{"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"},"statusCodeValue":200,"statusCode":"OK"}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Christian von Mering"],"species":["5691"],"full_dataset_link":["https://pax-db.org/dataset/5691/4092869827"],"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":["We report a global quantitative phosphoproteomic study of bloodstream and procyclic form Trypanosoma brucei using SILAC labeling of each lifecycle stage. Phosphopeptide enrichment by SCX and TiO2 led to the identification of a total of 10096 phosphorylation sites on 2551 protein groups and quantified the ratios of 8275 phosphorylation sites between the two lifecycle stages. More than 9300 of these sites (92%) have not previously been reported. Model-based gene enrichment analysis identified over representation of Gene Ontology terms relating to the flagella, protein kinase activity, and the regulation of gene expression. The quantitative data reveal that differential protein phosphorylation is widespread between bloodstream and procyclic form trypanosomes, with significant intraprotein differential phosphorylation. Despite a lack of dedicated tyrosine kinases, 234 phosphotyrosine residues were identified, and these were 3-4 fold over-represented among site changing >10-fold between the two lifecycle stages. A significant proportion of the T. brucei kinome was phosphorylated, with evidence that MAPK pathways are functional in both lifecycle stages. Regulation of gene expression in T. brucei is exclusively post-transcriptional, and the extensive phosphorylation of RNA binding proteins observed may be relevant to the control of mRNA stability in this organism."],"pubmed_title":["Global quantitative SILAC phosphoproteomics reveals differential phosphorylation is widespread between the procyclic and bloodstream form lifecycle stages of Trypanosoma brucei."],"pubmed_authors":["Urbaniak Michael D MD, Martin David M A DM, Ferguson Michael A J MA"],"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"],"description_synonyms":["sequence, E430039A18Rik, CD156., CD156a, MS/MS, tandem MS, primary structure of sequence macromolecule, MS2"],"pubmed_title_synonyms":["Trypanosoma, Trypanosoma brucei subgroup, Trypanosoma brucei bruceus, brucei brucei, bruceus, Trypanosoma bruceus, Phosphorylations, phosphorylation enrichment, Trypanosoma (Trypanozoon) brucei, brucei, Trypanosoma brucei., Trypanosoma brucei, phosphorylation"],"name_synonyms":["organism, multi-cellular organism, whole organism, body, MS/MS, MS2, Koerper, sequence, E430039A18Rik, whole body, CD156., animal, CD156a, tandem MS, primary structure of sequence macromolecule"],"pubmed_abstract_synonyms":["glycogen synthase kinase activity, ds RNA-Binding, para Tyrosine, ANT-C, DmErk, extracellular signal-regulated kinase activity, Trypanosoma brucei subgroup, pp44mapk, Materials, Gene Ontology Projects, protein kinase A activity, Bhlha41, Scx, SCX, determination, Ass-1, Mpk2, Antp1, mRNA Stability, bHLHa48, p42mapk, Progress Reports, protein, phosphorylation, prevention, Prp4 protein kinase activity, SR2-1, Trypanosoma, protein polypeptide chains, DSmurf, LeMPK3, Double Stranded RNA Binding Proteins, scx, ATP-protein transphosphorylase activity, Summary Report, p44mpk, AA408052, AntP1, ATP:protein phosphotransferase (non-specific) activity, kinase-related transforming protein, Project, fold, Dp38, mitogen-activated protein kinase activity, Kinase, protein aggregate, SAPK2, animal, mpk1, SEM, Sem, prevention and control, Summary Reports, RNA Binding Proteins, MAP-k, Erk/Map kinase, reference sample, Progress Report, pp42, 2-amino-3-(4-hydroxyphenyl)propanoic acid, 3-(p-Hydroxyphenyl)alanine, DERK-A, Dsor2, proteins, E(sina)7, Nannomonas, Y, sem, Rl, xscleraxis, Raf kinase activity, BG:DS07700.1, ASS, preventive measures, Progress, MP kinase activity, serine kinase activity, Double-Stranded RNA-Binding Protein, DERK, Field Reports, atypical protein kinase C activity, Smurf, bHLHa41, Tyr, ds RNA-Binding Proteins, MBP kinase II activity, mitogen-activated S6 kinase activity, ANT-P, protein-aspartyl kinase activity, stage, dERK, Decay, ATP Phosphotransferases, RNA Binding Protein, CG4943, ATP, D-smurf, ERK-A, p82 kinase activity, MAP kinase 2 activity, preventive therapy, dpERK, dpErk, Trypanosoma brucei bruceus, Mapk, protamine kinase activity, ds, Regulation of Gene Expression, 2-Amino-3-(p-hydroxyphenyl)propionic acid, betaIIPKC, Erk1, ERK1, ERK2, mapk1a, DmMAPK, para-Tyrosine, PMK-2, Double-Stranded, Lack, dp-ERK, PMK-1, Aus, PMK-3, Gene Action, Tyrosine, M phase-specific cdc2 kinase activity, Wee-kinase activity, Gene Expression, organism, Expression Regulation, Investigative Report, mapk1b, MapK, Tyrosine O phosphate, MAPK, BB114693, Double-Stranded RNA-Binding Proteins, pMAPK, pMapK, Genetic Materials, Ontology Projects, serine protein kinase activity, RNA Decay, erk2, Double-Stranded RNA-Binding, RNA Instability, Genetic Material, region, mapk, RNA-Binding Protein, Gene Ontologies, Koerper., Transphosphorylases, ERKa, phosphorylase B kinase kinase activity, Ontology, DmERKA, Ontologies, rl/MAPK, BcDNA:RE08694, whole organism, Projects, protein glutamyl kinase activity, DmelCG4943, RNA-Binding Proteins, Nannomona, l(2R)EMS45-39, Field, Trypanosoma bruceus, L-isomer, DmelCG12559, non-specific serine/threonine protein kinase activity, p38, INSDC_feature:gene, l(2)41Ac, mRNA Degradation, Transcript Degradation, Trypanosoma brucei, regulation of protein expression, L isomer, DpErk, DpERK, ErkA, ERKA, hydroxyalkyl-protein kinase activity, Report, CT34260, WEE1Hu, dpERk, Material, brucei brucei, serine-specific protein kinase activity, epsilon PKC, SAPK, HIPK2, dihydrogen phosphate (ester), cytidine 3', Tyrosine-O-phosphate, Cistron, L-Tyrosine, L-tyrosine, Wee 1-like kinase activity, Regulation, pERK, ribosomal S6 protein kinase activity, calcium/phospholipid-dependent protein kinase activity, multi-cellular organism, glycogen synthase A kinase activity, GroupII, dSmurf1, developmental stage, glycogen synthase kinase 3 activity, Double Stranded RNA Binding Protein, Degradation, 12559, DMANTPE1, Gene, Trypanosoma (Trypanozoon) brucei, Antp P1, Antp P2, protein-containing complex, SCXB, Gene Ontology Project, phosphorylase b kinase kinase activity, Gene Ontology, regulation of gene product expression, SCXA, EK2-1, protein amino acid phosphorylation, Stability, Investigative, polypeptide chain, Hu, MOD_RES Phosphotyrosine, Gene Products, serine(threonine) protein kinase activity, mRNA Transcript, 3.4, ribosomal protein S6 kinase II activity, Phosphotransferase, Erk, ERK, T-antigen kinase activity, PRKM1, galactosyltransferase-associated kinase activity, study, ANTC, PRKM2, protein-serine kinase activity, antp, ds RNA-Binding Protein, Genetic, xp42, STK32, labeling, Transphosphorylase, p42 mitogen-activated protein kinase activity, CG1028, CG18732, ATP:protein phosphotransferase (MAPKK-activated) activity, erk, ds RNA Binding Protein, protein kinase (phosphorylating) activity, d-smurf, Trypanosomes, protein-cysteine kinase activity, L Tyrosine, Raf-1, Hpr kinase activity, bruceus, site, mRNA Transcript Degradation, rll, DmERK-A, species, AntP, Tyrosin, STK26, ANTP, Investigative Reports, p38-2, casein kinase (phosphorylating) activity, myelin basic protein kinase activity, Controlled, RNA Degradation, data, Controlling, RNA, ert1, Flagellum, Phosphotyrosine, protein complex, body, Proteins, prkm2, stress-activated kinase activity, Phosphorylations, prkm1, CT39192, MAP-2 kinase activity, whole body, protein serine kinase activity, DmAntp, Dsmurf, Cistrons, Phosphotransferases, protein phosphokinase activity, dSmurf, p38delta, twitchin kinase activity, Phosphopeptide, PKA, native protein, macromolecular stability of mRNA, natural protein, PKC, tirosina, Smurf ubiquitin ligase, stress-activated protein kinase activity, Research Reports, Protein, chemical analysis, mapk2, AP50 kinase activity, mapk1, MBP kinase I activity, mRNA Instability, phosphorylation enrichment, gene regulation, l(3)84Ba, mRNA Decay, brucei, protein kinase p58 activity, Xp42, serine/threonine protein kinase activity, Ontology Project, threonine-specific protein kinase activity, Ant, CG12559, mRNA, Kinases, mitogen activated kinase activity, prophylaxis, Su(Raf)2B, dpERK1, EY2-2, dsk1, 5'-cyclic monophosphate-responsive protein kinase activity, atypical PKC activity, Trypanosome, Protein Gene Products, Gene Action Regulation, Gene Proteins, Ns, D-ERK, DmelCG1028, Reports, dpMAPK, control, DRO15DC96Z, assay, Summary, Instability, protein serine-threonine kinase activity, SAP kinase activity, Field Report, Scl, MAP kinase 1 activity, A-kinase activity"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"T.brucei - Whole organism, sequence+MS2 intensity (Urbaniaketal,jproteomeres2013)","description":"abundance based on sequence+MS2 intensity, Interaction consistency score: 17.7, Coverage: 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