PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering3702https://pax-db.org/dataset/3702/2805505816mering@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.Research interest in proteomics is increasingly shifting toward the reverse genetic characterization of gene function at the proteome level. In plants, several distinct gene defects perturb photosynthetic capacity, resulting in the loss of chlorophyll and an albino or pale-green phenotype. Because photosynthesis is interconnected with the entire plant metabolism and its regulation, all albino plants share common characteristics that are determined by the switch from autotrophic to heterotrophic growth. Reverse genetic characterizations of such plants often cannot distinguish between specific consequences of a gene defect from generic effects in response to perturbations in photosynthetic capacity. Here, we set out to define common and specific features of protein accumulation in three different albino/pale-green plant lines. Using quantitative proteomics, we report a common molecular phenotype that connects the loss of photosynthetic capacity with other chloroplast and cellular functions, such as protein folding and stability, plastid protein import, and the expression of stress-related genes. Surprisingly, we do not find significant differences in the expression of key transcriptional regulators, suggesting that substantial regulation occurs at the posttranscriptional level. We examine the influence of different normalization schemes on the quantitative proteomics data and report all identified proteins along with their fold changes and P values in albino plants in comparison with the wild type. Our analysis provides initial guidance for the distinction between general and specific adaptations of the proteome in photosynthesis-impaired plants.Common and specific protein accumulation patterns in different albino/pale-green mutants reveals regulon organization at the proteome level.Motohashi Reiko R, Rödiger Anja A, Agne Birgit B, Baerenfaller Katja K, Baginsky Sacha SAdd, 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, ratioDH65B, CG10118, organisation, organizational structure, protein complex, Proteins, DmelCG10118, total expressed protein, Gene, Th, organization and administration, Non-Governmental Organizations, protein, protein-containing complex, pale, protein polypeptide chains, Ank-1, native protein, natural protein, polypeptide chain, skc35, Protein, Proteomes., Gene Products, nb, Non-Governmental, pale/ple, protein aggregate, DTH, Nongovernmental Organizations, administrative management, Organization, Ple, Nongovernmental, administrative structure, palet, common, albino, Regulons, proteins, Protein Gene Products, Gene Proteins, c, Non Governmental Organizations, Non-Governmental Organization, dTH65B, Pale, organizational management, TH, dTH1, VII, Organizations, organization, Nongovernmental Organizationplantae, Plant, organism, whole body, multi-cellular organism, whole organism, animal, body, viridiplantae., Koerper, Pflanzebiochemical pathways, IPP2A2, Metabolic Process, Materials, land plants., Activity, Globular Protein Folding, determination, Laboratory, Ass-1, Feature, Pflanze, postnatal development, Metabolic Concepts, A4, growth and development, protein, Progress Reports, beta-tubulin folding, Photosynthetic Carbon Fixation, Social Controls, Leukoplast, viridiplantae, 5730420M11Rik, dysfunctional, protein polypeptide chains, Ank-1, skc35, Summary Report, AA408052, Concepts, fold, pale/ple, Research Activity, Metabolism Concept, protein aggregate, Phenomenon, Laboratory Research, Carbon Fixation, Formal Social Controls, Summary Reports, IKKg, Phyllobilins, KEY, Key, Priorities, SET, Progress Report, TAF-I, catabolism, plants, metabolic process resulting in cell growth, proteins, Calvin-Benson-Bassham, Chloroplast, Folding, genetic, Social, DmelCG4299, chaperonin-mediated tubulin folding, ASS, Progress, c, IGAAD, set, Field Reports, DmelCG10574, biotransformation, Calvin, TH, Research Priority, Chromoplast, Catabolism, phapii, Process, land plants, metabolism resulting in cell growth, familial, DmelCG10118, StF-IT-1, Research Priorities, Th, Calvin Benson Cycle, partial functionality, chaperone activity, DmIKKgamma, Globular Protein, co-chaperonin activity, Investigative Report, dIKK, Kenny, Genetic Materials, secretion, alpha-tubulin folding, Protein Foldings, Genetic Material, Research and Development, HLA-DR-associated protein II, growth pattern, DI-2, non-developmental growth, I-2Dm, Field, IKK-gamma, Plant, palet, Control, common, Calvin Benson Bassham Cycle, INSDC_feature:gene, CG4299, Leukoplasts, Controls, lacks function of type, Features, Leucoplasts, low functionality, Activities, loss of, I-2PP1, Phenotypes, higher plants, Report, co-chaperone activity, DMDA, TAF-IBETA, Globular Protein Foldings, DmelCG16910, Material, multichaperone pathway, Cistron, inherited genetic, TAF-Ibeta, Regulation, i2pp2a, Proteomes, Regulations, Amyloplast, Peptidomics, Processes, number, Foldings, Gene, impaired, Reductive Pentose Phosphate Cycle, Leucoplast, Metabolic Processes, protein-containing complex, presence, dIKK-gamma, TYPE, pale, PHAPII, DAGA4, Investigative, polypeptide chain, Metabolism, chaperonin ATPase activity, DmIKK-gamma, Chlorophylls, Photosynthesis Dark Reactions, Cycle, Gene Products, non-chaperonin molecular chaperone ATPase activity, glycoprotein-specific chaperone activity, dmIKKgamma, IKK[[gamma]], MAM, Metabolism Phenomena, Globular, SCG3, plantae, Genetic, Research, Plastid, dysfunction, ipp2a2, Metabolic Concept, 2pp2a, albino, CG10574, Etioplast, 2PP2A, Chromoplasts, IKK, taf-ibeta, Protein Folding, Pale, dSET, dSet, Calvin-Benson-Bassham Cycle, Development and Research, Characteristics, dTH1, Investigative Reports, constitutitional genetic, Dark Reactions of Photosynthesis, protein uptake, DH65B, data, CG10118, degradation, Formal Social Control, protein complex, Photosynthetic, Proteins, Photosynthesis Dark Reaction, igaad, total expressed protein, function, Etioplasts, Cistrons, group, LGMD2C, Concept, Metabolic Phenomena, Chlorophyll 740, development, Metabolism Concepts, IKKgamma, count in organism, Priority, Characteristic, native protein, natural protein, Social Control, I-2PP2A, Dm I-2, Protein, Research Reports, chemical analysis, Research Activities, Phenomena, I2PP2A, Calvin-Benson Cycle, nb, DTH, metabolism, protein complex assembly, Metabolic Phenomenon, multicellular organism metabolic process, Ple, distinct, biodegradation, DMDA1, Metabolic, ensemble, Dmikkgamma, postnatal growth, CG16910, Amyloplasts, Protein Gene Products, Gene Proteins, dSET/TAF-Ibeta, having decreased function, single-organism metabolic process, 2610030F17Rik, Reports, Calvin Cycle, dTH65B, SCARMD2, regulation, assay, VII, Calvin-Benson, AA407739, Summary, hereditary, growth, Field Report, Anabolism0falseA.thaliana - Whole organism (Motohashi,plant_physiol,2012)abundance based on MAPPED_BY_AUTHORS, Interaction consistency score: 5.7, Coverage: 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