{"database":"PAXDB","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["http://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Christian von Mering"],"species":["4113"],"full_dataset_link":["https://pax-db.org/dataset/4113/3769969026"],"submitter_email":["mering@imls.uzh.ch"],"submitter_affiliation":["University of Zurich"],"sample_protocol":[""],"repository":["PAXDB"],"data_protocol":["For the rescaling, the\ndatasets are first parsed or processed such that the data reflect\nproportional abundances of whole protein molecules\n(i.e. proportionality to counts of complete, individual protein\nmolecules, not to molecular weights, protein volumes, or digested\npeptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up\nto one million; this means the abundance of each protein of\ninterest is finally expressed in (parts per million,) relative to\nall other proteins in a sample. \nFor a given protein abundance dataset, we then compute\nthe absolute log abundance ratios of all pairs of proteins\nannotated to be functionally linked. The median of these absolute\nlog abundance ratios represents an indirect quality\nmetric: the closer it is to zero, the better (i.e. the more there\nis consistency between abundance values and functional annotations\nsuch as protein complexes or pathways). We then\ncompute a background expectation for this metric, by permuting\nthe abundance values in a given dataset randomly,\nand recomputing the median log abundance ratios. The permutation\nis repeated several times, yielding a distribution of\nmedians. The actually observed median is then expressed as a\nZ-score distance to the random distribution ofmedians—this\ndistance is termed the interaction consistency score."],"pubmed_abstract":["In order to get a better understanding of protein association during <i>Solanum tuberosum</i> (cv. Sarpo Mira)⁻<i>Phytophthora infestans</i> incompatible interaction, we investigated the proteome dynamics of cv. Sarpo Mira, after foliar application of zoospore suspension from <i>P. infestans</i> isolate, at three key time-points: zero hours post inoculation (hpi) (Control), 48 hpi (EI), and 120 hpi (LI); divided into early and late disease stages by the tandem mass tagging (TMT) method. A total of 1229 differentially-expressed proteins (DEPs) were identified in cv. Sarpo Mira in a pairwise comparison of the two disease stages, including commonly shared DEPs, specific DEPs in early and late disease stages, respectively. Over 80% of the changes in protein abundance were up-regulated in the early stages of infection, whereas more DEPs (61%) were down-regulated in the later disease stage. Expression patterns, functional category, and enrichment tests highlighted significant coordination and enrichment of cell wall-associated defense response proteins during the early stage of infection. The late stage was characterized by a cellular protein modification process, membrane protein complex formation, and cell death induction. These results, together with phenotypic observations, provide further insight into the molecular mechanism of <i>P. infestans</i> resistance in potatos."],"pubmed_title":["Quantitative Proteomics of Potato Leaves Infected with <i>Phytophthora infestans</i> Provides Insights into Coordinated and Altered Protein Expression during Early and Late Disease Stages."],"pubmed_authors":["Xiao Chunfang C, Gao Jianhua J, Zhang Yuanxue Y, Wang Zhen Z, Zhang Denghong D, Chen Qiaoling Q, Ye Xingzhi X, Xu Yi Y, Yang Guocai G, Yan Lei L, Cheng Qun Q, Chen Jiaji J, Shen Yanfen Y"],"data_synonyms":["Add, DmelCG43443, ADD, ADD-87, Hts-RC, data, AU023367, Data Set, protein complex, supply, Proteins, Ovhts, Gene, HtsRC, CG9325, protein, neutral molecular compounds, protein-containing complex, Dmel_CG9325, Xt, Peptide, 1B1, add, Polypeptides, anon-EST:Posey9, protein polypeptide chains, native protein, peptido, htsRC, GLI3-190, natural protein, polypeptide chain, Add-hts, Protein, CG43443, Gene Products, l(2)k14523, Dmel_CG34197, l(2)00634, median, Ovhts-RC, background, supply and distribution, protein aggregate, all_pairs, molecule, Bph, molecula, Random selection by shearing, oligonucleotide random primer, proportion, HTS-R1, HTS, Hts, molecules, peptides, l(2)k06121, adducin, GLI3FL, distribution, AI854843, proportionality, add-like, HTS-RC, rate, proteins, Molekuel, Pdn, sample population, introduction, Protein Gene Products, Gene Proteins, Adducin, RANDOM, 10^[-6], ppm, sample, supply., quotient, Peptid, peptidos, Polypeptide, Attention Deficit Hyperactivity Disorder, l(2)01103, EST D, CG34197, HtsF, ratio"],"description_synonyms":["IGO, 14.1, IGL1, VPREB2, AGM2, IGL5, IGVPB., IGLJ14.1, CD179b, IGLL"],"pubmed_title_synonyms":["other disease, Potatoes, tuberosum, Peptidomics, protein complex, Solanum tuberosum subsp. tuberosum, Proteins, Potato, disorders, Gene, protein, protein-containing complex, Phytophthora infestan, Fs(3)Sz11, protein polypeptide chains, potato late blight agent, native protein, natural protein, polypeptide chain, diseases, Solanum tuberosums, Protein, Botrytis infestans, Diseases, Gene Products, disease or disorder, potato late blight, condition, infestans, diseases and disorders, DmF2, tuberosums, protein aggregate, Fs(3)Hor, lod, potatoes, DmelCG2684, human disease, potato, proteins, NTef2, Lds, Solanum, Phytophthora, early, Protein Gene Products, non-neoplastic, Gene Proteins, disease, Solanum aracc-papa, Horka, CG2684, Fs(3)Horka, disorder, Homo sapiens disease, medical condition., potato late blight fungus"],"name_synonyms":["exact)., exact), hoja (Spanish, 葉 (Japanese"],"pubmed_abstract_synonyms":["other disease, type 1, tuberosum, Procedures, Effects, Solanum tuberosum subsp. tuberosum, developmental stage, FBN, Infestations and Infections, Gene, protein, protein-containing complex, Phytophthora infestan, dIKK-gamma, Long Term, prevention, 11, Readability, protein polypeptide chains, method, Techniques, potato late blight agent, 11E, polypeptide chain, diseases, ECTOL1, Method, macromolecular complex assembly, Associations, type I, DmIKK-gamma, method used in an experiment, Botrytis infestans, Gene Products, Studies, disease or disorder, diseases and disorders, DmF2, dmIKKgamma, Mir, MIR, protein aggregate, IKK[[gamma]], Fs(3)Hor, Effect, prevention and control, Technique, IKKg, WMS, KEY, Key, Walls, Miranda, HPI, lod, Cell Walls, DmelCG2684, human disease, protein modification, reference sample, accidental cell death., Longterm, proteins, potato, mir, Long-Term, NTef2, Phytophthora, clinical infection, non-neoplastic, OCTD, preventive measures, Study, 13-epoxyoctadeca-9, Infestation and Infection, IKK, hydroperoxide isomerase activity, Methodological Studies, Suspension, (9Z, 13-hydro-lyase activity, HYRPRO1, cellular protein-containing complex assembly, disorder, Homo sapiens disease, Long-Term Effect, stage, process resulting in protein modification, 14Z)-(13S)-hydroperoxyoctadeca-9, Infections and Infestations, necrosis, potato late blight fungus, GPHYSD2, cellular protein modification process, Long-Term Effects, thiol methyltransferase activity, Controlled, SGS, Potatoes, Controlling, preventive therapy, defense/immunity protein activity, protein complex, Proteins, Potato, disorders, Longterm Effect, total expressed protein, medical condition, Procedure, antimicrobial peptide activity, Cell, Fs(3)Sz11, ACMICD, CG12249, chaperone activity, IKKgamma, DmIKKgamma, TPSG1, S-adenosyl-L-methionine:thiol S-methyltransferase activity, native protein, natural protein, dIKK, Protein, Solanum tuberosums, Long Term Effects, Kenny, Diseases, Infection, defence response, potato late blight, condition, infestans, linoleate hydroperoxide isomerase, MFS1, DmelCG12249, tuberosums, Death, protein complex assembly, macromolecule complex assembly, WMS2, 14-trienoate 12, cellular macromolecule complex assembly, potatoes, Wall, hydroperoxide dehydratase activity, physiological defense response, Dmikkgamma, prophylaxis, Mira, IKK-gamma, protein complex formation, Infection and Infestation, MASS, Methodological, Understanding, CG16910, Lds, Solanum, Methodological Study, Longterm Effects, early, Protein Gene Products, 11-dienoate-forming], plan specification, Gene Proteins, linoleic acid hydroperoxide isomerase, disease, Solanum aracc-papa, DmelCG16910, control, Horka, SSKS, PRSS31, cellular protein complex assembly, MIRA, CG2684, hyperprolinemia, Fs(3)Horka, 13-hydro-lyase [(9Z)-(13S)-12, TMT, Proteomes"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Stuberosum - Leaf, SC (Xiaoetal,intjmolsci.2019)","description":"abundance based on Spectral counting, Interaction consistency score: 14.1, Coverage: 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