PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering121845https://pax-db.org/dataset/121845/3479534116mering@imls.uzh.chUniversity of ZurichPAXDBFor the rescaling, the datasets are first parsed or processed such that the data reflect proportional abundances of whole protein molecules (i.e. proportionality to counts of complete, individual protein molecules, not to molecular weights, protein volumes, or digested peptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up to one million; this means the abundance of each protein of interest is finally expressed in (parts per million,) relative to all other proteins in a sample. For a given protein abundance dataset, we then compute the absolute log abundance ratios of all pairs of proteins annotated to be functionally linked. The median of these absolute log abundance ratios represents an indirect quality metric: the closer it is to zero, the better (i.e. the more there is consistency between abundance values and functional annotations such as protein complexes or pathways). We then compute a background expectation for this metric, by permuting the abundance values in a given dataset randomly, and recomputing the median log abundance ratios. The permutation is repeated several times, yielding a distribution of medians. The actually observed median is then expressed as a Z-score distance to the random distribution ofmedians—this distance is termed the interaction consistency score.'Candidatus Liberibacter asiaticus' (CLas), the bacterial pathogen associated with citrus greening disease, is transmitted by Diaphorina citri, the Asian citrus psyllid. Interactions among D. citri and its microbial endosymbionts, including 'Candidatus Profftella armatura', are likely to impact transmission of CLas. We used quantitative mass spectrometry to compare the proteomes of CLas(+) and CLas(-) populations of D. citri, and found that proteins involved in polyketide biosynthesis by the endosymbiont Profftella were up-regulated in CLas(+) insects. Mass spectrometry analysis of the Profftella polyketide diaphorin in D. citri metabolite extracts revealed the presence of a novel diaphorin-related polyketide and the ratio of these two polyketides was changed in CLas(+) insects. Insect proteins differentially expressed between CLas(+) and CLas(-) D. citri included defense and immunity proteins, proteins involved in energy storage and utilization, and proteins involved in endocytosis, cellular adhesion, and cytoskeletal remodeling which are associated with microbial invasion of host cells. Insight into the metabolic interdependence between the insect vector, its endosymbionts, and the citrus greening pathogen reveals novel opportunities for control of this disease, which is currently having a devastating impact on citrus production worldwide.Metabolic Interplay between the Asian Citrus Psyllid and Its Profftella Symbiont: An Achilles' Heel of the Citrus Greening Insect Vector.Ramsey John S JS, Johnson Richard S RS, Hoki Jason S JS, Kruse Angela A, Mahoney Jaclyn J, Hilf Mark E ME, Hunter Wayne B WB, Hall David G DG, Schroeder Frank C FC, MacCoss Michael J MJ, Cilia Michelle MAdd, 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, ratiopolypeptide, peptide, Polypeptides, Peptid, peptidos, Polypeptide, peptido, peptides, Peptide, count.Seville Orange Tree, Citrus bergamias, Pummelo Tree, Bitter Orange, Profftella, Citrus medica, Bitter, Mandarin Orange Trees, medicas, Lemon, Orange Tree, Seville, Citrus hystrix, aurantium, Pummelo Trees, bergamia, Tree, Mandarin Orange, Asian citrus psyllid, Trees, Sour Orange, Mandarin Orange Tree, Citron, Insects, Tangerine Trees, Kaffir Lime, Sinus Tarsi, Sinus Tarsus, Pomelo Trees, Citrus medicas, Sour, reticulata, Citrus reticulata, Sour Orange Trees, Heels, 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, Seville Orange Trees, Insect., Citrus hystrices, Citrus Fruit, Bitter Orange Tree, Sour Orange Tree, Citrus aurantiumpolypeptide, peptide, Polypeptides, organism, multi-cellular organism, whole organism, peptido, peptides, body, Koerper, Peptid, peptidos, whole body, Polypeptide, animal, Peptide, count.other disease, Pummelo Tree, Bitter Orange, number, Pummelo Trees, secondary metabolites, Gene, Endocytoses, Spectrum Analyses, nonselective vesicle endocytosis, Ximpact, presence, Mandarin Orange, prevention, Asian citrus psyllid, Liberibacter asiaticus, Candidatus Liberobacter asiaticus, Ketides, entry into host via enzymatic degradation of host cuticle, primary metabolites, Mandarin Orange Tree, polyketide biosynthesis, diseases, insects, Atelocerata, Mass, Gene Products, Polyketide, Citron, disease or disorder, diseases and disorders, Analysis, prevention and control, Citrus medicas, Mass Spectroscopy, Sour, Mass Spectrum Analysis, reticulata, entry into host via a specialized structure during symbiotic interaction, Immune Processes, human disease, Immune Responses, Sour Orange Trees, reference sample, Analyses, Seville Orange, penetration into host via a specialized structure, maxima, proteins, entry into host via enzymatic degradation of host anatomical structure, polyketide synthesis, retention, Citrus bergamia, non-neoplastic, preventive measures, Immune Response, Immune, Pomelo, Citrus, Citrus grandis, Citrus grandi, disorder, Homo sapiens disease, Citron Trees, polyketide anabolism, Seville Orange Trees, Immune Process, Citrus hystrices, Citrus Fruit, Citrus aurantium, polyketide formation, Controlled, Seville Orange Tree, Citrus bergamias, Controlling, preventive therapy, Profftella, Sour Orange., Citrus medica, Bitter, Process, plasma membrane invagination, Mandarin Orange Trees, medicas, Lemon, Orange Tree, Seville, Citrus hystrix, aurantium, Proteins, disorders, entry into cell of other organism during symbiotic interaction, bergamia, medical condition, Tree, Spectrum Analysis, impact-a, Cell, Trees, Sour Orange, Spectroscopy, count in organism, Insect Protein, MS, native protein, Protein, Diseases, condition, Insects, Uniramia, Tangerine Trees, Kaffir Lime, Pomelo Trees, Mass Spectrum Analyses, Mass Spectrum, Citrus reticulata, Lemon Tree, storage, prophylaxis, Pummelo, Lime, Citrus limon, Spectrometry, metabolite, hexapods, Citrus maxima, hystrices, Mandarin, Pomelo Tree, Kaffir, Citrus aurantiums, Insect, Profftella armatura, Orange Trees, Protein Gene Products, Bitter Orange Trees, Gene Proteins, disease, Fruit, entry into host cell via penetration peg, Lemon Trees, control, Citron Tree, Citrus reticulatas, metabolites, Response, penetration into host via a specialized structure during symbiotic interaction, Tangerine Tree, Tangerine, sequestering, E430016J11Rik, Proteomes, Bitter Orange Tree, Sour Orange Tree, RWDD5, Tracheata0falseDcitri - Whole organism, Normalized peptide spectral count numbers (Ramseyetal,plosone2015)abundance based on Normalized peptide spectral count numbers, Interaction consistency score: 2.4, Coverage: 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