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pmid:25216269
Proteomic evidences for rex regulation of metabolism in toxin-producing Bacillus cereus ATCC 14579.
Sabrina Laouami · Géremy Clair · Jean Armengaud · Catherine Duport
PloS one · 2014 doi:10.1371/journal.pone.0107354
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Complete file
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The B. cereus genome comprises a gene encoding a protein with high similarities to the redox regulator, Rex, which is a central regulator of anaerobic metabolism in Bacillus subtilis and other Gram-positive bacteria. Here, we showed that B. cereus rex is monocistronic and down-regulated in the absence of oxygen. The protein encoded by rex is an authentic Rex transcriptional factor since its DNA binding activity depends on the NADH/NAD+ ratio. Rex deletion compromised the ability of B. cereus to cope with external oxidative stress under anaerobiosis while increasing B. cereus resistance against such stress under aerobiosis. The deletion of rex affects anaerobic fermentative and aerobic respiratory metabolism of B. cereus by decreasing and increasing, respectively, the carbon flux through the NADH-recycling lactate pathway. We compared both the cellular proteome and exoproteome of the wild-type and Δrex cells using a high throughput shotgun label-free quantitation approach and identified proteins that are under control of Rex-mediated regulation. Proteomics data have been deposited to the ProteomeXchange with identifier PXD000886. The data suggest that Rex regulates both the cross-talk between metabolic pathways that produce NADH and NADPH and toxinogenesis, especially in oxic conditions.", "claims": [{"id": "claim-method", "statement": "MS/MS spectral counts were compared with the TFold method using the PatternLab software program 2.0.0.13 [33] using a p-value cut-off set at 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25216269", "locator": "sections[10] \"Proteomic sample preparation and nanoLC-MS/MS analysis of tryptic peptides\" paragraph 2", "quote": "MS/MS spectral counts were compared with the TFold method using the PatternLab software program 2.0.0.13 [33] using a p-value cut-off set at 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The authors confirm that all data underlying the findings are fully available without restriction. Our MS/MS data are deposited on the PRIDE repository database http://www.ebi.ac.uk/pride/; Username: reviewer73547@ebi.ac.uk; Password: 0EbXtIq9.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25216269", "locator": "sections[33] \"Data Availability\" paragraph 2", "quote": "The authors confirm that all data underlying the findings are fully available without restriction. 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"section[14]/table-wrap[1]#pone-0107354-t001", "version": null, "note": "Results from controlled batch cultures of Δrex mutant and its parent strain, B. cereus ATCC 14579a.", "structure": {"pmcid": "PMC4162614", "section_index": 14, "section_title": "Rex regulates glucose catabolism in B. cereus", "row_count": 15, "column_count": 5}, "table": {"label": "Table 1", "caption": "Results from controlled batch cultures of Δrex mutant and its parent strain, B. cereus ATCC 14579a.", "rows": [["", "Anaerobic fermentative growth", "Aerobic respiratory growth"], ["", "WTb", "Δrex", "WTb", "Δrex"], ["Maximal specific growth rate (µmax) (h−1)", "0.84±0.04", "0.90±0.02*", "1.22±0.11", "1.41±0.04*"], ["Final biomass (g.liter−1)", "0.78±0.01", "0.83±0.06", "2.38±0.12", "2.31±0.12"], ["Yglucose (g of cells. mol of glucose−1)", "26±1", "28±1", "79±1", "77±1"], ["Maximal specific glucose consumption(mmol.g−1.h−1)", "32±2", "32±2", "15±1", "18±2"], ["Yields of end products (mol.mol glucose−1)c", "", "", 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"available", "identifier": "section[24]/table-wrap[1]#pone-0107354-t002", "version": null, "note": "Cellular abundance level changes of cell membrane, transport, stress response, transcriptional regulation, virulence and phage-related proteins in Δrex mutant relative to wild-type under anaerobiosis and aerobiosis.", "structure": {"pmcid": "PMC4162614", "section_index": 24, "section_title": "(iii) Impact of Rex on other relevant cellular pathways", "row_count": 59, "column_count": 8}, "table": {"label": "Table 2", "caption": "Cellular abundance level changes of cell membrane, transport, stress response, transcriptional regulation, virulence and phage-related proteins in Δrex mutant relative to wild-type under anaerobiosis and aerobiosis.", "rows": [["", "", "", "", "Abundance level change and significance"], ["", "", "", "", "Anaerobiosis", "Aerobiosis"], ["Accession no (NP)", "Proteinname", "Gene number", "Functionnal annotation", "log2(fold-change)a", "p-value", "log2(fold-change)", 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"BC_0874", "Arginine ABC transporter ATP-binding protein", "−0,396", "0,349", "−1,218", "0,024"], ["NP_832817.1", "CutC", "BC_3071", "Copper tansport", "0,903", "0,007", "−0,358", "0,341"], ["NP_830432.1", "-", "BC_0615", "Di-/tripeptide transporter", "−0,837", "0,047", "0,422", "0,232"], ["NP_830429.1", "-", "BC_0612", "L-lactate permease", "0,748", "0,026", "−0,644", "0,261"], ["", "", "", "Stress response-related proteins", "", "", "", ""], ["NP_831381.1", "-", "BC_1603", "Cold shock protein", "−1,120", "0,037", "−0,474", "0,277"], ["NP_830286.1", "TelA", "BC_0447", "Tellurite resistance protein", "0,084", "0,432", "0,840", "0,008"], ["NP_833675.1", "-", "BC_3956", "GTP-binding protein TypA/BipA", "0,310", "0,049", "0,043", "0,419"], ["NP_833972.1", "-", "BC_4258", "Hydroxyacylglutathione hydrolase", "0,824", "0,028", "−0,578", "0,213"], ["NP_833576.1", "-", "BC_3855", "Alkaline-shock protein", "0,014", "0,488", "0,740", "0,026"], ["NP_834187.1", "OhrA", "BC_4475", "Organic hydroxyperoxide protein A", "0,189", "0,340", "2,029", "0,015"], ["NP_829959.1", "Hsp15", "BC_0062", "Heat shock protein 15", "0,799", "0,082", "1,667", "0,007"], ["NP_830216.1", "AhpC", "BC_0377", "Alkyl hydroperoxide reductase C22", "−0,136", "0,426", "−1,029", "0,007"], ["NP_830941.1", "KatE", "BC_1155", "Catalase", "1,111", "0,014", "−0,074", "0,466"], ["NP_834345.1", "-", "BC_4639", "Thiol peroxidase", "−0,044", "0,463", "−0,737", "0,034"], ["", "", "", "Transcriptional Regulation", "", "", "", ""], ["NP_833888.1", "ArgR2", "BC_4174", "Arginine biosynthesis repressor", "1,511", "0,030", "1,269", "0,079"], ["NP_833771.1", "-", "BC_4053", "Transcriptional regulator, GntR family", "0,895", "0,019", "0,227", "0,399"], ["NP_833799.1", "-", "BC_4081", "MarR family transcriptional regulator", "0,029", "0,464", "1,903", "0,001"], ["NP_834861.1", "-", "BC_5197", "MarR family transcriptional regulator", "0,345", "0,029", "0,604", "0,123"], ["NP_832113.1", "-", "BC_2351", "MerR family transcriptional regulator", "0,485", "0,276", "1,170", "0,045"], ["NP_830532.1", "TenA", "BC_0742", "Transcriptional activator", "0,791", "0,046", "−0,621", "0,193"], ["NP_834137.1", "-", "BC_4425", "Transcriptional regulator", "0,632", "0,044", "−1,029", "0,051"], ["NP_831310.1", "-", "BC_1531", "Transcriptional regulatory protein", "−0,029", "0,471", "1,480", "0,004"], ["NP_831256.1", "ResD", "BC_1477", "Transcriptional regulatory protein", "0,356", "0,008", "−0,599", "0,119"], ["NP_830596.1", "-", "BC_0806", "BigG family transcription antiterminator", "0,485", "0,276", "1,922", "0,000"], ["", "", "", "Virulence-related proteins", "", "", "", ""], ["NP_834769.1", "HlyI", "BC_5101", "Hemolysin I", "−0,152", "0,438", "2,611", "0,001"], ["NP_832488.1", "Npr2", "BC_2735", "Bacillolysin", "−1,089", "0,193", "−2,120", "0,013"], ["NP_833332.1", "HhoA", "BC_3600", "Protease", "0,485", "0,098", "−1,690", "0,026"], ["NP_831147.1", "-", "BC_1366", "SSEB protein", "1,163", "0,036", "1,269", "0,055"], ["", "", "", "Phage-related proteins", "", "", "", ""], ["NP_831667.1", "-", "BC_1894", "Phage protein", "3,023", "0,014", "−1,358", "0,286"], ["NP_831632.1", "-", "BC_1859", "Phage protein", "2,526", "0,039", "−0,644", "0,261"], ["NP_831635.1", "-", "BC_1862", "Phage protein", "1,714", "0,027", "−0,761", "0,302"], ["NP_831673.1", "-", "BC_1901", "Phage protein", "1,727", "0,012", "−1,889", "0,205"], ["NP_831676.1", "-", "BC_1904", "Phage protein", "1,975", "0,038", "−0,515", "0,367"]], "row_count": 59, "column_count": 8, "numeric_cells": 303, "header_rows": 3, "locator": "section[24]/table-wrap[1]#pone-0107354-t002"}}, {"id": "asset:table:pmid:25216269:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ee151df068088bd167cfbe8a3c4c50e9d7a1f592671429e6954a837157b66620", "bytes": 1533, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[26]/table-wrap[1]#pone-0107354-t003", "version": null, "note": "Changes in mRNA and protein abundance of toxins and putative toxins induced by Δrex mutation under anaerobic and aerobic growth conditions#.", "structure": {"pmcid": "PMC4162614", "section_index": 26, "section_title": "(i) Focus on toxin-related proteins", "row_count": 18, "column_count": 8}, "table": {"label": "Table 3", "caption": "Changes in mRNA and protein abundance of toxins and putative toxins induced by Δrex mutation under anaerobic and aerobic growth conditions#.", "rows": [["Protein name", "", "Log2(fold-change) in B. cereus Δrex vs wild-typea"], ["", "Gene", "Anaerobiosis", "Aerobiosis"], ["", "", "mRNA", "Protein", "mRNA", "Protein"], ["", "", "", "cellular", "extracellular", "s", "cellular", "extracellular"], ["CytK", "BC_1110", "NS", "NSa", "NS", "NS", "NS", "1,72 ( p = 0.001)"], ["EntA", "BC_5239", "NS", "NS", "0,29 ( p = 0.035)", "NS", "NS", "0,53 ( p = 0.001)"], ["EntB", "BC_2952", "NS", "NS", "NS", "NS", "NS", "NS"], ["EntC", "BC_0813", "NS", "NS", "0,37 ( p = 0.042)", "−1,29 (p<0.05)", "NS", "0,75 ( p = 0.002)"], ["EntFM", "BC_1953", "NS", "NS", "NS", "−1,49 (p<0.05)", "NS", "0,68 ( p = 0.000)"], ["HblB", "BC_3102", "NS", "NS", "NS", "NS", "NS", "1,38 ( p = 0.001)"], ["HblB'", "BC_3101", "NS", "NS", "NS", "NS", "NS", "1,28 ( p = 0.002)"], ["HblL1", "BC_3103", "NS", "NS", "0,32 ( p = 0.039)", "NS", "NS", "1,09 ( p = 0.006)"], ["HblL2", "BC_3104", "NS", "NS", "NS", "NS", "NS", "1,29 ( p = 0.000)"], ["HlyI", "BC_5101", "NS", "NS", "NS", "NS", "2,61( p = 0.001)", "NS"], ["HlyII", "BC_3523", "NS", "NS", "NS", "NS", "NS", "2,45 ( p = 0.000)"], ["NheA", "BC_1809", "NS", "NS", "0,47 ( p = 0.003)", "NS", "NS", "1,35 ( p = 0.002)"], ["NheB", "BC_1810", "NS", "NS", "0,42 ( p = 0.008)", "NS", "NS", "1,34 ( p = 0.001)"], ["NheC", "BC_1811", "NS", "NS", "0,83 ( p = 0.001)", "NS", "NS", "1,70 ( p = 0.001)"]], "row_count": 18, "column_count": 8, "numeric_cells": 35, "header_rows": 4, "locator": "section[26]/table-wrap[1]#pone-0107354-t003"}}, {"id": "asset:table:pmid:25216269:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5a344c45944a2d9a7f557431e73f7dc239a66b3eed572277f57e63e4602ccad8", "bytes": 8358, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[27]/table-wrap[1]#pone-0107354-t004", "version": null, "note": "Changes in protein abundances in Δrex exoproteome compared to wild-type exoproteome under anaerobiosis and aerobiosis.", "structure": {"pmcid": "PMC4162614", "section_index": 27, "section_title": "(ii) Other predicted extracellular proteins", "row_count": 88, "column_count": 10}, "table": {"label": "Table 4", "caption": "Changes in protein abundances in Δrex exoproteome compared to wild-type exoproteome under anaerobiosis and aerobiosis.", "rows": [["", "", "", "", "", "", "Log2 fold-change and significancea"], ["Proteinname", "Gene", "Accession no. (NP)", "Functional annotation", "TM domain", "Export Signal peptide", "Anaerobiosis", "Aerobiosis"], ["", "", "", "", "", "", "log2-fold-change", "p-value", "log2-fold-change", "p-value"], ["Degradative enzymes and adhesins", "", "", "", "", "", ""], ["ColC", "BC_0556", "NP_830373", "Collagenase", "N", "Y", "0,4", "0,03", "1,9", "0,00"], ["NprB", "BC_5351", "NP_835012", "Bacillolysin", "N", "Y", "0,67", "0,00", "1,97", "0,00"], ["NprP2", "BC_2735", "NP_832488", "Bacillolysin", "N", "Y", "1,58", "0,00", "2,6", "0,01"], ["HhoA", "BC_3600", "NP_833332", "Protease", "N", "Y", "0,176", "0,241", "0,6", "0,03"], ["Tgc", "BC_1991", "NP_831760", "Putative murein endopeptidase", "N", "Y", "0,45", "0,01", "1,71", "0,00"], ["PlcB", "BC_0670", "NP_830483", "phospholipase C", "N", "Y", "0,6", "0,00", "2,25", "0,00"], ["PlcA", "BC_3761", "NP_833485", "Phosphatidylinositol phosphodiesterase", "N", "Y", "0,48", "0,02", "2,55", "0,00"], ["InhA2", "BC_0666", "NP_830479", "Immune inhibitor A precursor", "N", "Y", "1,59", "0,01", "3,43", "0,00"], ["PgdA", "BC_2929", "NP_832677", "Peptidoglycan deacetylase", "N", "Y", "0,585", "0,055", "0,87", "0,04"], ["Sph", "BC_0671", "NP_830484", "Sphingomyelin phosphodiesterase", "N", "Y", "0,82", "0,03", "2,82", "0,00"], ["Flagella components", "", "", "", "", "", ""], ["FlaA", "BC_1659", "NP_831436", "Flagellin", "N", "N", "0,516", "0,117", "0,6", "0,02"], ["FlgK", "BC_1636", "NP_831414", "Flagellar hook-associated protein", "N", "N", "0,96", "0,01", "1,04", "0,05"], ["FlgL", "BC_1637", "NP_831415", "Flagellar hook-associated protein", "N", "N", "0,78", "0,04", "1,28", "0,00"], ["FliD", "BC_1638", "NP_831416", "Flagellar capping protein", "N", "N", "0,526", "0,063", "1,22", "0,00"], ["FlgB", "BC_1641", "NP_831419", "Flagellar basal body rod protein", "N", "N", "0,111", "0,411", "0,9", "0,01"], ["Cell wall and membrane-related proteins", "", "", "", "", "", ""], ["FtsI", "BC_4270", "NP_833984", "Penicillin-binding protein", "Y", "N", "0,189", "0,145", "1,73", "0,02"], ["YvgJ1", "BC_2932", "NP_832680", "Phosphoglycerol transferase", "Y", "N", "−0,03", "0,462", "1,25", "0,03"], ["YvgJ2", "BC_5232", "NP_834895", "phosphoglycerol transferase", "Y", "N", "−0,03", "0,463", "0,71", "0,00"], ["CwlD", "BC_5196", "NP_834860", "N-acetylmuramoyl-L-alanine amidase", "N", "Y", "0,485", "0,022", "0,67", "0,00"], ["CwlB", "BC_0902", "NP_830688", "N-acetylmuramoyl-L-alanine amidase", "N", "Y", "1,091", "0,187", "−1,1", "0,04"], ["Metabolism", "", "", "", "", "", ""], ["Eno", "BC_5135", "NP_834803", "Phosphopyruvate hydratase", "N", "N", "−1,2", "0,01", "−0,12", "0,385"], ["PfkA", "BC_4600", "NP_834306", "6-Phosphofructokinase", "N", "N", "−0,9", "0,04", "−0,18", "0,377"], ["PykA", "BC_4599", "NP_834305", "Pyruvate kinase", "N", "N", "−0,15", "0,429", "−4,6", "0,01"], ["Pgi", "BC_4898", "NP_834571", "Glucose-6-phosphate isomerase", "N", "N", "−1", "0,04", "0,014", "0,493"], ["AtpA", "BC_3230", "NP_832971", "F0F1 ATP synthase subunit alpha", "N", "Y", "−0,03", "0,448", "1,75", "0,00"], ["GapA", "BC_5140", "NP_834805", "Glyceraldehyde-3-phosphate dehydrogenase", "N", "N", "−0,62", "0,144", "−2,9", "0,00"], ["PtA", "BC_5387", "NP_835048", "Phosphotransacetylase", "N", "N", "−1,6", "0,01", "−2,1", "0,03"], ["GapN", "BC_0868", "NP_830654", "NADP-dependent glyceraldehyde-3-phosphate dehydrogenase", "N", "N", "−3,6", "0,00", "−1,32", "0,054"], ["FbA", "BC_5335", "NP_834997", "Fructose-bisphosphate aldolase", "N", "N", "−0,76", "0,298", "−3,6", "0,03"], ["Hpr", "BC_4049", "NP_833767", "Phosphocarrier protein HPr", "N", "N", "−2,4", "0,03", "−1,18", "0,079"], ["Bdh", "BC_0868", "NP_830481", "(R,R)-butanediol dehydrogenase", "N", "N", "−3,32", "0,06", "−3,6", "0,02"], ["PtsA", "BC_4048", "NP_833766", "Phosphotransferase", "N", "N", "−2,12", "0,058", "−3,2", "0,00"], ["SfcA", "BC_4604", "NP_834310", "NAD-dependent malic enzyme", "N", "N", "−0,86", "0,187", "−1,6", "0,04"], ["GlmM", "BC_0188", "NP_830056", "Phosphoglucosamine mutase", "N", "N", "−1,32", "0,058", "−3,8", "0,00"], ["GdhA", "BC_4162", "NP_833877", "Leucine dehydrogenase", "N", "N", "−1,8", "0,04", "−2,4", "0,081"], ["-", "BC_4366", "NP_834078", "Cystathionine beta-lyase", "N", "N", "0,151", "0,447", "−2", "0,03"], ["AdsS", "BC_5468", "NP_835123", "Adenylosuccinate synthetase", "N", "N", "−1,8", "0,04", "−1,15", "0,202"], ["-", "BC_3799", "NP_833521", "Aspartate-semialdehyde dehydrogenase", "N", "N", "−2,56", "0,079", "−3,2", "0,01"], ["ThiG", "BC_0749", "NP_830539", "Thiazole synthase", "N", "N", "ND", "ND", "−2,2", "0,01"], ["-", "BC_0071", "NP_829966", "Phosphoribosyltransferase", "N", "N", "−0,23", "0,425", "−3,5", "0,00"], ["DeoD", "BC_1463", "NP_831242", "Purine nucleoside phosphorylase", "N", "N", "−2,6", "0,02", "−1,06", "0,185"], ["-", "BC_0015", "NP_829919", "Pyridoxine biosynthesis protein", "N", "N", "−1,8", "0,01", "−3,6", "0,00"], ["-", "BC_3981", "NP_833700", "tetrahydrodipicolinate -acetyltransferase", "N", "N", "ND", "ND", "−3,3", "0,00"], ["MoaB", "BC_4758", "NP_834462", "Molybdenum cofactor", "N", "N", "−0,94", "0,187", "−2,3", "0,02"], ["FrvB", "BC_4571", "NP_834277", "Deblocking aminopeptidase", "N", "N", "−3,2", "0,00", "−0,92", "0,215"], ["PepT", "BC_4143", "NP_833858", "Peptidase T", "N", "N", "−1,6", "0,04", "−1,94", "0,061"], ["Stress-related proteins", "", "", "", "", "", ""], ["AhpC", "BC_0377", "NP_830216", "Alkyl hydroperoxide reductase C22", "N", "N", "−0,94", "0,154", "−2,2", "0,00"], ["GrpE", "BC_4313", "NP_834025", "Chaperon", "N", "N", "−1,4", "0,04", "−0,38", "0,335"], ["GroEL", "BC_0295", "NP_830146", "Chaperon", "N", "N", "−0,69", "0,214", "−2,3", "0,01"], ["Dps2", "BC_5044", "NP_834714", "Non-specific DNA-binding protein", "N", "N", "−2,4", "0,00", "−1", "0,165"], ["Dps1", "BC_2011", "NP_831779", "Non-specific DNA-binding protein", "N", "N", "−1", "0,04", "0", "0,499"], ["Sod", "BC_5445", "NP_835106", "Superoxide dismutase [Mn]", "N", "N", "−2,4", "0,03", "−0,92", "0,226"], ["AhpF", "BC_0376", "NP_830215", "Alkyl hydroperoxide reductase subunit F", "N", "N", "ND", "ND", "−2,4", "0,02"], ["TerD", "BC_0443", "NP_830282", "tellurium resistance protein", "N", "N", "−2,7", "0,00", "−0,97", "0,064"], ["Translation", "", "", "", "", "", ""], ["RpsF", "BC_5476", "NP_835129", "30 S ribosomal protein S6", "N", "N", "−2,3", "0,01", "−2,32", "0,073"], ["RpsG", "BC_0126", "NP_830007", "30 S ribosomal protein S7", "N", "N", "0,566", "0,2", "−1,8", "0,01"], ["RpsH", "BC_0145", "NP_830025", "30 S ribosomal protein S8", "N", "N", "1,709", "0,059", "−1,8", "0,00"], ["RpsJ", "BC_0130", "NP_830010", "30 S ribosomal protein S10", "N", "N", "ND", "ND", "−2,7", "0,01"], ["RplJ", "BC_0119", "NP_830000", "50 S ribosomal protein L10", "N", "N", "−0,58", "0,16", "−4,3", "0,00"], ["RplK", "BC_5075", "NP_834743", "50 S ribosomal protein L11", "N", "N", "−0,94", "0,187", "−2,4", "0,02"], ["RplL", "BC_0120", "NP_830001", "50 S ribosomal protein L7/L12", "N", "N", "−1,7", "0,03", "−1,1", "0,03"], ["RpsT", "BC_4320", "NP_834032", "30 S ribosomal protein S20", "N", "N", "ND", "ND", "−2", "0,03"], ["RplX", "BC_0142", "NP_830022", "50 S ribosomal protein L24", "N", "N", "−2,2", "0,03", "−0,79", "0,154"], ["RpmD", "BC_0149", "NP_830029", "50 S ribosomal protein L30", "N", "N", "−1,03", "0,095", "−2,4", "0,02"], ["Frr", "BC_3822", "NP_833543", "Ribosome recycling factor", "N", "N", "−1,6", "0,04", "−0,23", "0,405"], ["RaiA", "BC_5190", "NP_834854", "SSU ribosomal protein S30P", "N", "N", "−2,3", "0,04", "−2,6", "0,02"], ["EftS", "BC_3824", "NP_833545", "Elongation factor Ts", "N", "N", "1,263", "0,204", "−3,1", "0,01"], ["Transcriptional Regulation", "", "", "", "", "", ""], ["AbrB", "BC_0042", "NP_829939", "Transcription state regulator", "N", "N", "−1,15", "0,082", "−3,3", "0,00"], ["CodY", "BC_3826", "NP_833547", "Transcriptional repressor", "N", "N", "ND", "ND", "−2,6", "0,02"], ["-", "BC_3728", "NP_833453", "DNA-binding protein HU", "N", "N", "−0,23", "0,422", "−2,5", "0,00"], ["Other", "", "", "", "", "", ""], ["-", "BC_1984", "NP_831667", "Phage protein", "N", "N", "3,113", "0,134", "4,77", "0,01"], ["-", "BC_1012", "NP_830798", "unknown", "N", "N", "−0,81", "0,291", "−3,5", "0,00"], ["-", "BC_5360", "NP_835021", "unknown", "Y", "Y", "0,299", "0,134", "2,38", "0,00"], ["-", "BC_0002", "NP_829890", "unknown", "N", "N", "−4,1", "0,00", "−3,1", "0,01"], ["-", "BC_2077", "NP_831845", "unknown", "N", "N", "−4,6", "0,00", "−0,01", "0,477"], ["-", "BC_4062", "NP_833780", "unknown", "Y", "N", "0,31", "0,363", "0,9", "0,01"], ["-", "BC_2705", "NP_832458", "unknown", "N", "N", "−1,89", "0,084", "−3,6", "0,00"]], "row_count": 88, "column_count": 10, "numeric_cells": 466, "header_rows": 3, "locator": "section[27]/table-wrap[1]#pone-0107354-t004"}}], "gaps": ["asset:data:geo:PXD000856 not downloaded", "asset:data:geo:PXD000856 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "MS/MS spectral counts were compared with the TFold method using the PatternLab software program 2.0.0.13 [33] using a p-value cut-off set at 0.05."}}], "targets": [], "gaps": ["method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["PXD000856", "DOI 10.6019/PXD000856"], "resolved_accessions": ["PXD000856"], "statements": ["The authors confirm that all data underlying the findings are fully available without restriction. Our MS/MS data are deposited on the PRIDE repository database http://www.ebi.ac.uk/pride/; Username: reviewer73547@ebi.ac.uk; Password: 0EbXtIq9."], "basis": "The paper names PXD000856 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. 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