PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering121845https://pax-db.org/dataset/121845/3925505146mering@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.Huanglongbing (HLB), also known as citrus greening disease, is the most serious disease of citrus plants. It is associated with the Gram-negative bacterium ' Candidatus Liberibacter asiaticus' ( CLas), which is transmitted between host plants by the hemipteran insect vector Diaphorina citri in a circulative, propagative manner involving specific interactions with various insect tissues including the hemolymph, fluid that occupies the body cavity akin to insect blood. High resolution quantitative mass spectrometry was performed to investigate the effect of CLas exposure on D. citri hemolymph at the proteome level. In contrast to the broad proteome effects on hundreds of proteins and a diverse array of metabolic pathways previously reported in gut and whole insect proteome analyses, the effect of CLas on the hemolymph was observed to be highly specific, restricted to key immunity and metabolism pathways, and lower in magnitude than that previously observed in the whole insect body and gut. Vitellogenins were abundantly expressed and CLas-responsive. Gene-specific RNA expression analysis suggests that these proteins are expressed in both male and female insects and may have roles outside of reproductive vitellogenesis. Proteins for fatty acid synthesis were found to be up-regulated, along with metabolic proteins associated with energy production, supported at the organismal level by the previously published observation that D. citri individuals experience a higher level of hunger when reared on CLas-infected plants. Prediction of post-translational modifications identified hemolymph proteins with phosphorylation and acetylation upon CLas exposure. Proteins derived from the three most prominent bacterial endosymbionts of the psyllid were also detected in the hemolymph, and several of these have predicted secretion signals. A DNAK protein, the bacterial HSP70, detected in the hemolymph expressed from Wolbachia pipientis was predicted to encode a eukaryotic nuclear localization signal. Taken together, these data show specific changes to immunity and metabolism in D. citri hemolymph involving host and endosymbiont proteins. These data provide a novel context for proteomic changes seen in other D. citri tissues in response to CLas and align with organismal data on the effects of CLas on D. citri metabolism and reproduction.Candidatus Liberibacter asiaticus Minimally Alters Expression of Immunity and Metabolism Proteins in Hemolymph of Diaphorina citri, the Insect Vector of Huanglongbing.Kruse Angela A, Ramsey John S JS, Johnson Richard R, Hall David G DG, MacCoss Michael J MJ, Heck 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, ratiocount.biochemical pathways, Metabolic Process, Process, degradation, Processes, metabolism resulting in cell growth, Proteins, Metabolic Concepts, Gene, Metabolic Processes, Concept, Metabolic Phenomena, Asian citrus psyllid, Liberibacter asiaticus, Candidatus Liberobacter asiaticus, Metabolism Concepts, native protein, Metabolism, Protein, Phenomena, Gene Products, Concepts, secretion, Insects, Metabolism Concept, Phenomenon, Hemolymphs, Metabolism Phenomena, metabolism, Metabolic Phenomenon, Immune Processes, multicellular organism metabolic process, Immune Responses, biodegradation, Metabolic, catabolism, Metabolic Concept, metabolic process resulting in cell growth, proteins, Protein Gene Products, Gene Proteins, single-organism metabolic process, Immune Response, Immune, Response, biotransformation, Immune Process, Insect., Catabolism, AnabolismHemolymphs, count.Metabolic Networks, ATHSP70, Ribonucleic, Bowel, Materials, coelom, l(3)L3929, Metabolic Concepts, Hsc-4, scd, fluid, phosphorylation, protein polypeptide chains, insects, Atelocerata, Analysis, Metabolism Concept, coelomic cavity lumen, Non Polyadenylated, Citrus medicas, irp94, DmelCG6489, reticulata, DmelCG18743, hsp70 Ba, Analyses, catabolism, Vitellogenin, Tissue, alimentary tract, HSPH2, Pathways, Bodily, HS24/P52, maxima, proteins, metabolic process resulting in cell growth, Hsp70Bc, Hsp70Bb, hsp70 Aa, Hsp70Bd, Secretion, g, Secretions, reproductive physiological process, Citrus grandis, Periods, Homo sapiens disease, adult alimentary canal, alimentary system, Citrus Fruit, hsc70, Hsp70b, Citrus bergamias, Pathway, Hsp70a, Indices, Index, Orange Tree, land plants, metabolism resulting in cell growth, fatty acid anabolism, acetylation, bergamia, Spectrum Analysis, female, HS24|P52, predicted, HSP70Bbb, Trees, Hsp70B, exocrine gland fluid/secretion, Bodily Secretion, DmIKKgamma, Hsp70A, Nuclear Localization, Dm-hsp70, dIKK, Human Reproductive Indices, Reproductive Periods., secretion, Ribonucleic acids, Uniramia, Tangerine Trees, Hemolymphs, ARABIDOPSIS HEAT SHOCK PROTEIN 70, Acid, DmelCG4264, body cavity, whole organism, maleate, IKK-gamma, Spectrometry, hexapods, Citrus maxima, INSDC_feature:gene, Pomelo Tree, Orange Trees, hsp-70, higher plants, gastrointestinal system, Material, Citrus reticulatas, Hsp70A7d, Koerper, dhsp70, HSC70-4, Vitellogenin II, CG31449, exocrine gland secretion, Bitter Orange Tree, Sour Orange Tree, CG5834, l(3)j7A4, Pummelo Tree, multi-cellular organism, Processes, number, Pummelo Trees, enteric tract, hs70, Metabolic Processes, protein-containing complex, Signals, dIKK-gamma, bs17d06.y1, Asian citrus psyllid, Human, 87A, Gus, Gur, Gut, hsp70RY, DmIKK-gamma, DMHSP7A2, Gene Products, disease or disorder, yolk formation, hsp70Bb-prime, portion of blood, gut, DMHSP7D1, BAP74, Hsp 70, Signal, Metabolic Concept, CG31359, Hsc70, Reproductive Indices, space of body compartment, CG31354, Citrus bergamia, Pomelo, bodily secretion, HSC70, Hsp-70Aa, Hsc4p, Human Reproductive, CG31366, Seville Orange Tree, Reproductive, RNA, NLS Peptides, Citrus medica, whole blood, degradation, female human body, body, Seville, Proteins, disorders, Reproductive Period, Phosphorylations, whole body, RNS, Hsp70ab, Concept, gut tube, IKKgamma, hsp70A, hsp70B, E(csp)1545, MS, native protein, hsc70-4, chemical analysis, condition, phosphorylation enrichment, metabolism, Mass Spectrum Analyses, Metabolic Pathways, Metabolic Phenomenon, hsp70a, multicellular organism metabolic process, dhsp70Aa, hsp70b, l(3)03550, Lemon Tree, Dmikkgamma, Pummelo, i190, Gus-u, Gus-t, Gus-s, Gus-r, Ribonucleic Acid, CG16910, Mandarin, Kaffir, yolk production, male human body, Gene Proteins, DmHSP70AA, DmelCG31449, Tangerine, Hsp70Bbc, HSP70Bc, Hsp70aB, Anabolism, biochemical pathways, Networks, host organism, Metabolic Process, Bitter Orange, celom, coelomic cavity, determination, Hsp70, Human Reproductive Indexes, protein, heat shock protein 70, NLS Peptide, Mandarin Orange, Candidatus Liberobacter asiaticus, HSP70, APG-2, diseases, Hsp110, Citron, Concepts, diseases and disorders, protein aggregate, Phenomenon, animal, IKKg, RNA Gene Products, Sour, KEY, Key, male, Mass Spectrum Analysis, Human Reproductive Index, Immune Processes, human disease, Immune Responses, RY, Sour Orange Trees, Seville Orange, DmelCG5834, hsc4, Vitellogeneses, xhsp70, NLS, plants, DmelCG31359, Immune, GRP78, digestive tube, biotransformation, asd, DmelCG31366, Citron Trees, CG4264, Seville Orange Trees, Catabolism, wide/broad, Bitter, Process, Mandarin Orange Trees, medicas, ribose nucleic acid, dHsp70, Lemon, external secretion, ribonucleic acids, Metabolic Network, fatty acid formation, Spectroscopy, Reproductive Index, organism, main body cavity, Ribonukleinsaeure, Diseases, Kenny, Genetic Materials, pentosenucleic acids, Genetic Material, HSC4, Neu Laxova syndrome, Hsc4, AI747421, Hsp70-BC, Hsp70-Ab, Citrus limon, Plant, Citrus aurantiums, Bitter Orange Trees, disease, wide, DmelCG16910, microarray, Cistron, CG6489, fatty acid biosynthesis, Proteomes, other disease, digestive canal, ventral body cavity, exocrine gland fluid, exocrine gland fluid or secretion, Gene, hsp70(87A), hsp70Ab, Network, hsp70Aa, HEL-S-5a, Spectrum Analyses, broad, presence, Liberibacter asiaticus, Hsp70-1, Nuclear Localization Signal, Mandarin Orange Tree, polypeptide chain, Metabolism, body fluid, Mass, hsp70Ba, dmIKKgamma, hsp70Bc, hsp70Bb, IKK[[gamma]], Metabolism Phenomena, Hsp-c4, Mass Spectroscopy, dhsc70, Genetic, Acetylations, Nuclear Localization Signal Peptide, Microvitellogenin, hsp70 87A, hsp70 87C, non-neoplastic, coelome, Non-Polyadenylated RNA, secreted substance, Immune Response, hemocoel, IKK, Citrus, anon-WO0118547.237, Citrus grandi, disorder, fatty acid synthesis, Immune Process, Citrus hystrices, intestines, Citrus aurantium, Peptides, data, Males, protein complex, vertebrate blood, Citrus hystrix, aurantium, total expressed protein, medical condition, Tree, Cistrons, Peptide, Sour Orange, Metabolic Phenomena, Metabolism Concepts, HSC-70, count in organism, hsp68, natural protein, Period, yeast nucleic acid, Protein, Phenomena, hsp70, Insects, Kaffir Lime, Hsp70(87C), Pomelo Trees, alimentary canal, CG18743, HLB, Hsp70.1, Mass Spectrum, ribonucleic acid, Citrus reticulata, biodegradation, Metabolic, Non Polyadenylated RNA, E(nd)195, Lime, Non-Polyadenylated, hystrices, Insect, Protein Gene Products, Fruit, single-organism metabolic process, Lemon Trees, hsp 70, Indexes, Citron Tree, Response, Metabolic Pathway, Tangerine Tree, assay, responsive, Females, Tracheata0falseDcitri - Hemolymph, spectral count (Kruseetal,jproteomeres2018)abundance based on spectral count, Interaction consistency score: 0.3, Coverage: 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