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pmid:26322068
2-DE proteomics analysis of drought treated seedlings of Quercus ilex supports a root active strategy for metabolic adaptation in response to water shortage.
Lyudmila P Simova-Stoilova · Maria C Romero-Rodríguez · Rosa Sánchez-Lucas · Rafael M Navarro-Cerrillo · J Alberto Medina-Aunon · Jesús V Jorrín-Novo
Frontiers in plant science · 2015 doi:10.3389/fpls.2015.00627
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Complete file
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Despite being well adapted to dry hot climate, drought is the main cause of mortality post-transplanting in reforestation programs. An active response to drought is critical for tree establishment and survival. Applying a gel-based proteomic approach, dynamic changes in root proteins of drought treated Quercus ilex subsp. Ballota [Desf.] Samp. seedlings were followed. Water stress was applied on 20 day-old holm oak plantlets by water limitation for a period of 10 and 20 days, each followed by 10 days of recovery. Stress was monitored by changes in water status, plant growth, and electrolyte leakage. Contrary to leaves, holm oak roots responded readily to water shortage at physiological level by growth inhibition, changes in water status and membrane stability. Root proteins were extracted using trichloroacetate/acetone/phenol protocol and separated by two-dimensional electrophoresis. Coomassie colloidal stained gel images were analyzed and spot intensity data subjected to multivariate statistical analysis. Selected consistent spots in three biological replicas, presenting significant changes under stress, were subjected to MALDI-TOF mass spectrometry (peptide mass fingerprinting and MS/MS). For protein identification, combined search was performed with MASCOT search engine over NCBInr Viridiplantae and Uniprot databases. Data are available via ProteomeXchange with identifier PXD002484. Identified proteins were classified into functional groups: metabolism, protein biosynthesis and proteolysis, defense against biotic stress, cellular protection against abiotic stress, intracellular transport. Several enzymes of the carbohydrate metabolism decreased in abundance in roots under drought stress while some related to ATP synthesis and secondary metabolism increased. Results point at active metabolic adjustment and mobilization of the defense system in roots to actively counteract drought stress.", "claims": [{"id": "claim-method", "statement": "Data were statistically analyzed by ANOVA using the following settings: error model max (average, actual), 0.01 proportions of highest variance values to be removed before variance averaging, 10° of freedom for the Bayesian error model, 0.05 FDR threshold, and zero permutations.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26322068", "locator": "sections[6] \"Image analysis and selection of spots of interest\" paragraph 2", "quote": "Data were statistically analyzed by ANOVA using the following settings: error model max (average, actual), 0.01 proportions of highest variance values to be removed before variance averaging, 10° of freedom for the Bayesian error model, 0.05 FDR threshold, and zero permutations."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available with identifier PXD002484.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26322068", "locator": "sections[8] \"Data submission\" paragraph 2", "quote": "Data are available with identifier PXD002484."}], "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:26322068"], "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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11}, "table": {"label": "Table 3", "caption": "Main functional groups and subgroups of identified proteins and the tendencies of changes in individual proteins within groups.", "rows": [["Protein name/Species of closest homology", "SSP", "Accession No.", "Mr/pI", "Mascot scores", "Spot volume ratio changes"], ["", "", "", "Experimental", "Theoretical", "Protein score/C.I", "Total ion score/ C.I.", "D10/C10", "R10/C20", "D20/C20", "C20/C10"], ["GLYCOLYSIS AND GLYOXYLATE BYPASS"], ["Glucose-6-phosphate isomerase", "", "", "", "", "", "", "", "", "", ""], ["Pop.trichocarpa", "1401", "tr|B9GV29|B9GV2", "45.56/5.8", "68.1/5.55", "367/100", "275/100", "1.301", "0.835", "1.415*", "0.914"], ["Phosphofructokinase", "", "", "", "", "", "", "", "", "", ""], ["Citrus paradisi", "4707", "tr|Q9ZST3|Q9ZST", "65.7/6.71", "62.23/6.1", "163/100", "129/100", "0.672*", "0.722", "0.584*", "1.137"], ["Phosphoglycerate mutase", "", "", "", "", "", "", "", "", "", ""], ["Ricinus communis", "1702", "sp|P35493|PMGI_", "70.51/5.9", "61.01/5.5", "249/100", "205/100", "0.532*", "0.356*", "0.312*", "1.086"], ["", "2701", "tr|B9S1V6|B9S1V", "69.86/6.1", "", "306/100", "255/100", "0.549*", "0.813", "0.464*", "0.967"], ["Enolase", "", "", "", "", "", "", "", "", "", ""], ["Jatropha curcas", "1504", "tr|E6NU46|E6NU4", "55.7/5.92", "52.69/6.3", "384/100", "319/100", "1.799", "1.089", "1.719*", "0.911"], ["Spinacia oleracea", "1507", "tr|Q9LEE0|Q9LEE", "55.25/6.0", "48.37/5.5", "187/100", "134/100", "1.121", "0.207*", "0.851", "1.463"], ["Alnus glutinosa", "3503", "sp|Q43321|ENO_A", "56.84/6.4", "47.79/5.4", "460/100", "396/100", "0.746", "1.362", "0.477*", "0.718"], ["Ricinus communis", "5602", "tr|B9R9N6|B9R9N", "58.52/6.8", "48.15/5.7", "461/100", "400/100", "0.243*", "0.409*", "0.181*", "1.099"], ["Glucose-1-phosphate adenylyl transferase", "", "", "", "", "", "", "", "", "", ""], ["Glycine max", "1407", "tr|I1JJP2|I1JJP", "51.01/6.03", "56.71/6.3", "574/100", "445/100", "1.565", "0.393*", "1.413", "1.235"], ["6-phospho-fructokinase 3 PFK3", "", "", "", "", "", "", "", "", "", ""], ["Arabidopsis thaliana", "7605", "sp|Q94AA4|K6PF3", "61.41/7.4", "54.09/6.61", "317/100", "268/100", "0.609", "1.174", "0.578*", "0.964"], ["Phosphoglucomutase", "", "", "", "", "", "", "", "", "", ""], ["Populus tremula", "3707", "sp|Q9ZSQ4|PGMC_", "74.14/6.4", "63.37/5.5", "240/100", "145/100", "", "R+", "", ""], ["Triosephosphate isomerase", "", "", "", "", "", "", "", "", "", ""], ["Solanum tuberosum", "5106", "tr|Q3HRV9|Q3HRV", "20.82/6.8", "27.92/5.9", "378/100", "321/100", "0.564", "0.379*", "0", "2.005*"], ["Malic enzyme", "", "", "", "", "", "", "", "", "", ""], ["Oryza brachyantha", "7701", "tr|J3L3Y9|J3L3Y", "76.28/7.1", "71.65/8.8", "123/100", "116/100", "0", "1.564", "0", "0.99"], ["Fructose-bisphosphate aldolase, cytoplasmic isozyme 2", "", "", "", "", "", "", "", "", "", ""], ["Pisum sativum", "7306", "sp|P46257|ALF2_", "43.39/7.43", "38.64/6.77", "104/100", "83/100", "", "R+", "", ""], ["Aconitate hydratase, cytoplasmic", "", "", "", "", "", "", "", "", "", ""], ["Cucurbita maxima", "5806", "sp|P49608|ACOC_", "98.54/6.9", "98.57/5.7", "166/100", "118/100", "0.441*", "0.948", "0.305*", "1.222"], ["TRICARBOXYLIC ACID CYCLE"], ["Isocitrate dehydrogenase", "", "", "", "", "", "", "", "", "", ""], ["Ricinus communis", "2303", "tr|B9SRZ2|B9SRZ", "41.8/6.11", "40.63/7.0", "327/100", "258/100", "1.587*", "0.74", "1.447", "0.712"], ["Pyruvate dehydrogenase E1 beta", "", "", "", "", "", "", "", "", "", ""], ["Pisum sativum", "1201", "sp|P52904|ODPB_", "38.03/5.8", "38.99/5.9", "251/100", "234/100", "1.085", "0.681", "1.522*", "0.811"], ["Dihydrolipoyl lysine-residue acetyltransferase", "", "", "", "", "", "", "", "", "", ""], ["Arabidopsis thaliana", "1502", "sp|Q5M729|OPD23", "54.32/5.8", "58.89/7.9", "350/100", "324/100", "0.743", "0.182*", "0.701", "1.227"], ["AMINO ACID METABOLISM"], ["Glutamine synthetase", "", "", "", "", "", "", "", "", "", ""], ["Camellia sinensis", "3302", "tr|Q762D2|Q762D", "40.11/6.3", "39.41/5.5", "206/100", "188/100", "1.301", "0.751", "1.476*", "0.899"], ["Cysteine synthase", "", "", "", "", "", "", "", "", "", ""], ["Ricinus communis", "2102", "tr|B9RET4|B9RET", "31.66/6.2", "34.44/ 5.5", "409/100", "369/100", "1.255", "1.048", "1.288", "0.671*"], ["Alanine aminotransferase", "", "", "", "", "", "", "", "", "", ""], ["Oryza sativasubsp. japonica", "0606", "tr|Q7X7S9|Q7X7S", "56.56/5.5", "53.77/5.2", "227/100", "199/100", "0.687*", "0.332*", "0.489*", "0.885"], ["3-phosphoglycerate dehydrogenase", "", "", "", "", "", "", "", "", "", ""], ["Ricinus communis", "4702", "tr|B9RYA3|B9RYA", "64.92/6.5", "63.35/7.6", "210/100", "162/100", "0.511*", "1.053", "0.94", "1.031"], ["Glutamate dehydrogenase", "", "", "", "", "", "", "", "", "", ""], ["Populus trichocarpa", "7402", "tr|B9IPQ2|B9IPQ", "45.2/7.15", "44.72/6.84", "338/100", "281/100", "1.729*", "1.555*", "1.308", "1.587*"], ["ONE CARBON METABOLISM"], ["S-adenosylmethionine synthase", "", "", "", "", "", "", "", "", "", ""], ["Camellia sinensis", "2402", "sp|Q9LDQ7|METK_", "48.07/6.1", "43.23/5.3", "555/100", "403/100", "1.401", "0.349", "0.454*", "2.449"], ["Elaeagnus umbellata", "2405", "sp|Q9AT55|METK", "47.84/6.2", "43.56/5.5", "731/100", "563/100", "1.579*", "0.772", "0.674", "1.081"], ["Vit.b12 indep. methionine synthase", "", "", "", "", "", "", "", "", "", ""], ["Pop. trichocarpa", "6801", "tr|B9HQI3|B9HQI", "87.0/6.97", "85.03/6.2", "566/100", "499/100", "2.555", "2.484", "1.998*", "0.889"], ["Formate dehydrogenase", "", "", "", "", "", "", "", "", "", ""], ["Quercus robur", "7302", "tr|Q7XHJ0|Q7XHJ", "43.52/7.1", "40.85/6.5", "509/100", "365/100", "1.291", "1.299", "0.966", "0.763*"], ["", "7408", "tr|Q7XHJ0|Q7XHJ", "44.88/7.4", "", "489/100", "368/100", "1.587", "2.649*", "1.361", "0.531*"], ["Methylene tetrahydro folate reductase", "", "", "", "", "", "", "", "", "", ""], ["Arabidopsis thaliana", "4704", "sp|O80585|MTHR", "65.2/6.62", "67.39/5.3", "104/100", "95/100", "1.007", "1.274", "0.279*", "1.114"], ["AMINE BIOSYNTHESIS"], ["Betaine aldehyde dehydrogenase", "", "", "", "", "", "", "", "", "", ""], ["Amaranthus hypochondr.", "1603", "sp|O04895|BADH_", "63.69/5.8", "55.4/5.4", "246/100", "222/100", "1.877*", "0.77", "0.775", "1.009"], ["Corylus heterophylla", "1605", "tr|E9NRZ9|E9NRZ", "63.72/5.9", "55.2/5.44", "152/100", "127/100", "0.677", "0.36", "0.221*", "1.404"], ["ETHANOL FERMENTATION"], ["Pyruvate decarboxylase", "", "", "", "", "", "", "", "", "", ""], ["Prunus armeniaca", "3703", "tr|B0ZS79|B0ZS7", "69.93/6.3", "66.2/5.74", "244/100", "234/100", "0.345*", "1.54", "0.818", "0.451*"], ["", "3705", "", "70.07/6.4", "", "248/100", "230/100", "0.209*", "0.348*", "0", "1.128"], ["SECONDARY METABOLISM"], ["Chalcone synthase", "", "", "", "", "", "", "", "", "", ""], ["Juglans nigra xJuglans regia Malus domestica", "6403", "tr|Q42864|Q4286", "46.52/7.1", "42.9/6.3", "323/100", "235/100", "2.609*", "0.554*", "0.927", "1.317"], ["7401", "tr|B8R6A2|B8R6A", "46.7/7.12", "42.79/5.7", "494/100", "396/100", "2.472*", "0.709", "0.963", "1.252"], ["(+)-Neomenthol dehydrogenase", "", "", "", "", "", "", "", "", "", ""], ["Arabid.thaliana", "0104", "sp|Q9M2E2|SDR1_", "25.81/5.5", "33.07/5.4", "83/99.97", "68/99.997", "1.342*", "0.407*", "1.556*", "1.067"], ["Caffeoyl CoA 3-O-methyltransferase", "", "", "", "", "", "", "", "", "", ""], ["Betula platyphylla", "0105", "tr|Q5I2D1|Q5I2D", "23.07/5.5", "27.95/5.4", "433/100", "325/100", "1.718*", "0.603*", "1.051", "1.151"], ["Flavanone 3-hydroxylase", "", "", "", "", "", "", "", "", "", ""], ["Ampelopsis grossedentata", "3303", "tr|I6ZTY9|I6ZTY", "40.46/6.4", "41.2/5.3", "840/100", "606/100", "1.994*", "0.449*", "1.106", "1.252"], ["Dihydroflavonol 4-reductase", "", "", "", "", "", "", "", "", "", ""], ["P.suffruticosa", "6304", "tr|G4WCQ6|G4WCQ", "41.6/7.03", "41.4/5.67", "92/99.996", "76/100", "2.738*", "2.012*", "1.594*", "0.731"], ["Shikimate dehydrogenase", "", "", "", "", "", "", "", "", "", ""], ["Populus trichocarpa", "6601", "tr|B9HSF2|B9HSF", "64.05/6.9", "58.27/5.9", "96/99.998", "80/100", "2.154*", "1.066", "1.105", "0.95"], ["UDP-glucosyl transferase", "", "", "", "", "", "", "", "", "", ""], ["Ricinus communis", "4507", "tr|B9S1I8|B9S1I", "54.8/6.61", "52.97/6.21", "69/99.224", "59/99.987", "0", "0.194*", "0.382*", "1.814*"], ["ATP SYNTHESIS"], ["ATP synthase subunit beta", "", "", "", "", "", "", "", "", "", ""], ["Vitis vinifera", "1601", "tr|F6GTT2|F6GTT", "58.71/5.7", "59.3/5.9", "941/100", "741/100", "1.284", "0.943", "1.724*", "0.963"], ["NADH-ubiquinone oxidoreductase", "", "", "", "", "", "", "", "", "", ""], ["Zea mays", "3806", "tr|B6U2J0|B6U2J", "84.5/6.42", "81.67/6.1", "235/100", "212/100", "1.605*", "0.388*", "0.806", "0.926"], ["Gamma carbonic anhydrase", "", "", "", "", "", "", "", "", "", ""], ["A. thaliana", "5107", "sp|Q9FWR5|GCA1_", "23.46/6.91", "30.12/7.13", "115/100", "94/100", "2.505", "2.939*", "1.991", "0.712"], ["PROTEIN SYNTHESIS"], ["DEAD box RNA helicase", "", "", "", "", "", "", "", "", "", ""], ["Pisum sativum", "1509", "tr|Q8H1A5|Q8H1A", "50.52/5.5", "47.14/5.39", "310/100", "202/100", "1.784*", "0.495", "1.14", "1.509*"], ["Glycyl-tRNA synthetase", "", "", "", "", "", "", "", "", "", ""], ["Arabidopsis lyrata", "3805", "tr|D7KEM8|D7KEM", "78.97/6.5", "82.49/6.43", "443/100", "395/100", "0.411*", "0.558", "0.878", "0.466*"], ["PROTEIN FOLDING/PROCESSING"], ["Groes chaperonin", "", "", "", "", "", "", "", "", "", ""], ["Ricinus communis", "3007", "tr|B9RR63|B9RR6", "19.06/6.3", "26.58/8.89", "86/99.983", "53/99.912", "2.342*", "0.43*", "2.245*", "1.634"], ["Protein disulfide-isomerase", "", "", "", "", "", "", "", "", "", ""], ["Nicotiana tabacum", "1202", "tr|P93358|P9335", "38.81/5.8", "40.08/5.99", "201/100", "180/100", "0.884", "0.409*", "1.2", "0.834"], ["Chaperonin-60kD", "", "", "", "", "", "", "", "", "", ""], ["Ricinus communis", "1701", "tr|B9S582|B9S58", "66.69/5.7", "61.48/6.2", "393/100", "332/100", "0.646", "0.606*", "0.638", "0.987"], ["heat shock protein STI-like", "", "", "", "", "", "", "", "", "", ""], ["Glycine max", "4809", "tr|I1LGM2|I1LGM", "77.99/6.6", "65.86/6.26", "67/98.652", "54/99.95", "0.632*", "0.485*", "0.991", "0.795"], ["", "4810", "tr|I1J9X8|I1J9X", "78.27/6.6", "66.91/6.07", "68/99.023", "50/99.85", "0.405*", "0.414*", "0.912", "0.356*"], ["Chaperonin,TCP-1", "", "", "", "", "", "", "", "", "", ""], ["Malus domestica", "3604", "tr|D9ZJD1|D9ZJD", "63.5/6.33", "57.4/5.6", "292/100", "223/100", "0.398*", "0.379*", "1.254", "1.04"], ["Ricinus communis", "4705", "tr|B9RSN1|B9RSN", "70.46/6.6", "59.56/ 6.08", "362/100", "238/100", "0.917", "0.77", "0.692", "0.854"], ["Ricinus communis", "5701", "tr|B9SUJ3|B9SUJ", "69.96/6.8", "60.64/5.97", "157/100", "135/100", "0.161*", "0.509", "0.462", "1.138"], ["PROTEIN DEGRADATION"], ["Proteasome subunit beta type", "", "", "", "", "", "", "", "", "", ""], ["Glycine max", "2004", "tr|C6SVE5|C6SVE", "18.43/6.2", "25.17/5.3", "651/100", "592/100", "1.363", "0.671", "1.456*", "1.013"], ["Ricinus communis", "5004", "tr|B9SJ80|B9SJ8", "20.5/6.92", "30.6/7.6", "58/90.457", "47/99.745", "1.58*", "1.167", "1.216", "1.133"], ["Picea sitchensis", "7002", "tr|A9NZ27|A9NZ2", "19.97/7.4", "29.59/5.58", "224/100", "203/100", "1.281", "1.723*", "0.903", "0.951"], ["Xaa-Pro aminopeptidase", "", "", "", "", "", "", "", "", "", ""], ["Solanum lycopersicum", "3803", "tr|Q93X46|Q93X4", "79.52/6.4", "73.45/5.98", "88/99.99", "81/100", "1.58", "1.776*", "1.341", "0.923"], ["Mitochondrial processing peptidase", "", "", "", "", "", "", "", "", "", ""], ["Cucumis melo", "3607", "tr|Q9AXQ2|Q9AXQ", "62.57/6.5", "58.9/6.56", "656/100", "575/100", "1.25", "0.703*", "1.22*", "0.894"], ["Leucine aminopeptidase", "", "", "", "", "", "", "", "", "", ""], ["Medicago truncatula", "2603", "tr|G7JGP9|G7JGP", "58.61/6.1", "59.86/7.56", "292/100", "220/100", "0.577", "0.252*", "0.363*", "1.152"], ["26S protease regulatory subunit 6B", "", "", "", "", "", "", "", "", "", ""], ["M. truncatula", "1402", "tr|G7IV48|G7IV4", "51.86/5.9", "46.58/5.4", "540/100", "335/100", "0.786", "0.552*", "0.673*", "1.322*"], ["Ubiquitin-activating enzyme E1", "", "", "", "", "", "", "", "", "", ""], ["Ric.communis", "1901", "tr|B9SKZ1|B9SKZ", "117.4/5.8", "123.59/5.0", "87/99.988", "67/99.997", "2.059*", "0.758*", "0", "2.624*"], ["STRESS RESPONSE"], ["Aldo/keto reductase", "", "", "", "", "", "", "", "", "", ""], ["Manihot esculenta", "0203", "tr|Q52QX9|Q52QX", "35.02/5.6", "", "232/100", "210/100", "4.2*", "1.116", "2.516*", "1.422"], ["", "3205", "tr|Q52QX9|Q52QX", "38.15/6.3", "38.03/6.38", "325/100", "246/100", "2.025*", "0.785", "2.41*", "0.738"], ["", "4201", "tr|Q52QX9|Q52QX", "38.37/6.51", "", "327/100", "296/100", "0.341*", "0.178*", "1.203", "1.444"], ["Alcohol dehydrogenase", "", "", "", "", "", "", "", "", "", ""], ["Pyrus communis", "6302", "tr|G0Z9K2|G0Z9K", "41.76/6.9", "42.08/6.51", "611/100", "545/100", "0.119*", "1.149", "0.091", "0.889"], ["Short-chain dehydrogenase / reductase (SDR) family protein", "", "", "", "", "", "", "", "", "", ""], ["Solanum lycopers.", "0103", "tr|K4AZG5|K4AZG", "25.77/5.4", "35.46/5.39", "82/99.95", "78/100", "1.066", "0.323*", "1.185", "1.675*"], ["Aldehyde dehydrogenase", "", "", "", "", "", "", "", "", "", ""], ["Vitis vinifera", "6602", "tr|G9HQG0|G9HQG", "60.16/6.98", "52.53/6.18", "77/99.86", "63/99.993", "0.464*", "1.572*", "0.668", "1.039"], ["Peroxidase", "", "", "", "", "", "", "", "", "", ""], ["Linum usitatissimum", "0507", "tr|Q43782|Q4378", "48.17/5.4", "38.63/8.07", "77/99.865", "68/99.997", "0.332*", "0.406*", "3.295*", "0.96"], ["Stem-specific protein TSJT1", "", "", "", "", "", "", "", "", "", ""], ["Ricinus Communis", "0005", "tr|B9RTW0|B9RTW", "20.5/5.54", "25.5/5.56", "77/99.87", "70/99.998", "0.189*", "0.451*", "0.906", "1.298"], ["Hypersensitive induced response protein 3", "", "", "", "", "", "", "", "", "", ""], ["Triticum aestivum", "0108", "tr|B6D9L4|B6D9L", "24.68/5.67", "31.8/5.68", "231/100", "202/100", "0.395*", "1.238", "2.499*", "0.949"], ["Al induced protein", "", "", "", "", "", "", "", "", "", ""], ["Arabidopsis thaliana", "2105", "tr|Q9LIL3|Q9LIL", "22.29/5.96", "27.5/5.84", "94/99.997", "85/100", "0.179*", "0.837", "0.755", "0.305*"], ["CELL MOTILITY"], ["Actin 2", "", "", "", "", "", "", "", "", "", ""], ["Gossypium hirsutum", "0404", "tr|B8YPL4|B8YPL", "45.11/5.7", "41.94/5.38", "787/100", "597/100", "1.552", "1.01", "1.804*", "1.052"], ["Annona cherimola", "0703", "tr|H9A1W7|H9A1W", "65.5/5.51", "41.85/5.31", "788/100", "562/100", "0", "0.411", "0", "2.661"], ["PHOTOSYNTHESIS"], ["PsbP domain-containing protein", "", "", "", "", "", "", "", "", "", ""], ["M. truncatula", "0113", "tr|G7J6G5|G7J6G", "26.71/5.3", "27.95/6.92", "62/95.93", "55/99.96", "0.514", "0.056*", "0.889", "3.077"], ["Oxygen-evolving enhancer protein", "", "", "", "", "", "", "", "", "", ""], ["Populus euphratica", "0109", "sp|P84989|PSBO_", "24.86/5.5", "10.6/5.36", "423/100", "361/100", "0", "1.935", "5.33*", "0.605"], ["Rubisco LS", "", "", "", "", "", "", "", "", "", ""], ["Noronhia emarginata", "3706", "tr|Q06QN8|Q06QN", "66.65/6.4", "53.05/6.22", "197/100", "101/100", "0.354*", "0.727", "0", "0.825"]], "row_count": 153, "column_count": 11, "numeric_cells": 726, "header_rows": 2, "locator": "section[12]/table-wrap[1]#T3"}}], "gaps": ["asset:data:geo:PXD002484 not downloaded", "asset:data:geo:PXD002484 licence not read"]}, "analysis": {"state": "complete", "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": 1.0, "band": "verbatim", "quote": "Data were statistically analyzed by ANOVA using the following settings: error model max (average, actual), 0.01 proportions of highest variance values to be removed before variance averaging, 10° of freedom for the Bayesian error model, 0.05 FDR threshold, and zero permutations."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["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": ["PXD002484"], "resolved_accessions": ["PXD002484"], "statements": ["Data are available with identifier PXD002484."], "basis": "The paper names PXD002484 in ProteomeXchange repository 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:26322068", "data:geo:PXD002484", "asset:table:pmid:26322068:1", "asset:table:pmid:26322068:2", "asset:table:pmid:26322068:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD002484"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": null, "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 0, "usage": {}}, "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:26322068", "type": "paper", "label": "pmid:26322068"}, {"id": "source:pmid:26322068", "type": "manuscript", "label": "PMID 26322068 full text"}, {"id": "data:geo:PXD002484", "type": "dataset", "label": "GEO PXD002484"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26322068", "type": "paper", "label": "pmid:26322068"}, {"id": "source:pmid:26322068", "type": "manuscript", "label": "PMID 26322068 full text"}, {"id": "data:geo:PXD002484", "type": "dataset", "label": "GEO PXD002484"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26322068", "type": "extraction", "used": ["source:pmid:26322068"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD002484", "type": "accession_resolution", "used": ["data:geo:PXD002484"], "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:26322068", "parent_hash": "sha256:61c317c3acf12bfde97ebdb633c43590545b91571c831717ecd935fc8139136f", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD002484 licence not read", "asset:data:geo:PXD002484 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": 1.0, "evidence": ["Data were statistically analyzed by ANOVA using the following settings: error model max (average, actual), 0.01 proportions of highest variance values to be removed before variance averaging, 10° of freedom for the Bayesian error model, 0.05 FDR threshold, and zero permutations."], "order_basis": "analysis_only", "id": "assay:1"}]}