "structure": {"pmcid": "PMC6636172", "section_index": 7, "section_title": "Identification of lncRNAs and analysis of binding proteins", "row_count": 15, "column_count": 4}, "table": {"label": "Table 5", "caption": "Information of RNA-binding proteins of lncRNAs", "rows": [["Gene symbol", "Gene title", "Involved cell functions", "References"], ["EIF4B", "eukaryotic initiation factor 4B", "long-term plastic changes in neuron", "[34]"], ["PABPC1", "cytoplasmic poly(A)-binding protein 1", "inflammation", "[35]"], ["FUS", "fused in sarcoma", "motor neuron degeneration", "[36]"], ["Pum2", "pumilio 2", "neurogenesis", "[37]"], ["MBNL1", "muscleblind-like protein 1", "neuron development", "[38]"], ["ACO1", "aconitase 1", "neuron mitochondrial function", "[39]"], ["KHSRP", "KH-type splicing regulatory protein", "inflammation, neuron survival and growth", "[40]"], ["YTHDC1", "YTH domain-containing protein 1", "neuron development", "[41]"], ["SFRS9", "SR-family splicing factor 9", "neuronal stimulation", "[42]"], ["RBMX", "RNA binding motif protein X-linked gene", "neuron development", "[43]"], ["SFRS13A", "SR-family splicing factor 13A", "cholesterol homeostasis, AD risk", "[44]"], ["KHDRBS3", "KH RNA binding domain containing, signal transduction associated 3", "cell proliferation", "[45]"], ["ELAVL1", "ELAV-like protein 1", "neurogenesis, neuroprotection", "[46, 47]"], ["SFRS1", "SR-family splicing factor 1", "neuron differentiation and survival", "[48, 49]"]], "row_count": 15, "column_count": 4, "numeric_cells": 26, "header_rows": 1, "locator": "section[7]/table-wrap[1]#Tab5"}}, {"id": "asset:table:pmid:31346329:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4a39f4633b36cdbf6c88157b50be539233b517f7abbc5082995a5ddaa2bbd5ac", "bytes": 1040, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#Tab6", "version": null, "note": "Detailed information of hub genes", "structure": {"pmcid": "PMC6636172", "section_index": 8, "section_title": "Discussion", "row_count": 14, "column_count": 3}, "table": {"label": "Table 6", "caption": "Detailed information of hub genes", "rows": [["Hub genes", "Involved cell functions", "References"], ["Hippocampus"], ["CDC42", "actin cytoskeleton, gene expression, cell proliferation, Aβ neurotoxicity", "[69–72]"], ["VEGFA", "neurogenesis, neuronal migration", "[73–75]"], ["BDNF", "growth, survival and maintenance of neurons", "[76, 77]"], ["PDYN", "memory, learning, and cognitive functions; drug consumption and addiction", "[78–80]"], ["CALB", "long-term potentiation, synaptic plasticity, and memory functions", "[81, 82]"], ["TH", "memory and recognition functions", "[83, 84]"], ["CACNA1A", "learning and memory", "[85, 86]"], ["CD44", "inflammation-related functions", "[87–89]"], ["TAC1", "neurotrophic and inflammation related functions", "[90, 91]"], ["Entorhinal cortex"], ["OXT", "drug addiction, anxiety and memory formation", "[92–94]"], ["TAC1", "neurotrophic and inflammation related functions", "[90, 91]"]], "row_count": 14, "column_count": 3, "numeric_cells": 13, "header_rows": 1, "locator": "section[8]/table-wrap[1]#Tab6"}}], "gaps": ["asset:data:geo:GSE48350 not downloaded", "asset:data:geo:GSE48350 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": 0.7, "band": "medium", "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": ["GSE48350"], "resolved_accessions": ["GSE48350"], "statements": ["All data generated or analyzed during this study are included in this published article [and its supplementary information files]."], "basis": "The paper names GSE48350 in NCBI Gene Expression Omnibus (GEO) 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:31346329", "data:geo:GSE48350", "asset:table:pmid:31346329:1", "asset:table:pmid:31346329:2", "asset:table:pmid:31346329:3", "asset:table:pmid:31346329:4", "asset:table:pmid:31346329:5", "asset:table:pmid:31346329:6"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE48350"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:15:34Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 45993, "completion_tokens": 1158, "cached_tokens": 15624}}, "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:31346329", "type": "paper", "label": "pmid:31346329"}, {"id": "source:pmid:31346329", "type": "manuscript", "label": "PMID 31346329 full text"}, {"id": "data:geo:GSE48350", "type": "dataset", "label": "GEO GSE48350"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31346329", "type": "paper", "label": "pmid:31346329"}, {"id": "source:pmid:31346329", "type": "manuscript", "label": "PMID 31346329 full text"}, {"id": "data:geo:GSE48350", "type": "dataset", "label": "GEO GSE48350"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31346329", "type": "extraction", "used": ["source:pmid:31346329"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE48350", "type": "accession_resolution", "used": ["data:geo:GSE48350"], "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:31346329", "parent_hash": "sha256:34e1a74944cc736b339b2dbd5af22c31cbf8f0928b71f5328649ac130191857d", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE48350 licence not read", "asset:data:geo:GSE48350 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": "analysis_only", "id": "assay:1"}]}