GINS2 Functions as a Key Gene in Lung Adenocarcinoma by WGCNA Co-Expression Network Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32753902", "kind": "science-record", "revision": 8, "content_hash": "sha256:4d5f631eb97c111003c68dd1c2645f95da6afcce10226c0c46c7d072466c3ff5", "created_at": "2026-11-01T15:41:07Z", "updated_at": "2026-11-01T22:01:59Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "GINS2 Functions as a Key Gene in Lung Adenocarcinoma by WGCNA Co-Expression Network Analysis.", "doi": "10.2147/OTT.S255251", "pmid": "32753902", "authors": ["Wen Tian", "Xianglin Yang", "He Yang", "Baosen Zhou"], "journal": "OncoTargets and therapy", "year": 2020, "abstract": "BACKGROUND: Lung adenocarcinoma is one of the malignant tumors in the world. This study aimed to explore the biological mechanism of GINS2 in lung adenocarcinoma.\nMATERIALS AND METHODS: Raw data were downloaded from GEO. WGCNA co-expression network and PPI network were established to identify the hub gene. The expression profile and clinical features of GINS2 were collected from TCGA-LUAD cohort. Survival analysis in TCGA-LUAD cohort was plotted by R package. GSEA was analyzed via GSEA software. MTS, Transwell and apoptosis assays were used to detect the proliferation, migration and apoptotic abilities of lung adenocarcinoma cells.\nRESULTS: GINS2 was identified as the hub gene via WGCNA co-expression network and PPI network. Higher GINS2 expressions were observed in TCGA-LUAD cohort, GSE32863 and clinical samples dataset. Overexpression of GINS2 had a significantly negative connection with poor survival outcome. GSEA results revealed that GINS2 could be enriched in \"HALLMARK_G2M_CHECKPOINT\", \"HALLMARK_E2F_TARGETS\", \"HALLMARK_DNA_REPAIR\" and \"HALLMARK_MYC_TARGETS_V2\". Overexpression of GINS2 promoted tumor cell proliferation and migration and suppressed cell apoptosis.\nCONCLUSION: Our results explored that GINS2 functioned as an oncogene in lung adenocarcinoma, and suggested that GINS2 could act as a promising prognosis biomarker for lung adenocarcinoma.", "claims": [{"id": "claim-method", "statement": "Student`s test was performed to validate GINS2 expression differences between different groups via R ggplot2 package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32753902", "locator": "sections[12] \"Statistical Analysis\" paragraph 2", "quote": "Student`s test was performed to validate GINS2 expression differences between different groups via R ggplot2 package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "GSE32863 contained 58 lung adenocarcinoma and 58 adjacent non-tumor lung fresh frozen tissues. The gene expression profile of GSE32863 was downloaded.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32753902", "locator": "sections[3] \"Data Collection and DEGs Identification\" paragraph 2", "quote": "GSE32863 contained 58 lung adenocarcinoma and 58 adjacent non-tumor lung fresh frozen tissues. The gene expression profile of GSE32863 was downloaded."}], "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:32753902"], "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:GSE32863"], "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:GSE32863"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32753902", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/OTT.S255251", "sha256": "sha256:f00230a6c882938adc421e3d23ea85f8dbb117da89d3ad98a6cc811505af30a9", "bytes": 32028, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/OTT.S255251", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7354913", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE32863", "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=GSE32863", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE32863", "version": null, "note": "GSE32863 contained 58 lung adenocarcinoma and 58 adjacent non-tumor lung fresh frozen tissues. The gene expression profile of GSE32863 was downloaded.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "GSE32863 contained 58 lung adenocarcinoma and 58 adjacent non-tumor lung fresh frozen tissues. The gene expression profile of GSE32863 was downloaded.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM813411", "GSM813412", "GSM813413", "GSM813414", "GSM813415", "GSM813416", "GSM813417", "GSM813418", "GSM813419", "GSM813420", "GSM813421", "GSM813422", "GSM813423", "GSM813424", "GSM813425", "GSM813426", "GSM813427", "GSM813428", "GSM813429", "GSM813430", "GSM813431", "GSM813432", "GSM813433", "GSM813434", "GSM813435", "GSM813436", "GSM813437", "GSM813438", "GSM813439", "GSM813440", "GSM813441", "GSM813442", "GSM813443", "GSM813444", "GSM813445", "GSM813446", "GSM813447", "GSM813448", "GSM813449", "GSM813450", "GSM813451", "GSM813452", "GSM813453", "GSM813454", "GSM813455", "GSM813456", "GSM813457", "GSM813458", "GSM813459", "GSM813460", "GSM813461", "GSM813462", "GSM813463", "GSM813464", "GSM813465", "GSM813466", "GSM813467", "GSM813468", "GSM813469", "GSM813470", "GSM813471", "GSM813472", "GSM813473", "GSM813474", "GSM813475", "GSM813476", "GSM813477", "GSM813478", "GSM813479", "GSM813480", "GSM813481", "GSM813482", "GSM813483", "GSM813484", "GSM813485", "GSM813486", "GSM813487", "GSM813488", "GSM813489", "GSM813490", "GSM813491", "GSM813492", "GSM813493", "GSM813494", "GSM813495", "GSM813496", "GSM813497", "GSM813498", "GSM813499", "GSM813500", "GSM813501", "GSM813502", "GSM813503", "GSM813504", "GSM813505", "GSM813506", "GSM813507", "GSM813508", "GSM813509", "GSM813510", "GSM813511", "GSM813512", "GSM813513", "GSM813514", "GSM813515", "GSM813516", "GSM813517", "GSM813518", "GSM813519", "GSM813520", "GSM813521", "GSM813522", "GSM813523", "GSM813524", "GSM813525", "GSM813526"], "sample_count": 116, "group_sizes": null, "group_sizes_basis": null, "platform": "6884", "taxon": "Homo sapiens", "title": "Gene expression analysis of lung adenocarcinoma and matched adjacent non-tumor lung tissue", "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:32753902:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6645c0f30efd3843e1a1940bdc4fbdc90454012a95d6bbf0a693862238dd6deb", "bytes": 7085, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T0001", "version": null, "note": "The Differently Expressed Genes in GSE32863", "structure": {"pmcid": "PMC7354913", "section_index": 14, "section_title": "Identification of DEGs", "row_count": 3, "column_count": 3}, "table": {"label": "Table 1", "caption": "The Differently Expressed Genes in GSE32863", "rows": [["", "Number", "Gene Names"], ["Down-regulated genes", "339", "SPP1, GCNT3, SPINK1, MMP11, EEF1A2, CRABP2, COL1A1, CST1, CEACAM5, TOP2A, COMP, TUBB3, SLC2A1, PROM2, ITPKA, MMP9, SERINC2, PITX1, CDC20, SFN, HMGB3, FAM83A, C1orf106, CDH3, ETV4, PODXL2, GPT2, KRT8, SPDEF, TK1, SEMA4B, MUC20, SBK1, CTHRC1, LCN2, GSDMB, HOOK1, LMOD3, S100P, SLC29A4, OCIAD2, TMEM45B, CHPF, CDCA5, THBS2, CHMP4B, MAGT1, MUC21, GPX2, NQO1, BAIAP2L1, DSP, ITCH-IT1, CLDN3, USP49, AGRN, METTL7B, TNFRSF21, UHRF1, ZNF69, HSD17B7, FUT3, XPR1, SCG5, SLC16A3, TIMP1, ZNF14, PAFAH1B3, ST14, WDR66, ERO1A, CDCA7, CELSR3, CXCL14, ALPP, MARCKSL1, TTYH3, BLZF1, COL3A1, PPP1R14B, SSTR2, PFKP, PCP4, TESC, AOC4P, BCYRN1, CCNB2, ATP10B, PC, CAPN8, DUSP19, NUBPL, ZNF786, AURKA, SLC7A5, VSTM2L, YRDC, TMPRSS4, DDR1, KRT80, FAM83H, HIST1H2BD, LRRFIP1, COL5A2, 6-Mar, RHOD, STX1A, HES6, MAPK8IP3, PCSK1N, PRC1, RGS17, TUBB2B, CFB, MBD4, PTGR2, SPC24, CCNF, MCM4, TCN1, COL10A1, SLC25A51, TM4SF4, CDH1, PAICS, FUT2, NUSAP1, P3H4, SLC39A11, ADAM8, GALNT3, GINS2, IGFBP3, JUP, NMU, RRBP1, ZNF652, MGRN1, MUC16, STK39, CRLF1, ZNF223, CEACAM6, ELF3, PGGHG, TLCD1, UBE2T, AURKB, GLB1L2, MCM2, SLC22A18AS, SOX4, TDRD1, ANKRD22, TMEM132A, TMEM54, CAPN12, CERCAM, SLC4A5, SRPX2, SULF1, AGR2, AOC1, ASPM, F12, PDIA4, PHLDA2, ITPK1-AS1, RASEF, ARFGAP1, KCNK5, PSAT1, SIX4, SRPK1, CENPF, MX2, TXNDC17, ZNF486, CDC45, DEAF1, FAM63A, NRIP3, SORD, ZNF750, CNFN, IGF2BP3, PLOD2, SAPCD2, SCIN, SLC52A2, TRIM2, ABCA4, ARHGEF19, GNL3L, ST6GALNAC1, STIL, AHNAK2, CA9, KDELR2, KDM5B, MBTD1, SLC5A8, AIM2, ARHGAP39, CANT1, DNAH2, ECT2, EIF2AK4, KCNK1, ABCB6, HABP2, SLC16A9, WSB1, BOP1, CERS6, DBNDD1, E2F2, NARF, VARS, BAIAP2L2, FAM13A, GDF15, H1F0, FAM234A, HAUS2, HKDC1, LOC105375172, THY1, VWA1, FHL2, LDHA, MMP15, NPM3, PCDHB19P, PTGES, RAX2, REEP6, SMPDL3B, XKRX, CNOT11, GOLGA8A, HIST2H2AC, IGSF9, PSG1, RAB25, COL9A2, GALNT6, GFRA3, ITGA2, KIF1A, KIFC1, MRPL12, PA2G4, PLEK2, RHPN2, SPSB1, TSTA3, ALG1L, BRI3BP, ELMO3, FOXA3, NET1, SLC50A1, ATAD3A, BZW2, HACD4, ENC1, KIAA1522, KIF20A, KRT15, P4HB, PANX2, PPM1K, RMI2, CLPTM1L, H2AFX, HYOU1, LAPTM4B, PTPRF, PTTG3P, FGFRL1, GFPT1, GPR37, JSRP1, TFF1, GCAT, GJB2, ISG15, KCNK12, KISS1R, PDIA6, IL37, SERPINH1, SHMT2, SPIRE2, ACOT11, CLDN2, DDIT4L, DDX27, IDH2, KRT17, MST1R, PLXNA3, PRRC2A, PSME4, TMEM106C, TRIP13, ZNF827, DCBLD1, DHRS11, DPP9, FOXQ1, IRAK1, KRT19, BCAS4, TMEM63A, AKR1B10, CCDC34, DNTTIP1, FAM83E, KNTC1, MESP1, POC1A, SAC3D1, TAOK1, TNFRSF12A, TYMS, UBE2O, C17orf53, CHTF18, MTA3, SDHAP3, TIMELESS, TMEM62, TPX2, ALDH18A1, ENO2, L2HGDH, LRRC20"], ["Up-regulated genes", "628", "LOC401286, MCEMP1, HBB, CA4, HBA2, ITLN2, FCN3, FAM107A, HBA1, SCGB1A1, ADH1A, FABP4, SFTPC, CLEC3B, PGC, CAV1, GKN2, INMT, MFAP4, FOSB, GPIHBP1, FMO2, PLAC9, TMEM100, MARCO, ADIRF, CCL14, CFD, CRTAC1, SPOCK2, MT1M, S100A8, PEBP4, ITLN1, AGER, CAV2, RGCC, ACKR1, CPA3, MAMDC2, SEPP1, SDPR, CD52, LDB2, LYVE1, ADH1B, SPARCL1, GNG11, IL6, CYP4B1, TNNC1, CLDN5, PLA2G1B, TEK, HIGD1B, C7, FHL1, PRG4, PTGDS, DCN, SVEP1, HSD17B6, PCOLCE2, ANOS1, CDH5, SFTPD, ABCA8, OLR1, CACNA2D2, VSIG4, CLIC5, CPB2, DNASE1L3, ITM2A, LAMP3, TIMP3, SLPI, STX11, CLEC14A, FCN1, LYZ, MS4A7, CXCL2, IL33, ALOX5AP, GPC3, CD93, PGM5, SRPX, MME, PECAM1, SOX18, WIF1, C9orf24, EFEMP1, CA2, VWF, C2orf40, FPR1, MGP, ABI3BP, COX7A1, CRYAB, SCGB3A2, SMAD6, C1orf162, PDK4, TGFBR3, PI16, SEMA6A, SRGN, TPSAB1, TSPAN7, MMRN1, LPL, ALDH1A1, EPAS1, AGRP, ID3, GLIPR2, SOSTDC1, GPX3, COLEC12, HBEGF, HOXA5, JAM2, ADAMTS1, S100A4, DUOX1, TSC22D1, TYROBP, CD163, CYYR1, FBLN1, ADRB2, SUSD2, MYH11, VIPR1, WNT3A, ALPL, IL7R, C1QA, FCER1A, GYPC, ZFP36, AQP1, CALCRL, SLC39A8, ACTG2, CTSG, AIF1, CCM2L, DPT, CAMP, PPP1R14A, RASIP1, ANGPT1, SLC6A4, FOLR3, RAMP3, FCER1G, CYBRD1, GAS1, S100A3, GIMAP4, RETN, FBLN5, CGNL1, CCL2, FAM189A2, AQP9, CAT, ESAM, FAM150B, PLA2G4F, SCARA5, BTG2, GIMAP5, HSPB8, SLC31A2, FGD5, P3H2, HSPA12B, RASL12, ABCA3, ID2, WISP2, DUSP1, LTC4S, TGFBR2, GLDN, C4BPA, CLIC3, ENPP2, LRRC32, LTBP4, SCGB3A1, SLIT2, EVI2B, TACC1, CPED1, HEG1, PTPRB, SLC19A3, TMEM74B, ID1, ACVRL1, CD302, VSIG2, ALDH1A2, PID1, PPP1R15A, S1PR1, DPEP2, EMCN, STOM, FXYD6, KLF2, CCL21, GMFG, JAML, LMO2, SASH1, TOX2, AP1S2, COL6A6, CSRNP1, FZD4, LHFP, C1QB, EGR2, TCEAL2, ARHGEF6, CLEC1A, GJC2, ARHGAP44, CXCL12, GDF10, ANXA3, NOSTRIN, OLFML1, C10orf54, JCHAIN, LIMCH1, FMO3, PTPRM, SOCS2, SOX7, CXCR4, KLF9, LIMS2, NDN, TMEM204, FAM183A, GIMAP7, KANK2, LY86, VIM, ADAMTS8, CES1P1, CRTAP, CTNNAL1, EMP3, KANK3, ZNF385B, CD300LF, KLK11, MS4A2, MS4A6A, TEKT1, FCGR1B, HBG2, MYH10, PROS1, SLCO2B1, GSTM3, IL1B, PPM1F, STXBP6, SNCA, SPON1, CCND2, FCGR2A, HSPB6, MS4A15, MT1X, RHOJ, SGCE, C11orf88, FAM216B, FAM65A, HP, IFI30, LAMC3, SBSPON, GADD45B, GBP4, HSPC324, SIRPA, SLC15A3, SOCS3, ROPN1L, RPL13AP17, COX4I2, LPXN, MAP3K8, SLCO2A1, SLIT3, C5AR1, MT2A, NCF1, DOCK2, EFCAB1, S100A9, SERPING1, SPARC, ZBED2, CYB5A, DAB2, FAM167A, FAM212A, NKG7, ACKR3, DPYSL2, GHR, HBG1, PDPN, TCF21, DUOXA1, FERMT2, FGR, HLA-DRB3, IGFBP7, OSCAR, A2M, CD37, ICAM2, IFT57, AHNAK, BTK, CPVL, PTH1R, RNF144B, SESN1, ANKRD1, COL13A1, F13A1, METTL7A, PLEK, ADCY4, HLA-DRB6, PDLIM3, PLLP, CHPT1, GJA4, HSPB2, LAMA4, MTURN, SYT15, ADGRE5, C1orf21, CTGF, EMP1, FIGF, LCP1, LMO7, MAF, AGR3, C1orf115, EFEMP2, EGR1, EPB41L2, LGI3, MNDA, DES, MSLN, NDNF, SERPINA3, TRPV2, VNN2, WFS1, C1QC, ETS1, C6, FGFBP2, GSTA4, HCST, SLC2A3, ARMCX1, ETS2, FGL2, HLA-DPA1, LILRB3, SNURF, ALDH2, CYBB, CYR61, EML1, LUM, MAOB, CBX7, HCK, IRF8, LRRN3, PRKCH, SELENBP1, ZFP36L2, C1orf186, CH25H, CNN1, HPGD, TFRC, WFDC1, AVPI1, CD33, DENND2A, FCGR3B, KLRB1, LYL1, PAPSS2, PRKCDBP, TLR8, TSPAN32, UBL3, ZNF106, AADAC, ACP5, AK1, APOL3, C10orf67, CD53, GRASP, HEY1, NR4A2, OLFML2A, PTGIS, RAMP2, RNASE4, TUBB6, UBB, APOLD1, JUN, CD300C, CD83, ENG, ITPRIP, KLF13, LDLR, NPNT, PPP1R3C, RAB8B, CDO1, CHMP3, HLA-DRA, LRRK2, LST1, SGK1, SH3BGRL, SLC46A2, ACADL, ACSL4, GLIPR1, GSTO1, GZMH, LAPTM5, TBX2, ADGRL2, CNRIP1, KCNJ8, MATN2, MS4A8, NKD2, SECISBP2L, WASF3, FOLR1, FOLR2, MT1G, P2RY13, SBDSP1, SCN4B, SH3GL3, CAMK2N1, EPB41L3, FBP1, FGGY, GABARAPL1, GATA2, NOTCH4, AAMDC, CLEC12A, FGD3, GFOD1, LILRA2, MT1A, SOX17, TM6SF1, KLF6, RAB11FIP1, SNRPN, TUBA1A, BORCS7, C1orf198, CCL3, CIRBP, EMILIN2, FAM43A, MAL, NINJ2, RPL17, TMEM88, UBE2E2, ANXA2, ARAP3, CD14, HCLS1, HDC, NCF1C, PRX, RTKN2, SDCBP, TSPAN18, ZYX, AOC3, DYNLRB2, HHIP, HLA-DQB1, MSRA, NUPR1, SH2B3, ZEB2, CRBN, CXCL8, DOCK11, RGS5, SPI1, AOX1, ATOH8, C2, CCDC178, CD59, MYOM2, PAMR1, ACTG1, CALB2, CAPS, EDN1, GCHFR, PHACTR2, STARD8, UBE2L6, C8B, EIF1B, GNG10, GSTM5, MAOA, PRICKLE2, C3, CD9, DLL1, GPRC5A, HSD17B11, MSR1, RBP1, SEC22C, ANG, FLNC, FPR2, GALNT18, PLIN2, TMEM140, TNFRSF19, TSPAN4, VGLL3, DACT3, F10, H3F3B, INAFM1, JUNB, MT1E, S1PR4, SELE, ZNF331, ANO6, APOC1, AXIN2, BTG1, GJA1, IFNGR1, IL17D, NEDD4L, PPP1R16B, QDPR, REM1, TMOD1, TMSB15A, ADTRP, CCL18, CDH13, CDHR3, FGFR4, IRF1, LXN, RCAN1, RERG, RPL21, TNS3"]], "row_count": 3, "column_count": 3, "numeric_cells": 4, "header_rows": 1, "locator": "section[14]/table-wrap[1]#T0001"}}, {"id": "asset:table:pmid:32753902:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a5603656518872592b873e073c23221e255dbed9a06378c36c1fdaaef3459126", "bytes": 4433, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#T0002", "version": null, "note": "Each Number of Each Module in WGCNA", "structure": {"pmcid": "PMC7354913", "section_index": 15, "section_title": "WGCNA Co-Expression Network", "row_count": 9, "column_count": 3}, "table": {"label": "Table 2", "caption": "Each Number of Each Module in WGCNA", "rows": [["Colour", "Number", "Gene Names"], ["Black", "3", "MT1X, MT2A, MT1A"], ["Blue", "12", "C9orf24, C20orf85, FAM183A, TEKT1, C11orf88, C6, FAM216B, ROPN1L, EFCAB1, MS4A8 CAPS, DYNLRB2"], ["Brown", "5", "TYROBP, FCER1G, C1QA, C1QB, C1QC"], ["Green", "3", "LDB2, CD93 CYYR1"], ["Grey", "559", "SPP1, GCNT3, SPINK1, MMP11, EEF1A2, CRABP2, COL1A1, CEACAM5, TOP2A, CST1, COMP, DSP, CDH3, TUBB3, SLC2A1, PROM2, ITPKA, MMP9, SERINC2, PITX1, CDC20, SFN, HMGB3, ST14, FAM83A, C1orf106, ETV4, PODXL2, GPT2, KRT8, SPDEF, TK1, SEMA4B, MUC20, SBK1, CTHRC1, LCN2, GSDMB, HOOK1, S100P, SLC29A4, TIMP1, OCIAD2, TMEM45B, CHPF, CDCA5, THBS2, CHMP4B, MUC21, GPX2, NQO1, BAIAP2L1, CLDN3, AGRN, METTL7B, TNFRSF21, UHRF1, FUT3, XPR1, SCG5, SLC16A3, PAFAH1B3, PC, WDR66, ERO1A, CDCA, CELSR3, CXCL14, MARCKSL1, TTYH3, COL3A1, PPP1R14B, PFKP, PCP4, TESC, CCNB2, ATP10B, CAPN8, AURKA, SLC7A5, VSTM2L, TMPRSS, DDR1, KRT80, FAM83H, HIST1H2BD, COL5A2, RHOD, STX1A, HES6, MAPK8IP3, PCSK1N, PRC1, RGS17, CFB, TUBB2B, SPC2, CCNF, MCM4, TCN1, COL10A1, TM4SF4, CDH1, PAICS, FUT2, NUSAP1, MCM2, SLC39A11, ADAM8, GINS2, IGFBP3, JUP, NMU, RRBP1, MGRN1, MUC16, STK39, CRLF1, ELF3, CEACAM6, PGGHG, TLCD1, UBE2T, AURKB, GLB1L2, SLC22A18AS, SOX4, ANKRD22, P3H4, TMEM132A, TMEM54, CAPN12, CERCAM, F12, SRPX2, SULF1, AGR2, AOC1, ASPM, PDIA4, MX2, PHLDA2, RASEF, ARFGAP1, KCNK5, PSAT1, SIX4, SRPK1, CENPF, TXNDC17, CDC45, DEAF1, NRIP3, SORD, ZNF750, CNFN, IGF2BP3, PLOD2, SAPCD2, SCIN, SLC52A2, TRIM2, CA9, ABCA4, ARHGEF19, GNL3L, ST6GALNAC1, STIL, AHNAK2, KDELR2, KDM5B, AIM2, E2F2, ARHGAP39, CANT1, DNAH2, ECT2, KCNK1, ABCB6, HABP2, SLC16A9, BOP1, CERS6, NARF, DBNDD1, VARS, BAIAP2L2, FAM13A, GDF15, H1F0, FAM234A, HKDC1, LOC105375172, THY1, VWA1, FHL2, LDHA, MMP15, NPM3, PTGES, CA4, REEP6, SMPDL3B, XKRX, CNOT11, PSG1, GOLGA8A, HIST2H2AC, IGSF9, RAB25, KIF1A, COL9A2, GALNT6, GFRA3, ITGA2, KIFC1, MRPL12, PA2G4, PLEK2, RHPN2, SPSB1, TSTA3, ALG1L, BRI3BP, ELMO3, FOXA3, NET1, IDH2, SLC50A1, ATAD3A, BZW2, KIAA1522, KIF20A, KRT15, P4HB, PANX2, RMI2, CLPTM1L, ENC1, H2AFX, HYOU1, LAPTM4B, PTPRF, PTTG3P, FGFRL1, GFPT1, GPR37, JSRP1, TFF1, GCAT, GJB2, ISG15, KCNK12, KISS1R, PDIA6, IL37, SERPINH1, SHMT2, SPIRE2, ACOT11, CLDN2, DDIT4L, DDX27, KRT17, MST1R, PLXNA3, PRRC2A, PSME4, TMEM106C, TRIP13, ZNF827, DCBLD1, DHRS11, DPP9, FOXQ1, IRAK1, KRT19, TMEM63A, AKR1B10, CCDC34, DNTTIP1, CFD, FAM83E, KNTC1, MESP1, POC1A, SAC3D1, TAOK1, TNFRSF12A, TYMS, UBE2O, C17orf53, CHTF18, MTA3, SDHAP3, TIMELESS, TMEM62, TPX2, ALDH18A1, BCAS4, ENO2, L2HGDH, LRRC20, LOC401286, MCEMP1, HBB, HBA2, ITLN2, FCN3, FAM107A, HBA1, SCGB1A1, ADH1A, FABP4, SFTPC, PGC, CAV1, GKN2, INMT, MFAP4, FOSB, GPIHBP1, FMO2, PLAC9, TMEM100, MARCO, ADIRF, CCL14, CRTAC1, SPOCK2, MT1M, S100A8, PEBP4, ITLN1, AGER, CAV2, RGCC, ACKR1, CPA3, MAMDC2, SEPP1, SDPR, CD52, LYVE1, ADH1B, SPARCL1, GNG11, IL6, CYP4B1, TNNC1, CLDN5, PLA2G1B, C7, HIGD1B, FHL1, PRG4, PTGDS, DCN, SVEP1, HSD17B6, PCOLCE2, ANOS1, SFTPD, ABCA8, OLR1, CACNA2D2, VSIG4, CLIC5, CPB2, DNASE1L3, ITM2A, LAMP3, TIMP3, SLPI, STX11, CLEC14A, FCN1, LYZ, MS4A7, CXCL2, ALOX5AP, GPC3, PGM5, SRPX, MME, PECAM1, SOX18, WIF1, EFEMP1, CA2, VWF, C2orf40, FPR1, MGP, ABI3BP, COX7A1, CRYAB, SCGB3A2, SMAD6, C1orf162, PDK4, TGFBR3, PI16, SEMA6A, SRGN, TPSAB1, TSPAN7, MMRN1, LPL, ALDH1A1, AGRP, ID3, GLIPR2, SOSTDC1, GPX3, COLEC12, HBEGF, HOXA5, IL33, ADAMTS1, S100A4, DUOX1, TSC22D1, CD163, FBLN1, ADRB2, SUSD2, MYH11, VIPR1, WNT3A, ALPL, IL7R, FCER1A, GYPC, ZFP36, AQP1, CALCRL, SLC39A8, ACTG2, CTSG, AIF1, DPT, CAMP, PPP1R14A, RASIP1, ANGPT1, SLC6A4, FOLR3, RAMP3, CYBRD1, GAS1, JAM2, S100A3, GIMAP4, RETN, FBLN5, CGNL1, CCL2, FAM189A2, AQP9, CAT, ESAM, FAM150B, PLA2G4F, SCARA5, BTG2, GIMAP5, HSPB8, SLC31A2, FGD5, HSPA12B, RASL12, ABCA3, ID2, WISP2, DUSP1, LTC4S, P3H2, TGFBR2, GLDN, C4BPA, CLIC3, ENPP2, LRRC32, LTBP4, SCGB3A1, SLIT2, EVI2B, TACC1, CPED1, HEG1, PTPRB, SLC19A3, TMEM74B, ACVRL1"], ["Red", "3", "TEK, CDH5, EPAS1"], ["Turquoise", "40", "LMOD3, MAGT1, ITCH-IT1, USP49, ZNF69, HSD17B7, ZNF14, ALPP, BLZF1, SSTR2, AOC4P, BCYRN1, DUSP19, NUBPL, ZNF786, YRDC, LRRFIP1, 6-Mar, MBD4, PTGR2, SLC25A51, GALNT3, ZNF652, ZNF223, TDRD1, SLC4A5, ITPK1-AS1, ZNF486, FAM63A, MBTD1, SLC5A8, EIF2AK4, WSB1, HAUS2, PCDHB19P, RAX2, HACD4, PPM1K, CHMP3, GNG10"], ["Yellow", "3", "CLEC3B, CCM2L, COX4I2"]], "row_count": 9, "column_count": 3, "numeric_cells": 12, "header_rows": 1, "locator": "section[15]/table-wrap[1]#T0002"}}, {"id": "asset:table:pmid:32753902:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fcc4d74e83eddad41e33b0d30abf597af1ae46bdf3cf28b6416c9a73fd190ea2", "bytes": 672, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[2]#T0003", "version": null, "note": "Nine Hub Genes in the PPI Network Constructed by STRING", "structure": {"pmcid": "PMC7354913", "section_index": 15, "section_title": "WGCNA Co-Expression Network", "row_count": 10, "column_count": 3}, "table": {"label": "Table 3", "caption": "Nine Hub Genes in the PPI Network Constructed by STRING", "rows": [["Gene Names", "Description", "Score"], ["CDC20", "Cell division cycle 20", "0.999"], ["CDC45", "Cell division cycle 45", "0.999"], ["GINS2", "GINS complex subunit 2", "0.999"], ["MCM2", "Minichromosome maintenance complex component 2", "0.998"], ["MCM4", "Minichromosome maintenance complex component 4", "0.998"], ["CCNB2", "Cyclin B2", "0.997"], ["AURKB", "Aurora kinase B", "0.997"], ["KIF20A", "Kinesin family member 20A", "0.996"], ["TPX2", "TPX2 microtubule nucleation factor", "0.995"]], "row_count": 10, "column_count": 3, "numeric_cells": 18, "header_rows": 1, "locator": "section[15]/table-wrap[2]#T0003"}}, {"id": "asset:table:pmid:32753902:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d16435f85b118271fc13f3ac5a1af84129d354dfe417d2f203da79e66407adc6", "bytes": 472, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#T0004", "version": null, "note": "ROC Analyses Results of GSE32863, TCGA and Clinical Samples", "structure": {"pmcid": "PMC7354913", "section_index": 16, "section_title": "Expression and Clinical Value of GINS2 in Lung Adenocarcinoma", "row_count": 4, "column_count": 6}, "table": {"label": "Table 4", "caption": "ROC Analyses Results of GSE32863, TCGA and Clinical Samples", "rows": [["Dataset", "AUC", "95% CI", "Sensitivity", "1-Specificity", "P-value"], ["GSE32863", "0.894", "0.777–0.921", "0.983", "0.862", "<0.001"], ["TCGA-LUAD", "0.847", "0.814–0.879", "0.996", "0.817", "0.0023"], ["Clinical samples", "0.851", "0.799–0.903", "0.987", "0.883", "<0.001"]], "row_count": 4, "column_count": 6, "numeric_cells": 18, "header_rows": 1, "locator": "section[16]/table-wrap[1]#T0004"}}, {"id": "asset:table:pmid:32753902:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2db75cb7038c58cf176f195d721004e4b556c8191d7d1c6d561bb3abfeaa6db7", "bytes": 599, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[2]#T0005", "version": null, "note": "The Relationship Between GINS2 Expression and Clinical Features in Our Case-Control Study", "structure": {"pmcid": "PMC7354913", "section_index": 16, "section_title": "Expression and Clinical Value of GINS2 in Lung Adenocarcinoma", "row_count": 10, "column_count": 6}, "table": {"label": "Table 5", "caption": "The Relationship Between GINS2 Expression and Clinical Features in Our Case-Control Study", "rows": [["Variables", "GINS2 Expression Level", "χ2", "P-value"], ["Low (n=62)", "High (n=44)"], ["Age (years)", "<60", "11", "10", "0.399", "0.528"], ["≧60", "51", "34"], ["Gender", "Male", "14", "9", "0.068", "0.794"], ["Female", "48", "35"], ["Smokingstatue", "No", "33", "19", "1.039", "0.308"], ["Yes", "29", "25"], ["Clinical stage", "i+II", "49", "11", "30.588", "<0.001"], ["III+IV", "13", "33"]], "row_count": 10, "column_count": 6, "numeric_cells": 29, "header_rows": 2, "locator": "section[16]/table-wrap[2]#T0005"}}], "gaps": ["asset:data:geo:GSE32863 not downloaded", "asset:data:geo:GSE32863 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "analysis of variance"}}, {"id": "method-2", "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": "PPI"}}, {"id": "method-3", "family": null, "specific": null, "label": "Student's test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Student`s test was performed to validate GINS2 expression differences between different groups via R ggplot2 package."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["GSE32863"], "resolved_accessions": ["GSE32863"], "statements": ["GSE32863 contained 58 lung adenocarcinoma and 58 adjacent non-tumor lung fresh frozen tissues. The gene expression profile of GSE32863 was downloaded."], "basis": "The paper names GSE32863 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:32753902", "data:geo:GSE32863", "asset:table:pmid:32753902:1", "asset:table:pmid:32753902:2", "asset:table:pmid:32753902:3", "asset:table:pmid:32753902:4", "asset:table:pmid:32753902:5"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE32863"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:21:39Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 36267, "completion_tokens": 1723, "cached_tokens": 12296}}, "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:32753902", "type": "paper", "label": "pmid:32753902"}, {"id": "source:pmid:32753902", "type": "manuscript", "label": "PMID 32753902 full text"}, {"id": "data:geo:GSE32863", "type": "dataset", "label": "GEO GSE32863"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32753902", "type": "paper", "label": "pmid:32753902"}, {"id": "source:pmid:32753902", "type": "manuscript", "label": "PMID 32753902 full text"}, {"id": "data:geo:GSE32863", "type": "dataset", "label": "GEO GSE32863"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32753902", "type": "extraction", "used": ["source:pmid:32753902"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE32863", "type": "accession_resolution", "used": ["data:geo:GSE32863"], "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:32753902", "parent_hash": "sha256:797816b28dc0806945baeb0f119b20be235f62cfb6967a90e7c426cb0628d735", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE32863 licence not read", "asset:data:geo:GSE32863 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": ["alyzed via GSEA software. MTS, Transwell and apoptosis assays were used to detect the proliferation", "liferation and migration and suppressed cell apoptosis. CONCLUSION: Our results explored that GINS2"], "order_basis": "paper_text_order:569", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Materials and Methods Cell Culture and Transfection HBE and A549 were purchased from GeneChem (S", "105 cells were seeded into 6-well plates and transfected plasmids using jetPRIME transfection reagent", "ates and transfected plasmids using jetPRIME transfection reagent (Polyplus transfection, USA) accordi", "sing jetPRIME transfection reagent (Polyplus transfection, USA) according to the manufacturer`s instru"], "order_basis": "paper_text_order:1470", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["all cultured in RPMI-1640 (GIBCO, USA). All cell lines were maintained at 37°C in a humidified chamber with 5% CO2.", "ublic of China). HBE and A549 cells were all cultured in RPMI-1640 (GIBCO, USA). All cell lines were", "ethods Cell Culture and Transfection HBE and A549 were purchased from GeneChem (Shanghai, Peop", "anghai, People's Republic of China). HBE and A549 cells were all cultured in RPMI-1640 (GIBCO,"], "order_basis": "paper_text_order:1485", "id": "assay:3"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["analysis of variance"], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}