{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31889939", "kind": "science-record", "revision": 6, "content_hash": "sha256:93e0771d7f854241d5286034e6cbb98850df7c5ffc7c962931dc01dff5495bd1", "created_at": "2026-11-01T15:40:54Z", "updated_at": "2026-11-01T21:22:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Quantitative proteome analysis of Merkel cell carcinoma cell lines using SILAC.", "doi": "10.1186/s12014-019-9263-z", "pmid": "31889939", "authors": ["Ulana Kotowski", "Boban M Erović", "Julia Schnöll", "Victoria Stanek", "Stefan Janik", "Martin Steurer", "Goran Mitulović"], "journal": "Clinical proteomics", "year": 2019, "abstract": "BACKGROUND: Merkel cell carcinoma (MCC) is an aggressive neuroendocrine tumour of the skin with growing incidence. To better understand the biology of this malignant disease, immortalized cell lines are used in research for in vitro experiments. However, a comprehensive quantitative proteome analysis of these cell lines has not been performed so far.\nMETHODS: Stable isotope labelling by amino acids in cell culture (SILAC) was applied to six MCC cell lines (BroLi, MKL-1, MKL-2, PeTa, WaGa, and MCC13). Following tryptic digest of labelled proteins, peptides were analysed by mass spectrometry. Proteome patterns of MCC cell lines were compared to the proteome profile of an immortalized keratinocyte cell line (HaCaT).\nRESULTS: In total, 142 proteins were upregulated and 43 proteins were downregulated. Altered proteins included mitoferrin-1, histone H2A type 1-H, protein-arginine deiminase type-6, heterogeneous nuclear ribonucleoproteins A2/B1, protein SLX4IP and clathrin light chain B. Furthermore, several proteins of the histone family and their variants were highly abundant in MCC cell lines.\nCONCLUSIONS: The results of this study present a new protein map of MCC and provide deeper insights in the biology of MCC. Data are available via ProteomeXchange with identifier PXD008181.", "claims": [{"id": "claim-method", "statement": "p-values where corrected for multitesting according to Benjamini Hochberg.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31889939", "locator": "sections[7] \"Term enrichment analysis\" paragraph 2", "quote": "p-values where corrected for multitesting according to Benjamini Hochberg."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data availabilityThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD008181 and 10.6019/pxd008181.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31889939", "locator": "sections[21] \"notes\" paragraph 1", "quote": "Data availabilityThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD008181 and 10.6019/pxd008181."}], "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:31889939"], "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. 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the PRIDE partner repository with the dataset identifier PXD008181 and 10.6019/pxd008181.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data availabilityThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD008181 and 10.6019/pxd008181.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteome analysis of Merkel cell carcinoma cell lines using SILAC", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31889939:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9b82ce6553dfb8722e11b5460dfdbba731469cc9f96035d764052283d6982536", "bytes": 9681, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#Tab1", "version": null, "note": "An overview of upregulated proteins identified in Merkel cell carcinoma cell lines", "structure": {"pmcid": "PMC6921584", "section_index": 6, "section_title": "Nano-HPLC separation and MS detection", "row_count": 143, "column_count": 5}, "table": {"label": "Table 1", "caption": "An overview of upregulated proteins identified in Merkel cell carcinoma cell lines", "rows": [["Cell line", "UniProt entry name", "Protein name", "Gene symbol", "Ratio (H/L)"], ["BroLi", "MFRN1_HUMAN", "Mitoferrin-1", "SLC25A37", "9.64"], ["SF01_HUMAN", "Splicing factor 1", "SF1", "1.92"], ["N4BP1_HUMAN", "NEDD4-binding protein 1", "N4BP1", "1.65"], ["MKL-1", "H2A1H_HUMAN", "Histone H2A type 1-H", "HIST1H2AH", "5.25"], ["HMGN2_HUMAN", "Non-histone chromosomal protein HMG-17", "HMGN2", "3.86"], ["C2C2L_HUMAN", "C2 domain-containing protein 2-like", "C2CD2L", "3.63"], ["DPY30_HUMAN", "Protein dpy-30 homolog", "DPY30", "3.56"], ["STON1_HUMAN", "Stonin-1", "STON1", "3.18"], ["PREX2_HUMAN", "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 2 protein", "PREX2", "3.11"], ["CCAR1_HUMAN", "Cell division cycle and apoptosis regulator protein 1", "CCAR1", "2.96"], ["RFC1_HUMAN", "Replication factor C subunit 1", "RFC1", "2.89"], ["ATPB_HUMAN", "ATP synthase subunit beta, mitochondrial", "ATP5B", "2.87"], ["ROAA_HUMAN", "Heterogeneous nuclear ribonucleoprotein A/B", "HNRNPAB", "2.64"], ["DJB14_HUMAN", "DnaJ homolog subfamily B member 14", "DNAJB14", "2.53"], ["SF3B1_HUMAN", "Splicing factor 3B subunit 1", "SF3B1", "2.47"], ["RL29_HUMAN", "60S ribosomal protein L29", "RPL29", "2.44"], ["HNRPM_HUMAN", "Heterogeneous nuclear ribonucleoprotein M", "HNRNPM", "2.39"], ["SUMO4_HUMAN", "Small ubiquitin-related modifier 4", "SUMO4", "2.38"], ["NDUS7_HUMAN", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial", "NDUFS7", "2.29"], ["HSP7C_HUMAN", "Heat shock cognate 71 kDa protein", "HSPA8", "2.19"], ["CH60_HUMAN", "60 kDa heat shock protein, mitochondrial", "HSPD1", "2.10"], ["BSDC1_HUMAN", "BSD domain-containing protein 1", "BSDC1", "2.06"], ["RS30_HUMAN", "40S ribosomal protein S30", "FAU", "2.01"], ["MXRA5_HUMAN", "Matrix-remodeling-associated protein 5", "MXRA5", "1.96"], ["ROA2_HUMAN", "Heterogeneous nuclear ribonucleoproteins A2/B1", "HNRNPA2B1", "1.89"], ["ROA1_HUMAN", "Heterogeneous nuclear ribonucleoprotein A1", "HNRNPA1", "1.89"], ["ROA3_HUMAN", "Heterogeneous nuclear ribonucleoprotein A3", "HNRNPA3", "1.89"], ["NPM_HUMAN", "Nucleophosmin", "NPM1", "1.80"], ["CH10_HUMAN", "10 kDa heat shock protein, mitochondrial", "HSPE1", "1.70"], ["STK24_HUMAN", "Serine/threonine-protein kinase 24", "STK24", "1.70"], ["HNRPC_HUMAN", "Heterogeneous nuclear ribonucleoproteins C1/C2", "HNRNPC", "1.66"], ["H2B1O_HUMAN", "Histone H2B type 1-O", "HIST1H2BO", "1.60"], ["PABP1_HUMAN", "Polyadenylate-binding protein 1", "PABPC1", "1.58"], ["I23O2_HUMAN", "Indoleamine 2,3-dioxygenase 2", "IDO2", "1.54"], ["MKL-2", "PADI6_HUMAN", "Protein-arginine deiminase type-6", "PADI6 PAD6", "9.47"], ["CTL2_HUMAN", "Choline transporter-like protein 2", "SLC44A2", "6.74"], ["SRSF3_HUMAN", "Serine/arginine-rich splicing factor 3", "SRSF3", "5.87"], ["HMGN2_HUMAN", "Non-histone chromosomal protein HMG-17", "HMGN2", "5.10"], ["PABP1_HUMAN", "Polyadenylate-binding protein 1", "PABPC1", "4.02"], ["NDUS7_HUMAN", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial", "NDUFS7", "3.84"], ["H2B1H_HUMAN", "Histone H2B type 1-H", "HIST1H2BH", "3.15"], ["COF1_HUMAN", "Cofilin-1", "CFL1", "2.30"], ["LRRT3_HUMAN", "Leucine-rich repeat transmembrane neuronal protein 3", "LRRTM3", "2.27"], ["CH10_HUMAN", "10 kDa heat shock protein, mitochondrial", "HSPE1", "2.20"], ["ACM2_HUMAN", "Muscarinic acetylcholine receptor M2", "CHRM2", "2.14"], ["S38AA_HUMAN", "Putative sodium-coupled neutral amino acid transporter 10", "SLC38A10", "2.14"], ["ROA1_HUMAN", "Heterogeneous nuclear ribonucleoprotein A1", "HNRNPA1", "2.08"], ["WDR62_HUMAN", "WD repeat-containing protein 62", "WDR62", "2.02"], ["ROA2_HUMAN", "Heterogeneous nuclear ribonucleoproteins A2/B1", "HNRNPA2B1", "2.01"], ["STMN1_HUMAN", "Stathmin", "STMN1", "1.80"], ["TM266_HUMAN", "Transmembrane protein 266", "TMEM266", "1.77"], ["H2B2E_HUMAN", "Histone H2B type 2-E", "HIST2H2BE", "1.66"], ["TBA1A_HUMAN", "Tubulin alpha-1A chain", "TUBA1A", "1.64"], ["TBA1B_HUMAN", "Tubulin alpha-1B chain", "TUBA1B", "1.64"], ["HNRPK_HUMAN", "Heterogeneous nuclear ribonucleoprotein K", "HNRNPK", "1.60"], ["PRDX2_HUMAN", "Peroxiredoxin-2", "PRDX2", "1.50"], ["PeTa", "ROA2_HUMAN", "Heterogeneous nuclear ribonucleoproteins A2/B1", "HNRNPA2B1", "4.46"], ["ROA3_HUMAN", "Heterogeneous nuclear ribonucleoprotein A3", "HNRNPA3", "4.46"], ["H2A1B_HUMAN", "Histone H2A type 1-B/E", "HIST1H2AB", "4.23"], ["H2AJ_HUMAN", "Histone H2A.J", "H2AFJ", "4.23"], ["ROA1_HUMAN", "Heterogeneous nuclear ribonucleoprotein A1", "HNRNPA1", "2.98"], ["NIBL1_HUMAN", "Niban-like protein 1", "FAM129B", "2.97"], ["CTL2_HUMAN", "Choline transporter-like protein 2", "SLC44A2", "2.96"], ["REPS2_HUMAN", "RalBP1-associated Eps domain-containing protein 2", "REPS2", "2.72"], ["URGCP_HUMAN", "Up-regulator of cell proliferation", "URGCP", "2.69"], ["H14_HUMAN", "Histone H1.4", "HIST1H1E", "2.67"], ["H33_HUMAN", "Histone H3.3", "H3F3A", "2.39"], ["K0895_HUMAN", "Uncharacterized protein KIAA0895", "KIAA0895", "2.36"], ["H15_HUMAN", "Histone H1.5", "HIST1H1B", "2.17"], ["H2B1N_HUMAN", "Histone H2B type 1-N", "HIST1H2BN", "1.91"], ["H2B2E_HUMAN", "Histone H2B type 2-E", "HIST2H2BE", "1.90"], ["PRDX2_HUMAN", "Peroxiredoxin-2", "PRDX2", "1.80"], ["WaGa", "SLX4I_HUMAN", "Protein SLX4IP", "SLX4IP", "33.84"], ["TMM56_HUMAN", "Transmembrane protein 56", "TMEM56", "8.88"], ["S38AA_HUMAN", "Putative sodium-coupled neutral amino acid transporter 10", "SLC38A10", "6.38"], ["COQ6_HUMAN", "Ubiquinone biosynthesis monooxygenase COQ6, mitochondrial", "COQ6", "4.57"], ["NEK5_HUMAN", "Serine/threonine-protein kinase Nek5", "NEK5", "4.36"], ["PEX16_HUMAN", "Peroxisomal membrane protein PEX16", "PEX16", "4.33"], ["PEAK1_HUMAN", "Pseudopodium-enriched atypical kinase 1", "PEAK1", "3.95"], ["PCBP2_HUMAN", "Poly(rC)-binding protein 2", "PCBP2", "3.83"], ["HS71A_HUMAN", "Heat shock 70 kDa protein 1A", "HSPA1A", "3.66"], ["FBX41_HUMAN", "F-box only protein 41", "FBXO41", "3.59"], ["HNRPC_HUMAN", "Heterogeneous nuclear ribonucleoproteins C1/C2", "HNRNPC", "3.55"], ["HMMR_HUMAN", "Hyaluronan mediated motility receptor", "HMMR", "3.37"], ["SMYD5_HUMAN", "SET and MYND domain-containing protein 5", "SMYD5", "3.27"], ["MBNL2_HUMAN", "Muscleblind-like protein 2", "MBNL2", "2.47"], ["H4_HUMAN", "Histone H4", "HIST1H4A", "2.45"], ["HNF4A_HUMAN", "Hepatocyte nuclear factor 4-alpha", "HNF4A", "2.35"], ["ASPG_HUMAN", "N(4)-(beta-N-acetylglucosaminyl)-l-asparaginase", "AGA", "2.20"], ["H2B1O_HUMAN", "Histone H2B type 1-O", "HIST1H2BO", "1.99"], ["H2B1D_HUMAN", "Histone H2B type 1-D", "HIST1H2BD", "1.97"], ["TBB5_HUMAN", "Tubulin beta chain", "TUBB", "1.89"], ["UGGG1_HUMAN", "UDP-glucose:glycoprotein glucosyltransferase 1", "UGGT1", "1.80"], ["UB2J1_HUMAN", "Ubiquitin-conjugating enzyme E2 J1", "UBE2J1", "1.80"], ["RLA2_HUMAN", "60S acidic ribosomal protein P2", "RPLP2", "1.77"], ["SF01_HUMAN", "Splicing factor 1", "SF1", "1.71"], ["HNRL2_HUMAN", "Heterogeneous nuclear ribonucleoprotein U-like protein 2", "HNRNPUL2", "1.71"], ["ROAA_HUMAN", "Heterogeneous nuclear ribonucleoprotein A/B", "HNRNPAB", "1.70"], ["POP1_HUMAN", "Ribonucleases P/MRP protein subunit POP1", "POP1", "1.69"], ["PRDX2_HUMAN", "Peroxiredoxin-2", "PRDX2", "1.68"], ["CE57L_HUMAN", "Centrosomal protein CEP57L1", "CEP57L1", "1.67"], ["CCDC6_HUMAN", "Coiled-coil domain-containing protein 6", "CCDC6", "1.67"], ["KCTD9_HUMAN", "BTB/POZ domain-containing protein KCTD9", "KCTD9", "1.66"], ["ADCY1_HUMAN", "Adenylate cyclase type 1", "ADCY1", "1.59"], ["S35E2_HUMAN", "Solute carrier family 35 member E2", "SLC35E2", "1.55"], ["ATP5J_HUMAN", "ATP synthase-coupling factor 6, mitochondrial", "ATP5J", "1.51"], ["ATPA_HUMAN", "ATP synthase subunit alpha, mitochondrial", "ATP5A1", "1.50"], ["MCC13", "CLCB_HUMAN", "Clathrin light chain B", "CLTB", "4.71"], ["HSPB1_HUMAN", "Heat shock protein beta-1", "HSPB1", "3.23"], ["SNX4_HUMAN", "Sorting nexin-4", "SNX4", "2.83"], ["RL23A_HUMAN", "60S ribosomal protein L23a", "RPL23A", "2.82"], ["PROF1_HUMAN", "Profilin-1", "PFN1", "2.51"], ["H2B1C_HUMAN", "Histone H2B type 1-C/E/F/G/I", "HIST1H2BC", "2.47"], ["ZN407_HUMAN", "Zinc finger protein 407", "ZNF407", "2.44"], ["H2B1K_HUMAN", "Histone H2B type 1-K", "HIST1H2BK", "2.42"], ["OPRD_HUMAN", "Delta-type opioid receptor", "OPRD1", "2.42"], ["HGB1A_HUMAN", "Putative high mobility group protein B1-like 1", "HMGB1P1", "2.35"], ["PSME1_HUMAN", "Proteasome activator complex subunit 1", "PSME1", "2.29"], ["PRDX1_HUMAN", "Peroxiredoxin-1", "PRDX1", "2.22"], ["CAC1G_HUMAN", "Voltage-dependent T-type calcium channel subunit alpha-1G", "CACNA1G", "2.20"], ["H2B2F_HUMAN", "Histone H2B type 2-F", "HIST2H2BF", "2.18"], ["K2C5_HUMAN", "Keratin, type II cytoskeletal 5", "KRT5", "2.17"], ["RL4_HUMAN", "60S ribosomal protein L4", "RPL4", "2.15"], ["LDHB_HUMAN", "l-Lactate dehydrogenase B chain", "LDHB", "2.14"], ["MT1E_HUMAN", "Metallothionein-1E", "MT1E", "2.14"], ["ILRL2_HUMAN", "Interleukin-1 receptor-like 2", "IL1RL2", "1.94"], ["MYPC2_HUMAN", "Myosin-binding protein C, fast-type", "MYBPC2", "1.93"], ["NONO_HUMAN", "Non-POU domain-containing octamer-binding protein", "NONO", "1.84"], ["LMNA_HUMAN", "Prelamin-A/C", "LMNA", "1.82"], ["K2C8_HUMAN", "Keratin, type II cytoskeletal 8", "KRT8", "1.66"], ["NUCL_HUMAN", "Nucleolin", "NCL", "1.64"], ["PDLI1_HUMAN", "PDZ and LIM domain protein 1", "PDLIM1", "1.64"], ["RLA1_HUMAN", "60S acidic ribosomal protein P1", "RPLP1", "1.64"], ["BAF_HUMAN", "Barrier-to-autointegration factor", "BANF1", "1.63"], ["NPM_HUMAN", "Nucleophosmin", "NPM1", "1.61"], ["HNRPK_HUMAN", "Heterogeneous nuclear ribonucleoprotein K", "HNRNPK", "1.61"], ["YBOX1_HUMAN", "Nuclease-sensitive element-binding protein 1", "YBX1", "1.60"], ["H2AJ_HUMAN", "Histone H2A.J", "H2AFJ", "1.56"], ["RL34_HUMAN", "60S ribosomal protein L34", "RPL34", "1.55"], ["ROA1_HUMAN", "Heterogeneous nuclear ribonucleoprotein A1", "HNRNPA1", "1.52"], ["RS28_HUMAN", "40S ribosomal protein S28", "RPS28", "1.52"], ["CQ047_HUMAN", "Uncharacterized protein C17orf47", "C17orf47", "1.52"]], "row_count": 143, "column_count": 5, "numeric_cells": 298, "header_rows": 1, "locator": "section[6]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:31889939:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:efe7594ff6b0d8d66d9d8527f147edfa0088750865b0fe80f40fecb9a9ace355", "bytes": 3066, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#Tab2", "version": null, "note": "An overview of downregulated proteins identified in Merkel cell carcinoma cell lines", "structure": {"pmcid": "PMC6921584", "section_index": 9, "section_title": "Differentially expressed proteins in MCC cell lines and the control cell line", "row_count": 44, "column_count": 5}, "table": {"label": "Table 2", "caption": "An overview of downregulated proteins identified in Merkel cell carcinoma cell lines", "rows": [["Cell line", "UniProt entry name", "Protein name", "Gene symbol", "Ratio (H/L)"], ["BroLi", "H10_HUMAN", "Histone H1.0", "H1F0", "0.45"], ["MGAP_HUMAN", "MAX gene-associated protein", "MGA", "0.17"], ["MKL-1", "ASXL1_HUMAN", "Putative Polycomb group protein ASXL1", "ASXL1", "0.48"], ["TBB5_HUMAN", "Tubulin beta chain", "TUBB TUBB5", "0.48"], ["TAF2_HUMAN", "Transcription initiation factor TFIID subunit 2", "TAF2", "0.45"], ["FBLN2_HUMAN", "Fibulin-2", "FBLN2", "0.45"], ["PRDX2_HUMAN", "Peroxiredoxin-2", "PRDX2", "0.44"], ["SEPT5_HUMAN", "Septin-5", "Sep-05", "0.44"], ["FUS_HUMAN", "RNA-binding protein FUS", "FUS", "0.44"], ["BICD2_HUMAN", "Protein bicaudal D homolog 2", "BICD2", "0.43"], ["SRRT_HUMAN", "Serrate RNA effector molecule homolog", "SRRT", "0.41"], ["MAK_HUMAN", "Serine/threonine-protein kinase MAK", "MAK", "0.40"], ["CBX5_HUMAN", "Chromobox protein homolog 5", "CBX5", "0.36"], ["CHSP1_HUMAN", "Calcium-regulated heat-stable protein 1", "CARHSP1", "0.34"], ["NUCB2_HUMAN", "Nucleobindin-2", "NUCB2", "0.31"], ["TPIS_HUMAN", "Triosephosphate isomerase", "TPI1", "0.26"], ["TRI13_HUMAN", "E3 ubiquitin-protein ligase TRIM13", "TRIM13", "0.22"], ["L37A3_HUMAN", "Leucine-rich repeat-containing protein 37A3", "LRRC37A3", "0.08"], ["CMGA_HUMAN", "Chromogranin-A", "CHGA", "0.03"], ["KCTD9_HUMAN", "BTB/POZ domain-containing protein KCTD9", "KCTD9", "0.02"], ["1433Z_HUMAN", "14-3-3 protein zeta/delta", "YWHAZ", "0.02"], ["MKL-2", "ALAT1_HUMAN", "Alanine aminotransferase 1", "GPT", "0.49"], ["GRP75_HUMAN", "Stress-70 protein, mitochondrial", "HSPA9", "0.40"], ["ULK2_HUMAN", "Serine/threonine-protein kinase ULK2", "ULK2", "0.34"], ["NUCL_HUMAN", "Nucleolin", "NCL", "0.24"], ["1433Z_HUMAN", "14-3-3 protein zeta/delta", "YWHAZ", "0.04"], ["PeTa", "KCTD9_HUMAN", "BTB/POZ domain-containing protein KCTD9", "KCTD9", "0.45"], ["WaGa", "TMX1_HUMAN", "Thioredoxin-related transmembrane protein 1", "TMX1", "0.39"], ["RS30_HUMAN", "40S ribosomal protein S30", "FAU", "0.38"], ["CPLX3_HUMAN", "Complexin-3", "CPLX", "0.37"], ["CA052_HUMAN", "UPF0690 protein C1orf52", "C1orf52", "0.27"], ["RSMB_HUMAN", "Small nuclear ribonucleoprotein-associated proteins B and B’", "SNRPB", "0.23"], ["RS28_HUMAN", "40S ribosomal protein S28", "RPS28", "0.22"], ["CQ047_HUMAN", "Uncharacterized protein C17orf47", "C17orf47", "0.22"], ["G3P_HUMAN", "Glyceraldehyde-3-phosphate dehydrogenase", "GAPDH", "0.21"], ["GRP75_HUMAN", "Stress-70 protein, mitochondrial", "HSPA9", "0.17"], ["SAE2_HUMAN", "SUMO-activating enzyme subunit 2", "UBA2", "0.09"], ["SRSF7_HUMAN", "Serine/arginine-rich splicing factor 7", "SRSF7", "0.06"], ["MARCS_HUMAN", "Myristoylated alanine-rich C-kinase substrate", "MARCKS", "0.05"], ["MCC13", "WNK4_HUMAN", "Serine/threonine-protein kinase WNK4", "WNK4", "0.48"], ["HNRPU_HUMAN", "Heterogeneous nuclear ribonucleoprotein U", "HNRNPU", "0.44"], ["RL18A_HUMAN", "60S ribosomal protein L18a", "RPL18A", "0.42"], ["FUBP1_HUMAN", "Far upstream element-binding protein 1", "FUBP1", "0.27"]], "row_count": 44, "column_count": 5, "numeric_cells": 92, "header_rows": 1, "locator": "section[9]/table-wrap[1]#Tab2"}}], "gaps": ["asset:data:geo:PXD008181 not downloaded", "asset:data:geo:PXD008181 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Benjamini Hochberg correction for multitesting", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "p-values where corrected for multitesting according to Benjamini Hochberg."}}], "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Benjamini Hochberg correction for multitesting), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["PXD008181"], "resolved_accessions": ["PXD008181"], "statements": ["Data availabilityThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD008181 and 10.6019/pxd008181."], "basis": "The paper names PXD008181 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:31889939", "data:geo:PXD008181", "asset:table:pmid:31889939:1", "asset:table:pmid:31889939:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD008181"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:17:44Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 32036, "completion_tokens": 945, "cached_tokens": 10888}}, "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:31889939", "type": "paper", "label": "pmid:31889939"}, {"id": "source:pmid:31889939", "type": "manuscript", "label": "PMID 31889939 full text"}, {"id": "data:geo:PXD008181", "type": "dataset", "label": "GEO PXD008181"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31889939", "type": "paper", "label": "pmid:31889939"}, {"id": "source:pmid:31889939", "type": "manuscript", "label": "PMID 31889939 full text"}, {"id": "data:geo:PXD008181", "type": "dataset", "label": "GEO PXD008181"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31889939", "type": "extraction", "used": ["source:pmid:31889939"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD008181", "type": "accession_resolution", "used": ["data:geo:PXD008181"], "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:31889939", "parent_hash": "sha256:679006a52f87cfc91ead61314a52535942b14035cbfeb50f747a6e38349dcfd3", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD008181 licence not read", "asset:data:geo:PXD008181 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["labelled proteins, peptides were analysed by mass spectrometry. Proteome patterns of MCC cell lines were co"], "order_basis": "paper_text_order:614", "id": "assay:1"}, {"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": ["om AddexBio (San Diego, CA, USA). Cells were cultured in RPMI buffer (Thermo Fisher Scientific, Walth", "er Scientific, Waltham, MA, USA). Cells were cultured for at least ten cell doublings. Three biolo", "doublings. Three biological replicates were cultured per each cell line, and these were merged in"], "order_basis": "paper_text_order:1580", "id": "assay:2"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T01:50:27+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}