{"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":["2711"],"full_dataset_link":["https://pax-db.org/dataset/2711/4285583629"],"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":["The citrus industry is facing an unprecedented challenge from Huanglongbing (HLB). All cultivars can be affected by the HLB-associated bacterium 'Candidatus Liberibacter asiaticus' (CLas) and there is no known resistance. Insight into HLB pathogenesis is urgently needed in order to develop effective management strategies. Here, we use Sec-delivered effector 1 (SDE1), which is conserved in all CLas isolates, as a molecular probe to understand CLas virulence. We show that SDE1 directly interacts with citrus papain-like cysteine proteases (PLCPs) and inhibits protease activity. PLCPs are defense-inducible and exhibit increased protein accumulation in CLas-infected trees, suggesting a role in citrus defense responses. We analyzed PLCP activity in field samples, revealing specific members that increase in abundance but remain unchanged in activity during infection. SDE1-expressing transgenic citrus also exhibit reduced PLCP activity. These data demonstrate that SDE1 inhibits citrus PLCPs, which are immune-related proteases that enhance defense responses in plants."],"pubmed_title":["An effector from the Huanglongbing-associated pathogen targets citrus proteases."],"pubmed_authors":["Clark Kelley K, Franco Jessica Yvette JY, Schwizer Simon S, Pang Zhiqian Z, Hawara Eva E, Liebrand Thomas W H TWH, Pagliaccia Deborah D, Zeng Liping L, Gurung Fatta B FB, Wang Pengcheng P, Shi Jinxia J, Wang Yinsheng Y, Ancona Veronica V, van der Hoorn Renier A L RAL, Wang Nian N, Coaker Gitta G, Ma Wenbo W"],"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"],"pubmed_title_synonyms":["Seville Orange Tree, Citrus bergamias, Pummelo Tree, Bitter Orange, Sour Orange., Citrus medica, Bitter, Mandarin Orange Trees, medicas, Lemon, Orange Tree, Seville, Citrus hystrix, aurantium, Pummelo Trees, bergamia, Tree, Mandarin Orange, Trees, Sour Orange, Mandarin Orange Tree, Citron, Tangerine Trees, Kaffir Lime, Pomelo Trees, Citrus medicas, Sour, reticulata, Citrus reticulata, Sour Orange Trees, Lemon Tree, Seville Orange, Pummelo, Lime, Citrus limon, maxima, Citrus maxima, hystrices, Mandarin, Pomelo Tree, Kaffir, Citrus aurantiums, Orange Trees, Citrus bergamia, Bitter Orange Trees, Fruit, Pomelo, Lemon Trees, Citron Tree, Citrus reticulatas, Citrus, Citrus grandis, Citrus grandi, Citron Trees, Tangerine Tree, Tangerine, associated, Seville Orange Trees, Citrus hystrices, Citrus Fruit, Bitter Orange Tree, Sour Orange Tree, Citrus aurantium"],"name_synonyms":["exact)., exact), hoja (Spanish, 葉 (Japanese"],"pubmed_abstract_synonyms":["Pummelo Tree, Sectors, Bitter Orange, land plants., Activity, regulation by symbiont of host system process, Tertiary Sectors, Pummelo Trees, positive regulation by symbiont of host non-apoptotic programmed cell death, Infestations and Infections, Gene, Protease, protein, protein-containing complex, infectivity, supernumerary, Mandarin Orange, Liberibacter asiaticus, Candidatus Liberobacter asiaticus, protein polypeptide chains, organ field, Mandarin Orange Tree, polypeptide chain, reduced, induction by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction, Roles, SILENCING DEFECTIVE 1, resistance, SEC, Gene Products, Citron, pathogenesis, Concepts, Cysteine Proteinases, field, Proteases, tiny, protein aggregate, acting on D-amino acid peptides, Citrus medicas, Sour, Industries, reticulata, T6K12_14, induction of non-apoptotic programmed cell death by other organism, viral infection, increased, modification by symbiont of host biological process, Sour Orange Trees, stimulation by symbiont of host programmed cell death, Seville Orange, developmental field, Selb, sec, hypoplasia, maxima, proteins, plants, causes, clinical infection, Proteinases, peptide hydrolase activity, Citrus bergamia, Infestation and Infection, SUPPRESSOR OF GENE SILENCING 2, Pomelo, acting on L-amino acid peptides, Role Concepts, causality, Citrus, Citrus grandis, Citrus grandi, TG, Citron Trees, acting on peptide bonds, Infections and Infestations, hydrolase, associated, Seville Orange Trees, Citrus hystrices, Citrus Fruit, Citrus aurantium, small, Seville Orange Tree, Citrus bergamias, protease activity, data, Proteinase, disruption by symbiont of host cell, activation by organism of non-apoptotic programmed cell death in other organism, Citrus medica, Bitter, hemolysin activity, Mandarin Orange Trees, medicas, protein complex, Lemon, Orange Tree, Seville, Citrus hystrix, aurantium, Proteins, Cysteine Proteinase, bergamia, future organ, Tree, Trees, Sour Orange, Concept, Tertiary, secret agent, Role Concept, native protein, natural protein, peptidase activity, Protein, modulation by symbiont of host system process, Pathogenicity, Role, Infection, Cysteine Protease, SGS2, Tangerine Trees, Kaffir Lime, Pomelo Trees, SDE1, HLB, T6K12.14, Cysteine, Citrus reticulata, Exhibit, Lemon Tree, underdeveloped, increased number, Pummelo, Lime, Citrus limon, Plant, Tromasin, Infection and Infestation, Citrus maxima, hystrices, Mandarin, Pomelo Tree, induction by organism of programmed cell death in other organism during symbiotic interaction, Kaffir, Citrus aurantiums, modification by symbiont of host morphology or physiology, Orange Trees, Protein Gene Products, Bitter Orange Trees, present in greater numbers in organism, Gene Proteins, Fruit, higher plants, Sector, proteinase activity, Lemon Trees, Citron Tree, Citrus reticulatas, activation by symbiont of host programmed cell death, RNA-dependent RNA polymerase 6, Tertiary Sector, virulence, Tangerine Tree, Tangerine, General activity, Bitter Orange Tree, Sour Orange Tree, accessory"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Csinensis - Leaf, iBAQ (Clarketal,natcommun2018)","description":"abundance based on iBAQ, Interaction consistency score: 7.2, Coverage: 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