{"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":["284590"],"full_dataset_link":["https://pax-db.org/dataset/284590/3047588386"],"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":["Omics analysis is a versatile approach for understanding the conservation and diversity of molecular systems across multiple taxa. In this study, we compared the proteome expression profiles of four yeast species (Saccharomyces cerevisiae, Saccharomyces mikatae, Kluyveromyces waltii, and Kluyveromyces lactis) grown on glucose- or glycerol-containing media. Conserved expression changes across all species were observed only for a small proportion of all proteins differentially expressed between the two growth conditions. Two Kluyveromyces species, both of which exhibited a high growth rate on glycerol, a nonfermentative carbon source, showed distinct species-specific expression profiles. In K. waltii grown on glycerol, proteins involved in the glyoxylate cycle and gluconeogenesis were expressed in high abundance. In K. lactis grown on glycerol, the expression of glycolytic and ethanol metabolic enzymes was unexpectedly low, whereas proteins involved in cytoplasmic translation, including ribosomal proteins and elongation factors, were highly expressed. These marked differences in the types of predominantly expressed proteins suggest that K. lactis optimizes the balance of proteome resource allocation between metabolism and protein synthesis giving priority to cellular growth. In S. cerevisiae, about 450 duplicate gene pairs were retained after whole-genome duplication. Intriguingly, we found that in the case of duplicates with conserved sequences, the total abundance of proteins encoded by a duplicate pair in S. cerevisiae was similar to that of protein encoded by nonduplicated ortholog in Kluyveromyces yeast. Given the frequency of haploinsufficiency, this observation suggests that conserved duplicate genes, even though minor cases of retained duplicates, do not exhibit a dosage effect in yeast, except for ribosomal proteins. Thus, comparative proteomic analyses across multiple species may reveal not only species-specific characteristics of metabolic processes under nonoptimal culture conditions but also provide valuable insights into intriguing biological principles, including the balance of proteome resource allocation and the role of gene duplication in evolutionary history."],"pubmed_title":["Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication."],"pubmed_authors":["Kito Keiji K, Ito Haruka H, Nohara Takehiro T, Ohnishi Mihoko M, Ishibashi Yuko Y, Takeda Daisuke D"],"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":["Saccharomyces oviformis, Yeast, Allocative, Peptidomics, Allocation of Resources, Duplications, total expressed protein, Saccharomyes cerevisiae, baker's yeast, Allocation, Gene, Efficiency, Saccharomyces uvarum var. melibiosus, Saccharomyces italicus, Saccaromyces cerevisiae, Allocative Efficiency, Sccharomyces cerevisiae, Duplication, Candida robusta, Resource, Saccharomyces capensis, yeast, Gene Duplications., Resources Allocation, brewer's yeast, Proteomes, lager beer yeast"],"name_synonyms":["Koerper., organism, whole body, multi-cellular organism, whole organism, animal, body"],"pubmed_abstract_synonyms":["biochemical pathways, protein translation, glucose biosynthetic process, Metabolic Process, Grain Alcohol, Materials, determination, Allocation of Resources, Feature, Glukose, postnatal development, Metabolic Concepts, Duplications, Saccharomyces lactis, Monohydrate, Ribosomal Protein, growth and development, CSMF, protein, (DL)-Isomer, 1-hydroxyethane, alcohol, Readability, protein polypeptide chains, Background, Kluyveromyces marxianus lactis, Carbon-12, Roles, Dextrose, Alkohol, Cultural, 1, Concepts, 10.5, 2, Gene Duplications, Metabolism Concept, protein aggregate, Phenomenon, 10.9, 3-Propanetriol, C, Ribosomal, ethnicity, Oelsuess, me75, Grain, F, enzymes, Genomes, DmelCG2328, proportionality to, catabolism, non-developmental growth of a unicellular organism, Ethyl, hypoplasia, Saccharomyes cerevisiae, Baker, proteins, metabolic process resulting in cell growth, V, Aethanol, Histories, Saccharomyces uvarum var. melibiosus, [CH2Me(OH)], D17Mit170, DL-glucose, T1, historical notes., Dehydrated ethanol, NOR-1, Saccharomyces capensis, Carbon, Role Concepts, cellular growth, Baker's, biotransformation, Mycoderma cerevisiae, brewer's yeast, Catabolism, spiritus vini, Glyceritol, protein anabolism, protein biosynthetic process, anatomical protrusion, CHN, Alcohol, Process, DP, Torulaspora lactis, metabolism resulting in cell growth, frequency, Efficiency, Ethyl alcohol, Tl3, historical aspects, Tl2, Absolute Alcohol, Baker's Yeasts, Vitreous, Cultural Background, Role Concept, Cultures, Saccharomyces diastaticus, Kluyveromyces marxianus var. drosophilarum, non-developmental cell growth, glycerol, protein formation, Role, Genetic Materials, secretion, VI, Resources Allocation, (alpha-D)-Isomer, [OEtH], Genetic Material, D-Glucose, Yeast, Gro, 20.35, EtOH, Cultural Beliefs, glycerine, growth pattern, non-developmental growth, 6C, proportionality, rate, INSDC_feature:gene, whole genome, Features, surveillance, alcohol etilico, Methylcarbinol, morbidity, Kluyveromyces marxianus var. lactis, Saccharomyces drosophilarum, Saccharomyces cerevisiae (Desm.) Meyen ex E.C. Hansen, Vitreous Carbon, protein synthesis, D Glucose, Material, spine, carbonium, Biocatalyst, eve2, Cistron, Duplicate Genes, Glucose Monohydrate, Proteomes, Brewer's Yeast, CG2328, 14.10, Allocative, Glucose, Biocatalysts, Processes, Aspect, glyoxylate bypass, Saccharomyces mikatii, etanol, Brewer's, baker's yeast, Gene, Torula sphaerica, carbon, Metabolic Processes, protein-containing complex, Saccharomyces italicus, Allocative Efficiency, protrusion, Aethylalkohol, Glycerine, Duplication, glycyl alcohol, Propanetriol, reduced, polypeptide chain, Metabolism, yeast, Trihydroxypropane, Gene Products, Duplicate Gene, Kluyveromyces lactis var. drosophilarum, Low, even, tiny, Metabolism Phenomena, lager beer yeast, Backgrounds, Zygofabospora waltii, study, proportion, Genetic, growth of cell, AI573420, occurrence, Absolute, Glycerin, prevalence, Metabolic Concept, Cultural Relativisms, Kluyveromyces drosophilarum, S. cerevisiae, C2H5OH, Kohlenstoff, S cerevisiae, Enzyme, Candida robusta, glycerolum, Customs, species, 1883, Characteristics, culture, Anhydrous, incidence, small, NOR1, Nor1, Candida sphaerica, cou, (beta-D)-Isomer, degradation, Saccharomyces cerevisiae 'var. diastaticus', protein complex, Kluyveromyces lactis var. lactis, Glyzerin, Proteins, total expressed protein, Kluyveromyces waltii, enzyme activity, Haploinsufficiencies, Cultural Backgrounds, Historical Aspects, carbone, Cistrons, Historical Aspect, Saccaromyces cerevisiae, Concept, Metabolic Phenomena, carbono, Sccharomyces cerevisiae, development, Metabolism Concepts, cell expansion, Lr, Characteristic, native protein, Resource, natural protein, chemical analysis, Protein, Phenomena, alcool ethylique, protein biosynthesis, Eve, EVE, metabolism, outbreaks, Metabolic Phenomenon, Saccharomyces oviformis, Ethyl Alcohol, 3-Trihydroxypropane, multicellular organism metabolic process, Exhibit, distinct, biodegradation, underdeveloped, Metabolic, MINOR, postnatal growth, l(2)46Ce, Allocation, glucose biosynthesis, Understanding, endemics, l(2)46Cg, Anhydrous Dextrose, Carbon 12, Protein Gene Products, l(2)46CFj, Gene Proteins, l(2)46CFh, hydroxyethane, single-organism metabolic process, l(2)46CFp, quotient, Bra, Relativisms, epidemics, TEC, assay, Baker's Yeast, Kluyveromyce, Aspects, Relativism, Duplicate, E(eve), Cultural Relativism, growth, Minor, Baker Yeast, l(2)46CFg, Historical, Glc, Anabolism"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Klactis - Whole organism, SC (Kitoetal.,molcellproteomics2016)","description":"abundance based on Spectral counting, Interaction consistency score: 12.7, Coverage: 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