Autologous chondrocyte implantation-derived synovial fluids display distinct responder and non-responder proteomic profiles.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28666451", "kind": "science-record", "revision": 8, "content_hash": "sha256:25a27d8fc49ad2af30885baa8bb7d3289d42000038900a08dc35d78b4a1ef3c8", "created_at": "2026-11-01T15:40:27Z", "updated_at": "2026-11-01T22:43:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Autologous chondrocyte implantation-derived synovial fluids display distinct responder and non-responder proteomic profiles.", "doi": "10.1186/s13075-017-1336-7", "pmid": "28666451", "authors": ["Charlotte H Hulme", "Emma L Wilson", "Mandy J Peffers", "Sally Roberts", "Deborah M Simpson", "James B Richardson", "Pete Gallacher", "Karina T Wright"], "journal": "Arthritis research & therapy", "year": 2017, "abstract": "BACKGROUND: Autologous chondrocyte implantation (ACI) can be used in the treatment of focal cartilage injuries to prevent the onset of osteoarthritis (OA). However, we are yet to understand fully why some individuals do not respond well to this intervention. Identification of a reliable and accurate biomarker panel that can predict which patients are likely to respond well to ACI is needed in order to assign the patient to the most appropriate therapy. This study aimed to compare the baseline and mid-treatment proteomic profiles of synovial fluids (SFs) obtained from responders and non-responders to ACI.\nMETHODS: SFs were derived from 14 ACI responders (mean Lysholm improvement of 33 (17-54)) and 13 non-responders (mean Lysholm decrease of 14 (4-46)) at the two stages of surgery (cartilage harvest and chondrocyte implantation). Label-free proteome profiling of dynamically compressed SFs was used to identify predictive markers of ACI success or failure and to investigate the biological pathways involved in the clinical response to ACI.\nRESULTS: Only 1 protein displayed a ≥2.0-fold differential abundance in the preclinical SF of ACI responders versus non-responders. However, there is a marked difference between these two groups with regard to their proteome shift in response to cartilage harvest, with 24 and 92 proteins showing ≥2.0-fold differential abundance between Stages I and II in responders and non-responders, respectively. Proteomic data has been uploaded to ProteomeXchange (identifier: PXD005220). We have validated two biologically relevant protein changes associated with this response, demonstrating that matrix metalloproteinase 1 was prominently elevated and S100 calcium binding protein A13 was reduced in response to cartilage harvest in non-responders.\nCONCLUSIONS: The differential proteomic response to cartilage harvest noted in responders versus non-responders is completely novel. Our analyses suggest several pathways which appear to be altered in non-responders that are worthy of further investigation to elucidate the mechanisms of ACI failure. These protein changes highlight many putative biomarkers that may have potential for prediction of ACI treatment success.", "claims": [{"id": "claim-method", "statement": "Statistical analysis was performed using ProgenesisQI™ software; briefly transformed normalised abundances were used for one-way analysis of variance (ANOVA) and all peptides (with p < 0.05) of an identified protein were included.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28666451", "locator": "sections[6] \"Mass spectrometry and label-free quantification\" paragraph 2", "quote": "Statistical analysis was performed using ProgenesisQI™ software; briefly transformed normalised abundances were used for one-way analysis of variance (ANOVA) and all peptides (with p < 0.05) of an identified protein were included."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Proteomic data has been deposited in the PRIDE ProteomeXchange and can be accessed using the identifier PXD005220.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28666451", "locator": "sections[17] \"ack\" paragraph 1", "quote": "Proteomic data has been deposited in the PRIDE ProteomeXchange and can be accessed using the identifier PXD005220."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used Ingenuity pathway analysis with a right-sided Fisher’s exact test and an independent DAVID pathway analysis, while the underlying proteomic source data were deposited in PRIDE ProteomeXchange under identifier PXD005220.", "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:28666451"], "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:PXD005220"], "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:PXD005220"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28666451", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s13075-017-1336-7", "sha256": "sha256:c098eae219b4c813614ad855bcebd23e82a42d28d0f8493f76b2eef7501212f2", "bytes": 50158, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s13075-017-1336-7", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5493128", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD005220", "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=PXD005220", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD005220", "version": null, "note": "Proteomic data has been deposited in the PRIDE ProteomeXchange and can be accessed using the identifier PXD005220.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Proteomic data has been deposited in the PRIDE ProteomeXchange and can be accessed using the identifier PXD005220.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteomic profiles of  synovial fluids derived from autologous chondrocyte implantation surgery", "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:28666451:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bc4afaf837a5d76c20b6ba7a8a43906f9d8bec36a19036c13386050a7233c8ea", "bytes": 1940, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Demographic data for patient participants whose samples from Stage I or Stage II were analysed who responded clinically (responders) or who did not respond (non-responders) to autologous chondrocyte implantation (ACI)", "structure": {"pmcid": "PMC5493128", "section_index": 3, "section_title": "Synovial fluid collection and storage", "row_count": 16, "column_count": 7}, "table": {"label": "Table 1", "caption": "Demographic data for patient participants whose samples from Stage I or Stage II were analysed who responded clinically (responders) or who did not respond (non-responders) to autologous chondrocyte implantation (ACI)", "rows": [["", "Stage I", "Stage II", "p value (A) R v NR SI; (B) R v NR SI", "p value (A) SI v SII R; (B) SI v SII NR"], ["Responders (n = 8)", "Non-responders (n = 7)", "Responders (n = 12)", "Non-responders (n = 12)"], ["Difference in Lysholm Score", "27 (17–38)", "–8 (–4 to –17)", "34 (17–54)", "–11 (–4 to –46)", "(A) 0.0003; (B) <0.0001", "(A) 0.21; (B) 0.55"], ["BMI (kg/m2)", "29 (23–31)", "27 (24–31)", "27 (23–48)", "29 (22–36)", "(A) 0.94; (B) 0.54", "(A) 0.73; (B) 0.68"], ["Age (years)", "32 (17–49)", "40 (25–50)", "40 (17–90)", "43 (25–52)", "(A) 0.28; (B) 0.92", "(A) 0.17; (B) 0.58"], ["Male (n)", "8", "7", "11", "10", "(A) >0.99; (B) >0.99", "(A) >0.99; (B) 0.51"], ["Smoker (n)", "1", "2", "1", "3", "(A) 0.54; (B) 0.59", "(A) >0.99; (B) >0.99"], ["Dilution factor of SF", "5 (3–9)", "4 (2–7)", "4 (1–9)", "3 (2–5)", "(A) 0.48; (B) 0.25", "(A) 0.53; (B) 0.50"], ["Total defect area (cm2)", "14 (0.4–24)", "6 (0.6–12)", "6 (1–20)", "5 (0.6–12)", "(A) 0.74; (B) 0.35", "(A) 0.45; (B) 0.28"], ["Patella defect (n)", "1", "1", "4", "2", "(A) >0.99; (B) 0.64", "(A) 0.60; (B) >0.99"], ["LFC defect (n)", "2", "0", "0", "0", "(A) 0.47; (B) >0.99", "(A) 0.15; (B) >0.99"], ["LTP defect (n)", "1", "0", "0", "0", "(A) >0.99; (B) >0.99", "(A) 0.15; (B) >0.99"], ["MFC defect (n)", "2", "2", "1", "6", "(A) >0.99; (B) 0.07", "(A) 0.54; (B) 0.63"], ["Trochlea defect (n)", "0", "3", "2", "1", "(A) 0.20; (B) >0.99", "(A) 0.49; (B) 0.12"], ["Multiple defects (n)", "1", "0", "1", "1", "(A) >0.99; (B) >0.99", "(A) >0.99; (B) >0.99"], ["Unknown defect location (n)", "1", "1", "4", "2", "(A) >0.99; (B) 0.64", "(A) 0.60; (B) >0.99"]], "row_count": 16, "column_count": 7, "numeric_cells": 88, "header_rows": 2, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:28666451:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:07b8c536a67e4cb2f70a7a828f3e6ff710462df9488e9ff9eba3142c1275cb21", "bytes": 5011, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#Tab2", "version": null, "note": "Fold-change of proteins that are differentially expressed in the synovial fluid collected at Stage I compared to Stage II of the ACI procedure in clinical non-responders. Proteins shown in italic were validated using enzyme linked immunosorbant assay", "structure": {"pmcid": "PMC5493128", "section_index": 11, "section_title": "Differential abundance of proteins after controlled cartilage injury (Stage I versus Stage II)", "row_count": 91, "column_count": 3}, "table": {"label": "Table 2", "caption": "Fold-change of proteins that are differentially expressed in the synovial fluid collected at Stage I compared to Stage II of the ACI procedure in clinical non-responders. Proteins shown in italic were validated using enzyme linked immunosorbant assay", "rows": [["Protein", "Fold change"], ["Description", "Accession"], ["Perilipin-4", "Q96Q06", "–4.3"], ["Syntaxin-7", "O15400", "–3.9"], ["Fermitin family homolog 3", "Q86UX7", "–3.7"], ["Deoxynucleoside triphosphate triphosphohydrolase SAMHD1", "Q9Y3Z3", "–3.7"], ["PDZ and LIM domain protein 1", "O00151", "–3.6"], ["Sorting nexin-5", "Q9Y5X3", "–3.3"], ["Neuroblast differentiation-associated protein AHNAK", "Q09666", "–3.2"], ["Signal recognition particle 14 kDa protein", "P37108", "–3.0"], ["Hyaluronan and proteoglycan link protein 3", "Q96S86", "–3.0"], ["Heterogeneous nuclear ribonucleoprotein K", "P61978", "–2.9"], ["ATP-citrate synthase", "P53396", "–2.9"], ["Fatty acid-binding protein, epidermal", "Q01469", "–2.8"], ["60S ribosomal protein L12", "P30050", "–2.7"], ["Fatty acid-binding protein, adipocyte", "P15090", "–2.6"], ["Insulin-like growth factor-binding protein 6", "P24592", "–2.6"], ["Protein canopy homolog 3", "Q9BT09", "–2.6"], ["Tripeptidyl-peptidase 1", "O14773", "–2.5"], ["PDZ and LIM domain protein 3", "Q53GG5", "–2.5"], ["Cellular nucleic acid-binding protein", "P62633", "–2.5"], ["Bifunctional glutamate/proline-tRNA ligase", "P07814", "–2.5"], ["Protein disulfide-isomerase A3", "P30101", "–2.4"], ["Peroxiredoxin-6", "P30041", "–2.4"], ["Tryptase alpha/beta-1", "Q15661", "–2.4"], ["Endoplasmic reticulum resident protein 29", "P30040", "–2.4"], ["Peroxiredoxin-1", "Q06830", "–2.4"], ["Na(+)/H(+) exchange regulatory cofactor NHE-RF1", "O14745", "–2.4"], ["Mitochondrial import inner membrane translocase subunit TIM14", "Q96DA6", "–2.4"], ["Mortality factor 4-like protein 1", "Q9UBU8", "–2.4"], ["Fructose-bisphosphate aldolase A", "P04075", "–2.3"], ["Microtubule-associated protein RP/EB family member 1", "Q15691", "–2.3"], ["Leucine zipper transcription factor-like protein 1", "Q9NQ48", "–2.3"], ["Transcription elongation factor A protein 1", "P23193", "–2.3"], ["2',3'-cyclic-nucleotide 3'-phosphodiesterase", "P09543", "–2.3"], ["Histamine N-methyltransferase", "P50135", "–2.3"], ["Protein S100-A13", "Q99584", "–2.3"], ["Acrosomal protein SP-10", "P26436", "–2.2"], ["AP-2 complex subunit beta", "P63010", "–2.2"], ["S-phase kinase-associated protein 1", "P63208", "–2.2"], ["High mobility group protein B3", "O15347", "–2.2"], ["Cytokine-like protein 1", "Q9NRR1", "–2.2"], ["Mitochondrial fission 1 protein", "Q9Y3D6", "–2.2"], ["Filamin-A", "P21333", "–2.2"], ["Nuclear migration protein nudC", "Q9Y266", "–2.1"], ["Cathepsin K", "P43235", "–2.1"], ["Prostaglandin E synthase 3", "Q15185", "–2.1"], ["Vinculin", "P18206", "–2.1"], ["Plastin-2", "P13796", "–2.1"], ["Coronin-1C", "Q9ULV4", "–2.1"], ["Ig heavy chain V-I region V35", "P23083", "–2.1"], ["Stress-induced-phosphoprotein 1", "P31948", "–2.1"], ["Putative phospholipase B-like 2", "Q8NHP8", "–2.1"], ["Gelsolin", "P06396", "–2.0"], ["Spectrin beta chain, erythrocytic", "P11277", "–2.0"], ["Stathmin", "P16949", "–2.0"], ["Hsc70-interacting protein", "P50502", "–2.0"], ["40S Ribosomal protein", "P23396", "–2.0"], ["Epidermal growth factor receptor substrate 15", "P42566", "22.5"], ["Hemoglobin subunit theta-1", "P09105", "6.1"], ["C-type lectin domain family 11 member A", "Q9Y240", "5.6"], ["Periostin", "Q15063", "5.1"], ["Collagen alpha-1(I) chain", "P02452", "4.7"], ["Spectrin alpha chain, erythrocytic 1", "P02549", "4.0"], ["Collagen alpha-1(V) chain", "P20908", "3.7"], ["Fibrinogen gamma chain", "P02679", "3.5"], ["Collagen alpha-1(XII) chain", "Q99715", "3.3"], ["Complement C1q tumor necrosis factor-related protein 3", "Q9BXJ4", "3.1"], ["Adiponectin", "Q15848", "3.0"], ["Adipocyte enhancer-binding protein 1", "Q8IUX7", "3.0"], ["Latent-transforming growth factor beta-binding protein 1", "Q14766", "3.0"], ["Fibrinogen beta chain", "P02675", "3.0"], ["Chondroitin sulfate proteoglycan 4", "Q6UVK1", "2.9"], ["Fibrinogen alpha chain", "P02671", "2.8"], ["Interstitial collagenase (MMP1)", "P03956", "2.7"], ["Secreted phosphoprotein 24", "Q13103", "2.7"], ["Collagen alpha-2(V) chain", "P05997", "2.6"], ["Ferritin light chain", "P02792", "2.6"], ["C4b-binding protein alpha chain", "P04003", "2.6"], ["Nucleobindin-1", "Q02818", "2.4"], ["C4b-binding protein beta chain", "P20851", "2.2"], ["Vitamin K-dependent protein S", "P07225", "2.2"], ["Fibronectin", "P02751", "2.2"], ["Prosaposin", "P07602", "2.1"], ["Integrin beta-like protein 1", "O95965", "2.1"], ["Adipocyte plasma membrane-associated protein", "Q9HDC9", "2.1"], ["Cytoplasmic dynein 1 heavy chain 1", "Q14204", "2.0"], ["Soluble scavenger receptor cysteine-rich domain-containing protein SSC5D", "A1L4H1", "2.0"], ["F-actin-capping protein subunit beta", "P47756", "2.0"], ["Mannan-binding lectin serine protease 1", "P48740", "2.0"], ["Thrombospondin-3", "P49746", "2.0"]], "row_count": 91, "column_count": 3, "numeric_cells": 220, "header_rows": 2, "locator": "section[11]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:28666451:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7aa5cdfc8280ec6a4158f1aa502218a473efd4500b5f6ef865567c4299dbb959", "bytes": 1577, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[2]#Tab3", "version": null, "note": "Proteins that are differentially expressed with a ≥2.0-fold-change in the synovial fluid collected at Stage I compared to Stage II of the ACI procedure in clinical responders", "structure": {"pmcid": "PMC5493128", "section_index": 11, "section_title": "Differential abundance of proteins after controlled cartilage injury (Stage I versus Stage II)", "row_count": 26, "column_count": 3}, "table": {"label": "Table 3", "caption": "Proteins that are differentially expressed with a ≥2.0-fold-change in the synovial fluid collected at Stage I compared to Stage II of the ACI procedure in clinical responders", "rows": [["Protein", "Fold change"], ["Description", "Accession"], ["Heat shock protein 75 kDa, mitochondrial", "Q12931", "–470.0"], ["Microtubule-associated protein 1B", "P46821", "–17.2"], ["Adenosylhomocysteinase", "P23526", "–3.7"], ["Complement factor H-related protein 3", "Q02985", "–2.8"], ["Mannose-1-phosphate guanyltransferase beta", "Q9Y5P6", "–2.7"], ["Peroxiredoxin-4", "Q13162", "–2.5"], ["Oxysterol-binding protein 1", "P22059", "–2.4"], ["Protein canopy homolog 3", "Q9BT09", "–2.1"], ["Spermatid perinuclear RNA-binding protein", "Q96SI9", "–2.0"], ["Ferritin light chain", "P02792", "2.2"], ["Secreted phosphoprotein 24", "Q13103", "2.2"], ["Chondroitin sulfate proteoglycan 4", "Q6UVK1", "2.3"], ["Collagen alpha-2(I) chain", "P08123", "2.3"], ["Collagen alpha-1(V) chain", "P20908", "2.5"], ["26S protease regulatory subunit 6A", "P17980", "2.7"], ["Collagen alpha-2(V) chain", "P05997", "2.9"], ["Collagen alpha-1(I) chain", "P02452", "3.3"], ["Spectrin alpha chain, erythrocytic 1", "P02549", "4.1"], ["Histidine triad nucleotide-binding protein 1", "P49773", "4.2"], ["Platelet factor 4", "P02776", "4.2"], ["Alpha-1-acid glycoprotein 2", "P19652", "4.3"], ["Protein 4.1", "P11171", "4.3"], ["Periostin", "Q15063", "4.5"], ["26S proteasome non-ATPase regulatory subunit 13", "Q9UNM6", "4.6"]], "row_count": 26, "column_count": 3, "numeric_cells": 65, "header_rows": 2, "locator": "section[11]/table-wrap[2]#Tab3"}}, {"id": "asset:table:pmid:28666451:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2199179b97fa41a5fd60b7dcf5cfc145981c31f82a8e5150228d816341d5dbaf", "bytes": 2352, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#Tab4", "version": null, "note": "Analysis of upstream regulators of interactome networks generated from protein changes between Stages I (SI) and II (SII) in either responders or non-responders to ACI were identified using Ingenuity Pathway Analysis software", "structure": {"pmcid": "PMC5493128", "section_index": 12, "section_title": "Identification of canonical pathways and protein networks associated with protein changes between Stage I and II", "row_count": 23, "column_count": 5}, "table": {"label": "Table 4", "caption": "Analysis of upstream regulators of interactome networks generated from protein changes between Stages I (SI) and II (SII) in either responders or non-responders to ACI were identified using Ingenuity Pathway Analysis software", "rows": [["Upstream regulators", "Activation z score (SII v SI)", "p value of overlap", "Target molecules in dataset"], ["Non-responders"], ["", "TGFB1", "–1.595", "9.46E–10", "APOB,APOC2,APOE,CD44,COL1A1,COL1A2,COL5A1,COMP,CSPG4,CTSD,ECM1,FETUB,FN1,FTL,GSN,HINT1,HSPG2,HTRA1,IGFBP6,LCAT,MYLK,PCOLCE2,PDXK,POSTN,RAP1A,S100A4,TGFBI"], ["DYSF", "NP", "2.01E–09", "CFD,FN1,FTL,LCP1,LYZ,PROS1,S100-A13,S100A4"], ["MYC", "3.046", "2.20E–09", "ALDOA,ANXA5,CCT3,CD44,COL1A1,COL1A2,COL5A1,CSPG4,CTSD,ECM1,FN1,HSPA9,LYZ,NCL,NUCB1,NUDC,PAM,PTN,RPL22,RPL30,TF"], ["COL9A1", "1.308", "2.79E–09", "COMP,FN1,HSPG2,TGFBI,THBS4"], ["Beta-estradiol", "2.271", "5.01E–09", "ALDOA,APOE,CD44,COL1A1,COL1A2,COMP,CTSD,F7,FN1,GMFB,HSPA2,HSPA8,HSPA9,HTRA1,IGFBP6,LTF,LYZ,MYLK,PAM,PDIA3,QSOX1,RAP1A,RPS13,S100-A13,SLC9A3R1,TF,THBS4"], ["Lipopolysaccharide", "–0.104", "5.96E–09", "ANXA5,APOB,APOC2,APOE,CD44,CFD,COL1A1,COL1A2,COL5A1,CSPG4,FN1,GSN,HDGFRP3,HMGB2,HSPA8,HTRA1,ITIH2,LBP,LTF,LYZ,PARK7,PCOLCE,PCOLCE2,PDIA3,PLG,TF"], ["Dihydrotestosterone", "–1.091", "1.03E–08", "ALDOA,APOE,CCT3,FN1,FTL,GSN,HINT1,LYZ,MYLK,NUCB1,PAM,POSTN,PROS1,RPL30,TF"], ["HRAS", "0.623", "2.52E–08", "CD44,COL1A1,COL1A2,ERP29,FN1,GSN,HSPA8,HTRA1,LYZ,MYH10,PDIA5,PLTP,POSTN,RPL30,S100A4"], ["KRAS", "2.226", "3.99E–08", "ALDOA,CD44,COL1A1,FN1,GBA,GSN,MYLK,PCOLCE,PDIA3,PSMA7,RNASE4,S100A4"], ["SMARCB1", "–1.195", "4.82E–08", "APOC4,CD44,COL1A1,COL1A2,GSN,LBP,POSTN,PTN,RAB14"], ["Responders"], ["", "CEBPB", "–1.067", "2.03E–07", "APOB,CFD,COL1A1,COL1A2,F7,HSPA8,PLG"], ["FLI1", "NP", "3.82E–07", "COL1A1,COL1A2,HSPA8,PF4"], ["S-adenosylhomocysteine", "NP", "1.21E–06", "COL1A1,COL1A2"], ["SCX", "NP", "1.65E–06", "COL1A1,COMP,POSTN"], ["Tgf beta (group)", "–1.454", "5.16E–06", "COL1A1,COL1A2,LCAT,POSTN,TGFBI"], ["ENTPD5", "NP", "1.21E–05", "COL1A1,COL1A2"], ["MKX", "NP", "1.21E–05", "COL1A1,COL1A2"], ["GATA4", "NP", "2.86E–05", "COL1A1,COL1A2,POSTN,TGFBI"], ["Nilotinib", "NP", "3.39E–05", "COL1A1,COL1A2"], ["TBX5", "NP", "5.50E–05", "COL1A1,COL1A2,POSTN"]], "row_count": 23, "column_count": 5, "numeric_cells": 40, "header_rows": 1, "locator": "section[12]/table-wrap[1]#Tab4"}}], "gaps": ["asset:data:geo:PXD005220 not downloaded", "asset:data:geo:PXD005220 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", 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"expected_value": 2.1, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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": ["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": ["PXD005220"], "resolved_accessions": ["PXD005220"], "statements": ["Proteomic data has been deposited in the PRIDE ProteomeXchange and can be accessed using the identifier PXD005220."], "basis": "The paper names PXD005220 in PRIDE ProteomeXchange and the accession resolves in the repository. 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