PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering9544https://pax-db.org/dataset/9544/1498921887mering@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.Type 2 diabetes mellitus (T2DM) is a severe metabolic disorder that affects more than 10% of the population worldwide. Obesity is a major cause of insulin resistance and contributes to the development of T2DM. Liver is an essential metabolic organ that plays crucial roles in the pathogenesis of obesity and diabetes. However, the underlying mechanisms of liver in the transition of obesity to diabetes are not fully understood. The nonhuman primate rhesus monkey is an appropriate animal for research of human diseases. Here, we first screened and selected three individuals of spontaneously diabetic rhesus monkeys. Interestingly, the diabetic monkeys were obese with a high body mass index at the beginning, but gradually lost their body weight during one year of observation. Furthermore, we performed stable isotope labeling with amino acids in cell culture-based quantitative proteomics to identify proteins and signaling pathways with altered expression in the liver of obese and diabetic monkeys. In total, 3,509 proteins were identified and quantified, of which 185 proteins displayed an altered expression level. Gene ontology analysis revealed that the expression of proteins involved in fatty acids β-oxidation and galactose metabolism was increased in obese monkeys; while proteins involved in oxidative phosphorylation and branched chain amino acid (BCAA) degradation were upregulated in diabetic monkeys. In addition, we observed mild apoptosis in the liver of diabetic monkeys, suggesting liver injury at the late onset of diabetes. Taken together, our liver proteomics may reveal a distinct metabolic transition from fatty acids β-oxidation in obese monkey to BCAA degradation in diabetic monkeys.SILAC-based quantitative proteomic analysis of the livers of spontaneous obese and diabetic rhesus monkeys.Wang Junlong J, Xu Shimeng S, Gao Jing J, Zhang Linqiang L, Zhang Zhiguo Z, Yang Wenhui W, Li Yunhai Y, Liao Shasha S, Zhou Hu H, Liu Pingsheng P, Liang Bin BAdd, 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, ratiorhesus macaque, Rhesus Macaque, Rhesus Macaques, Monkey, Macaque, Macaca mulatta lasiotas, obese, Obesity NOS, number, obesity disease, ob, OB, Adiposity, rhesus monkeys, rhesus macaques, OBESITY NOS, Overweight and obesity, Rhesus Monkeys, Macaca mulatta lasiota, presence, Adiposis, obesity, Chinese Rhesus Macaque, Obesity, Livers, Obese, count in organism, unspecified, proteomic analysis, Obesity [Ambiguous], Obese (finding), Cercopithecus mulatta, Rhesus., Rhesus monkey, Chinese Rhesus Macaques, Rhesus Monkey, Rhesus, Chinese, obesity disorder, Obesity (disorder)jecur, iecur., Liversacido graso, single-organism catabolic process, Adult-Onset Diabetes Mellitus, acidos grasos, Macaque, Laboratory, Physical, rhesus monkeys, Type 2 Diabetes Mellitus, growth and development, trauma, unspecified, Body Mass, Oxidative, Programmed, Non-Insulin Dependent Diabetes Mellitus, 1, 2, Research Activity, Laboratory Research, RBBP1L1, BCAA, Esterified, organ, Animalia, Priorities, modification by symbiont of host biological process, Thesaurismosis, amino acids, stimulation by symbiont of host programmed cell death, catabolism, Moods, Esterified Fatty, Weights, Age of onset, proteins, Bcaa, Ketosis-Resistant Diabetes Mellitus, NIDDM, Noninsulin-Dependent, Aliphatic Acids, Intrinsic Pathway Apoptosis, Diabetes mellitus, Homo sapiens disease, BRCAA1, db, single organism signaling, DM, Index, animalia, obese, Injury and Wounds, Rbp1l1, Research Priorities, Physical Traumas, Rhesus Monkeys, Fettsaeuren, galactose metabolism, alpha-amino carboxylic acids, OB-RGRP, bis(2-chloroethyl)sulfane, signaling (initiator) caspase activity, induction of apoptosis, Adult-Onset Diabetes, Old World monkeys, Quetelet's Index, Weight, Obesity [Ambiguous], OBESITY, Ontology Projects, secretion, Ketosis Resistant, Caspase-Dependent, Maturity-Onset Diabetes Mellitus, Culture Technique, Research and Development, Branched Chain Amino Acid, Acid, Phosphorylation, Ontology, Fatty Acid, breakdown, whole organism, Saturated Fatty Acid, Body Weights, Amino acids, Projects, Type II Diabetes, Adiposity, OBESITY NOS, human, Obr, Activities, Intrinsic Pathway Apoptoses, fatty acids, activation by symbiont of host programmed cell death, Koerper, Cell Cultures, Extrinsic Pathway, Research-Related Injuries, Acids, School-Age Population, obl, Slow-Onset, Saturated Fatty, T2DM - Type 2 Diabetes mellitus, Research Related Injuries, Esterified Fatty Acids, multi-cellular organism, Macaca mulatta lasiotas, Peptidomics, regulation by symbiont of host system process, number, obesity disease, Isotope-Coded Affinity, apoptotic programmed cell death, Injuries and Wounds, Gene Ontology Project, cellular catabolism, activation of apoptosis, Gene Ontology, jecur, Human, Wounds, IR, induction by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction, Insulin, Diabetes mellitus (disorder), Gene Products, metabolism disorder, disease or disorder, Branched Chain, Isotopically-Coded Affinity, noninsulin-dependent, Man, School-Age Populations, Fatty Acids, disease of metabolism, Injury, New World monkeys, obese-like, Population, man, Cell Culture Technique, BMI, bis(2-chloroethyl) sulphide, Oxidative Phosphorylations, anatomical unit, Diabetes Mellitus, Classic Apoptosis, execution phase of apoptotic process, body organ, Rhesus monkey, Development and Research, Apoptosis, cellular breakdown, disruption by symbiont of host cell, cell suicide, hemolysin activity, 1-chloro-2-[(2-chloroethyl)thio]ethane, degradation, body, Affects, Proteins, apoptotic cell death, disorders, Phosphorylations, MODY, whole body, alpha-amino acids, Cell, nev, primates, Fettsaeure, Drug resistance to insulin (disorder), T2D, native protein, traumatic injury, Wounds and Injury, Stable Isotope, disorder of metabolism NOS, Trauma, chemical analysis, Maturity-Onset, Slow-Onset Diabetes Mellitus, Resistance, condition, Obesity (disorder), Metabolic disorders, Ontology Project, Metabolic disease (disorder), LEPROT, apoptosis, metabolic disease, increased number, Obesity NOS, Branched-Chain Amino Acids, postnatal growth, wound, ob, OB, acide gras, Isotope Labeling, School Age Populations, Isotopically-Coded, Body, signalling, Classic Apoptoses, Gene Proteins, Quetelets Index, Metabolic Diseases, signalling process, apoptotic program, commitment to apoptosis, Stable Diabetes Mellitus, Severe, Modb1, biochemical pathways, multicellular organismal catabolic process, rhesus macaque, Gene Ontology Projects, single-organism developmental process, Activity, Monkeys, determination, Wound, postnatal development, Aminosaeure, positive regulation by symbiont of host non-apoptotic programmed cell death, Amino acid, Body fails to respond to insulin, type I programmed cell death, injury, diabetes mellitus type 2, Adiposis, element, School-Age, Obese, Tier, diseases, Extrinsic Pathway Apoptoses, pathogenesis, Project, Maturity Onset Diabetes, Saturated Fatty Acids, cellular degradation, Chinese Rhesus Macaques, diseases and disorders, Esterified Fatty Acid, Leprb, animal, Slow Onset, Research-Related, Isotopically-Coded Affinity Tagging, DM - Diabetes mellitus, increased, human disease, Rhesus Macaques, Monkey, Man (Taxonomy), Iprit, Metabolic disease, Aliphatic, iecur, Branched-Chain Amino Acid, 9330186M13, reaction, CG14648, Quetelet, Classic, signaling process, mustard gas, Classical Apoptosis, biotransformation, METABOLISM DISORDER NOS, Research Priority, MD - Metabolic disorders, Tagging, Non Insulin Dependent, Primate, Insulin Sensitivity, Stable Isotope Labeling, Primata, Anthropoidea., RBP1L1, cellular suicide, Growl, Caspase-Dependent Apoptosis, Anthropoidea, Aminokarbonsaeure, Modern, late, Adult-Onset, organism, weight, Intrinsic Pathway, School Age, Extrinsic Pathway Apoptosis, Obese (finding), Diseases, modulation by symbiont of host system process, monkeys, NOS, Physical Trauma, 6330417L24Rik, SAP180, Amino Acid, Gene Ontologies, Populations, METAB DIS, Ontologies, Aliphatic Acid, Cell Death, Type 2, induction by organism of programmed cell death in other organism during symbiotic interaction, modification by symbiont of host morphology or physiology, Diabetes NOS, Noninsulin-Dependent Diabetes Mellitus, disease, Non-Insulin Dependent Diabetes, induction of apoptosis by p53, Amino Acids, Rhesus, Research-Related Injury, Unspecified disorder of metabolism, Classical, Apoptoses, accessory, other disease, biological signaling, human being, Noninsulin Dependent, caspase-dependent programmed cell death, primate, Aminocarbonsaeure, Gene, Caspase Dependent Apoptosis, Yperite, alpha-amino acid, DIABETES MELLITUS TYPE 02, presence, supernumerary, Obesity, Generalized metabolic disorder, Homo sapiens, acides gras, 6720480E17Rik, Non-Insulin-Dependent, Mood, non-insulin-dependent diabetes mellitus, Mustard gas, Animal, Type I, 1'-thiobis(2-chloroethane), Cell Culture, Maturity-Onset Diabetes, Quetelet Index, T2DM, Generalized metabolic disorder (disorder), induction of non-apoptotic programmed cell death by other organism, Research, breakdown of chemical, Non-Insulin-Dependent Diabetes Mellitus, Having too much body fat, anon-WO0118547.126, 5930400I17, metazoa, Maturity Onset Diabetes Mellitus, Overweight and obesity, causes, growl, respiratory-chain phosphorylation, apoptosis activator activity, non-neoplastic, Lost, Noninsulin Dependent Diabetes Mellitus, Branched-Chain Amino, Stable, Traumas, causality, Isotope-Coded Affinity Tagging, Metabolic disorder, Sensitivity, disorder, Ketosis-Resistant, DmelCG14648, Branched-Chain, School Age Population, Chinese, programmed cell death by apoptosis, Diabetes, diabetes, sulfur mustard, Adult Onset, Rhesus Macaque, monkey, Culture Techniques, Saturated, activation by organism of non-apoptotic programmed cell death in other organism, medical condition, disorder of metabolism NOS (disorder), Labeling, obesity, diabetes mellitus (disease), Chinese Rhesus Macaque, development, Isotope, count in organism, Priority, Programmed Cell Death, Metazoa, Protein, Generalised metabolic disorder, Cercopithecus mulatta, Research Activities, Type 2 Diabetes Mellitus Non-Insulin Dependent, obesity disorder, Isotope Coded Affinity Tagging, breakdown of molecule, apoptosis signaling, Type 2 Diabetes, biodegradation, distinct, diabetes mellitus, Thesaurismoses, Senfgas, rhesus macaques, Amino, Age symptoms begin, Macaca mulatta lasiota, Affinity Tagging, Injuries, Protein Gene Products, Livers, present in greater numbers in organism, breakdown of substance, Modern Man, Anthropoids, Isotope-Coded, Rhesus Monkey, assay, Type II, growth, Maturity Onset0falseMmulatta - Liver, iBAQ with SILAC (Wangetal,amjphysiolendocrinolmetab2018)abundance based on iBAQ with SILAC, Interaction consistency score: 20.0, Coverage: 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