{"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":["4565"],"full_dataset_link":["https://pax-db.org/dataset/4565/3803621201"],"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":["Tritrophic interactions involving a biocontrol agent, a pathogen, and a plant have been analyzed predominantly from the perspective of the biocontrol agent. To explore the adaptive strategies of wheat in response to beneficial, pathogenic, and combined microorganisms, we performed the first comprehensive transcriptomic, proteomic, and biochemical analysis in wheat roots after exposure to <i>Bacillus velezensis</i> CC09, <i>Gaeumannomyces graminis</i> var. <i>tritici</i>, and their combined colonization, respectively. The transcriptional or translational programming of wheat roots inoculated with beneficial <i>B. velezensis</i> showed mild alterations compared with that of pathogenic <i>G. graminis</i> var. <i>tritici</i>. However, the combination of <i>B. velezensis</i> and <i>G. graminis</i> var. <i>tritici</i> activated a larger transcriptional or translational program than for each single microorganism, although the gene expression pattern was similar to that of individual infection by <i>G. graminis</i> var. <i>tritici</i>, suggesting a prioritization of defense against <i>G. graminis</i> var. <i>tritici</i> infection. Surprisingly, pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity made wheat pretreated with <i>B. velezensis</i> more sensitive to subsequent <i>G. graminis</i> var. <i>tritici</i> infection. Additionally, <i>B. velezensis</i> triggered a salicylic acid (SA)-dependent mode of induced systemic resistance that resembles pathogen-induced systemic acquired resistance. Wheat plants mainly depend on SA-mediated resistance, and not that mediated by jasmonic acid (JA), against the necrotrophic pathogen <i>G. graminis</i> var. <i>tritici.</i> Moreover, SA-JA interactions resulted in antagonistic effects regardless of the type of microorganisms in wheat. Further enhancement of SA-dependent defense responses such as lignification to the combined infection was shown to reduce the level of induced JA-dependent defense against subsequent infection with <i>G. graminis</i> var. <i>tritici</i>. Altogether, our results demonstrate how the hexaploid monocot wheat responds to beneficial or pathogenic microorganisms and prolongs the onset of take-all disease through modulation of cell reprogramming and signaling events."],"pubmed_title":["A Comparative Transcriptomic and Proteomic Analysis of Hexaploid Wheat's Responses to Colonization by <i>Bacillus velezensis</i> and <i>Gaeumannomyces graminis</i>, Both Separately and Combined."],"pubmed_authors":["Kang Xingxing X, Wang Lanhua L, Guo Yu Y, Ul Arifeen Muhammad Zain MZ, Cai Xunchao X, Xue Yarong Y, Bu Yuanqin Y, Wang Gang G, Liu Changhong C"],"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":["sequence, primary structure of sequence macromolecule."],"pubmed_title_synonyms":["Triticum durum, Ophiobolus graminis, Bacillus velesensis, Durum, Triticum vulgare, Triticum aestivum8, Triticum spelta, Triticum sativum, Triticum aestivam, Bacillus methylotrophicus, Triticum turgidum subsp. durum, Triticum aestivum subsp. aestivum, wheat, Rhaphidophora graminis., Tricum aestivum, common wheat, Bacillus velezensis, Bacillus amyloliquifaciens, bread wheat, Durum Wheats, Gaeumannomyces graminis var. graminis, Canadian hard winter wheat, proteomic analysis, Durum Wheat, Triticum turgidum, Bacillus oryzicola, Bacillus methylotrophicus Madhaiyan et al. 2010, Ophiochaeta graminis, Bacillus amyloliquefaciens subsp. plantarum, Wheat, Triticum aestivum, Bacillus methylotrophicus subsp. plantarum"],"name_synonyms":["all, sequence, primary structure of sequence macromolecule., aerial root (narrow), root, GRO:0005338, climbing root (narrow)"],"pubmed_abstract_synonyms":["Resistances, determination, Pflanze, Infestations and Infections, A4, sci, 2 Hydroxybenzoic Acid, viridiplantae, dmTAF[[II]]230, diseases, HOW, How, diseases and disorders, l(3)j5D5, Wheat, 2R)-3-oxo-2-(pent-2Z-enyl)-cyclopentaneacetic acid, 24B, human disease, Gene Expressions, TFIID TAF250, cel, stru, Age of onset, plants, l(3)S053606, wheat, CG10293, Tricum aestivum, common wheat, allergic reaction, l(3)j5B5, (1R, defence response signalling pathway, signaling process, Systemic Acquired Resistance, Durum Wheat, Triticum turgidum, ortho Hydroxybenzoic Acid, Homo sapiens disease, Infections and Infestations, associated, single organism signaling, ortho-Hydroxybenzoic, 0904/17, dTAF[[II]]230, ETI triggered of host innate immune response, 2-Hydroxybenzoic Acid, Triticum vulgare, land plants, TAF200, Bacillus methylotrophicus, effector-triggered induction of host innate immune response, Triticum turgidum subsp. durum, salicylic acid-dependent systemic resistance, TAFII-250, TAF250/230, results, Bacillus velezensis, 2-carboxyphenol, Programs, o-Hydroxybenzoic acid, TAFII250, <new synonym>, SZ1, 2R)-3-oxo-2-(2Z)-2-penten-ylcyclopentanacetic acid, Diseases, o-hydroxybenzoic acid, Salicylic, Bacillus methylotrophicus subsp. plantarum, activation of hypersensitive response, Acid, positive regulation by symbiont of host resistance gene-dependent defense response, Ophiobolus graminis, Bacillus velesensis, Rhaphidophora graminis, 2-{(1R, Triticum sativum, Plant, Jasmonate, Infection and Infestation, CG17603, TAF[[II]], activation of HR, avirulence protein, disease, higher plants, DMDA, Taf250, SR3-5, anon-EST:Liang-2.39, Ophiochaeta graminis, defence response signaling pathway, TAF230, Triticum aestivum, Induced, other disease, d230, biological signaling, P62, defense response signaling pathway, Gene, dTAFII250, (-)-Jasmonic acid, Triticum aestivum subsp. aestivum, EfW1, TYPE, DAGA4, dmTAF1, sensitive, Taf230, resistance, disease or disorder, MAM, SCG3, resistance gene-independent, sensitivity, Aggravating interaction, o-Hydroxybenzoic, TAF250, plantae, defense response signalling pathway, Taf200, jasmonate, dTAF[[II]]250, pattern, l(3)s2612, distribution, cell, Triticum aestivum8, Triticum spelta, o Hydroxybenzoic Acid, 7-epi-jasmonic acid, Triticum aestivam, effector-triggered immune signaling, o-Hydroxybenzoic Acid, Taf1p, 2R)-3-oxo-2-[(Z)-pent-2-enyl]cyclopentyl}acetate, Expressions, clinical infection, non-neoplastic, induction of effector-triggered immunity (ETI), dTAF250, Infestation and Infection, bread wheat, Gaeumannomyces graminis var. graminis, ortho-Hydroxybenzoic Acid, Induced Systemic, DmelCG10293, resistance gene-dependent, disorder, Induced Systemic Resistance, Expression, TAF, signalling., Triticum durum, TAF[[II]]250, Induced Systemic Resistances, clone 2.39, necrotrophic effector, disorders, 2-Hydroxybenzoic, l(3)84Ab, medical condition, BG:DS00004.13, qkr, l(3)S090417, Cell, LGMD2C, dTAF230, Bacillus amyloliquifaciens, effector-triggered induction of plant hypersensitive response by symbiont, p230, KH93F, Canadian hard winter wheat, chemical analysis, Infection, Resistance, TAF[[II]]250/230, condition, TFIID, Bacillus methylotrophicus Madhaiyan et al. 2010, Systemic Resistance, Bacillus amyloliquefaciens subsp. plantarum, effector-triggered necrosis, who, Taf[[II]]250, TAF[[II]]230, DMDA1, Durum, Systemic Resistances, 3-oxo-2-(2-pentenyl)cyclopentaneacetic acid, 2-HYDROXYBENZOIC ACID, (-)-jasmonic acid, TAF[II]250, Who/How, Age symptoms begin, o-carboxyphenol, Durum Wheats, DmelCG17603, signalling process, SCARMD2, qkr[93F], Bacillus oryzicola, assay, ETI-triggered of host innate immune response, TAF1"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Taestivum - Root, sequence+intensity from multiple files (Kangetal,molplantmicrobeinteract.2019)","description":"abundance based on sequence+intensity from multiple files, Interaction consistency score: 11.4, Coverage: 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