PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering4565https://pax-db.org/dataset/4565/760704831mering@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.Here, we conducted the first large-scale leaf phosphoproteome analysis of two bread wheat cultivars by liquid chromatography-tandem mass spectrometry. Altogether, 1802 unambiguous phosphorylation sites representing 1175 phosphoproteins implicated in various molecular functions and cellular processes were identified by gene ontology enrichment analysis. Among the 1175 phosphoproteins, 141 contained 3-10 phosphorylation sites. The phosphorylation sites were located more frequently in the N- and C-terminal regions than in internal regions, and ∼70% were located outside the conserved regions. Conservation analysis showed that 90.5% of the phosphoproteins had phosphorylated orthologs in other plant species. Eighteen significantly enriched phosphorylation motifs, of which six were new wheat phosphorylation motifs, were identified. In particular, 52 phosphorylated transcription factors (TFs), 85 protein kinases (PKs), and 16 protein phosphatases (PPs) were classified and analyzed in depth. All the Tyr phosphorylation sites were in PKs such as mitogen-activated PKs (MAPKs) and SHAGGY-like kinases. A complicated cross-talk phosphorylation regulatory network based on PKs such as Snf1-related kinases (SnRKs), calcium-dependent PKs (CDPKs), and glycogen synthase kinase 3 (GSK3) and PPs including PP2C, PP2A, and BRI1 suppressor 1 (BSU1)-like protein (BSL) was constructed and was found to be potentially involved in rapid leaf growth. Our results provide a series of phosphoproteins and phosphorylation sites in addition to a potential network of phosphorylation signaling cascades in wheat seedling leaves.Integrative network analysis of the signaling cascades in seedling leaves of bread wheat by large-scale phosphoproteomic profiling.Lv Dong-Wen DW, Lv Dong-Wen DW, Ge Pei P, Zhang Ming M, Cheng Zhi-Wei ZW, Li Xiao-Hui XH, Yan Yue-Ming YMAdd, 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, ratiobig, Plant Sprout, v&#225stago (Spanish, Triticum durum, scale tissue, biological signaling, Malted Grains, gyltl1b-b, Triticum vulgare, Mbp1, Triticum turgidum subsp. durum, peltate hair., Triticum aestivum subsp. aestivum, Sprout, froggy, Gyltl1a, large, Plant Sprouts, exact), MDDGA6, mKIAA0609, Canadian hard winter wheat, Sprouted Seed, 芽生え、実生 (Japanese, Malted, Seed, scales, myd, KIAA0609, Wheat, fg, Seeds, network topology analysis, Sprouts, Malted Grain, Grain, gyltl1b, scale, Durum, MDDGB6, Triticum aestivum8, Triticum spelta, plant peltate hair, Triticum sativum, mdc1d, Plant, Triticum aestivam, expanded, Mbp-1, LARGE, wheat, signalling, Tricum aestivum, common wheat, BPFD#36, Seedling, MDC1D, Grains, bread wheat, Durum Wheats, signalling process, enr, enlarged, signaling process, great, Sprouted Seeds, Sprouted, Durum Wheat, Triticum turgidum, single organism signaling, Triticum aestivumexact)., exact), hoja (Spanish, 葉 (JapanesePP2A[[C]], PR53, PR55, l(3)S026326, PP2A[B], pr53, anon-WO0118547.420, Dmsgg3, growth and development, PPS1, phosphorylation, bin4, protein polypeptide chains, DmelCG7109, B', DmelCG17746, l(3)S031807, AI481720, PP2A 28D, Bin4, BIN4, PP2A[C], zw3/sgg, Kinase, BIN1, myd, l(3)01436, l(3)S110815, calcio, F23K16_30, Grain, Pp2A, facio-genito-popliteal syndrome, PP2a, l(3)S026226, plant peltate hair, OFC6, dPPM1, l(3)S027313, 2-amino-3-(4-hydroxyphenyl)propanoic acid, 3-(p-Hydroxyphenyl)alanine, l(3)S141309, aar, Mbp-1, proteins, Y, wheat, pp2a, l(3)02414, Tricum aestivum, common wheat, DWF2, DmelCG6235, c, PR65, l(3)S035505b, hpo, PP2A, cleft lip/palate paramedian mucous cysts of the lower lip popliteal pterygium digital and genital anomalies, l(3)S048006, Sprouted, Durum Wheat, Triticum turgidum, Sgg, SGG, Pp2A-28D, l(3)S048013, PP2C, F23K16.30, Zw3, ATP Phosphotransferases, PP2A[A], Blood Coagulation Factor IV, Ca, single organism signaling, LC-MS2, l(3)S067915, anatomical protrusion, Coagulation, Triticum vulgare, CG7901, Triticum turgidum subsp. durum, VWS1, zw3, ZW3, chromosome 12, l(3)S091905, PP2-AB, BRASSINOSTEROID INSENSITIVE 1, serine/threonine protein phosphatase 2A, Plant Sprouts, Pallister Killian syndrome, Teschler-Nicola Killian syndrome, mKIAA0609, sgg-zw3, 1466/06, DmPp2A-28D, l(3)S029403, Ontology Projects, digital and genital anomalies, l(3)S033903, sgg39, CG7913, GSK-3betaSgg, fg, Zw3/GSK3, Seeds, Ontology, Wrd, Projects, l(3)S042630, CBB2, sgg46, expanded, popliteal pterygium, pp2A-B', 葉 (Japanese, GSK, mKIAA4175, MDC1D, Seedling, Grains, dPP2A A, l(3)S075902b, enr, wrd, A/PR65, liquid chromatography-tandem mass spectroscopy, l(3)S066813, l(3)S027127, B56-2, l(3)S042629, B56-1, Triticum aestivum, big, l(3)S063110, Plant Sprout, DmelCG17598, DWARF 2, LD02456, dPP2A-B56-1, dPP2A-B56-2, peltate hair, CG5643, protein-containing complex, Transcription Factor, Gene Ontology Project, Mosaic, Gene Ontology, l(3)S132907, large, Ppp2ce, zw[3], l(3)S069206a, l(3)S023141a, Factor IV, LC-MSMS, Sprouted Seed, Gene Products, CG17291, i234, l(3)S119908, Ca(0), plantae, l(3)j11C8, Transcription, l(3)S046918, exact)., DmelCG6525, zw3/GSK3beta, PP2A[B'-1], l(3)S088513, MDDGB6, dPP2A-Balpha, Triticum aestivum8, albino, dPP2A-C, SKIP, FBgn0082831, 5559, BEST:LD02456, PP2A[B'-2], DPR65, l(3)S029110, Pp2ce, species, Tyrosin, PP2Ac, PIT, ppp2r2c, pk17e, l(3)S076415, paramedian mucous cysts of the Lower Lip, l(3)S023938, DPR55, CG 7913, ZW-3, EP3559, Proteins, Phosphorylations, Spp, SPP, Factor, zw-3, Sprout, DmelCG5643, native protein, tirosina, chemical analysis, Canadian hard winter wheat, PKS complex, PP2A C, spp, PP2A A, VWS, phosphorylation enrichment, scales, PKS, Mitogen, Ontology Project, Calcium, l(2)02496, Sprouts, PP2Cepsilon, DmelCG17291, C86142, postnatal growth, l(2)s5286, l(3)S032303, l(3)S075110, hoja (Spanish, tws/aar, signalling, Polio and Post-Polio Syndrome, Cg17746, Phytomitogens, l(3)S105605, Gene Proteins, Durum Wheats, sgg/zw3, signalling process, Zw-3, ppp2r2b-a, 3-10, Sgg/Zw3/GSK3, CG6525, liquid chromatography tandem mass spectrometry, X-organ of Keilin, Pp2A29B, 8430431H08Rik, liquid chromatography tandem mass spectroscopy, GSK-3beta, scale tissue, Gene Ontology Projects, l(3)S025913, determination, popliteal pterygium syndrome, DmelCG7913, Pflanze, Calcium 40, postnatal development, Mbp1, protein, l(3)S060804, viridiplantae, Pallister-Killian mosaic syndrome, Zw3[sgg], l(3)S024838, l(3)S025806, l(3)S045519, exact), l(3)S043008b, skc35, gsk-3 Gene Product, skp1, Project, MDS1, Tws, PpS, 0318/07, PP2, l(3)S031006, GSK3beta, l(3)S053011, l(3)S080409, protein aggregate, Wheat, C62, DMSGG3, Malted Grain, GSK3Beta, LCMSMS, l(3)s1801, l(3)S049902, l(3)S067109b, TYPE 2A SERINE/THREONINE PROTEIN PHOSPHATASE, PPS, Pps, MTS/PP2A, posterior pharyngeal sensilla, Phosphoprotein, EG:BACR7C10.8, CCR1, Dm Zw3, v158, Tyr, R75353, signaling process, F20P5.30, ER2-6, ATP, l(3)S043029, F20P5_30, v&#225stago (Spanish, l(3)S024834a, tw, Organ X, GSKbeta, PP2a 28D, gyltl1b-b, l(3)S025832, l(1)G0335, PP2C1, l(3)S022440, zw3(sgg), gsk3-beta, LC-MS/MS, 2-Amino-3-(p-hydroxyphenyl)propionic acid, CG7109, B/PR55, l(3)S101413b, Pp2A-85F, 3222401G13, results, Killian syndrome, l(3)S023309, anon-WO03040301.132, PAS14, anon-WO03040301.254, CG7001, l(3)S110008a, larval pharyngeal sense organ, MDDGA6, Seed, KIAA0609, zw3[sgg], BcDNA:LD34343, OCAIA, l(3)S029701a, SHEP3, ptpa, Gene Ontologies, Hexasomy 12P, PP2A B', Transphosphorylases, gyltl1b, Factors, Ontologies, GSK-3, growth pattern, non-developmental growth, PTPA, mdc1d, Triticum sativum, Plant, SGG/GSK3b, CG6235, l(1)3Ba, l(3)S061915, Gsk-3, CG33297, l(3)S066017, l(3)S032708c, calcium, l(3)S023206, enlarged, spine, Isochromosome 12p syndrome, l(3)S134601a, GSK3beta/SGG, l(3)S022361, GSK3-beta, l(3)S061805, Protein Kinase, dpp2c1, gsk-3, biological signaling, DmelCG2621, DmelCG2984, PP2A-29B, Gene, Wdb, Pk?4, GSK3, dPP2A, Gsk-3beta, Gsk3, CABBAGE 2, l(3)S075515b, Triticum aestivum subsp. aestivum, l(3)S111515, EG:155E2.3, CG13383, froggy, Gyltl1a, LC-MS-MS, protrusion, dPR55, CAT1, gsk3, l(3)S048507, l(1)G0263, polypeptide chain, 7330414F15Rik, 20Ca, Phytomitogen, 芽生え、実生 (Japanese, Zw3-sh, Malted, Killian Teschler-Nicola syndrome, cleft Lip/palate, Phosphotransferase, DMZ3K25Z, dB56-2, CG12169, dB56-1, BcDNA:GM05554, PP2A-A, Calcium-40, B'/PR61, PP2A-B, l(3)S022205b, HAF3, PP2A-C, l(3)S146606, Triticum spelta, LPS, Triticum aestivam, LARGE, Transphosphorylase, ATP-protein phosphotransferase, BPFD#36, bread wheat, CMM8, GSK3betagr, great, l(3)S024455, AW045850, sgg10, Triticum durum, l(1)G0055, l(3)S060203, Malted Grains, protein complex, Mts, l(3)S023013, Kalzium, l(3)S028707, gsk3beta, l(3)S052810, Phosphotransferases, ATBRI1, development, LC/MS/MS, tetrasomy 12P, OCA1A, 5930404J21Rik, natural protein, Protein, Can, CG2621, CG2984, l(1)G0183, GSK-3B, scale, DmelCG12169, xgsk-3, Durum, Kinases, GLC2, Isochromosome 12P syndrome, faciogenitopopliteal syndrome, Protein Gene Products, BR INSENSITIVE 1, Coagulation Factor IV, l(1)zw3, Pallister mosaic syndrome, Sprouted Seeds, 2414, 6330556D22Rik, assay, growth, DmelCG70010falseTaestivum - Leaf, iBAQ (Lvetal,jproteomeres2014)abundance based on iBAQ, Interaction consistency score: 6.7, Coverage: 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