PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering10090https://pax-db.org/dataset/10090/1300563876mering@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.The suprachiasmatic nucleus (SCN) acts as the central clock to coordinate circadian oscillations in mammalian behavior, physiology and gene expression. Despite our knowledge of the circadian transcriptome of the SCN, how it impacts genome-wide protein expression is not well understood. Here, we interrogated the murine SCN proteome across the circadian cycle using SILAC-based quantitative mass spectrometry. Of the 2112 proteins that were accurately quantified, 20% (421 proteins) displayed a time-of-day-dependent expression profile. Within this time-of-day proteome, 11% (48 proteins) were further defined as circadian based on a sinusoidal expression pattern with a ∼24 h period. Nine circadianly expressed proteins exhibited 24 h rhythms at the transcript level, with an average time lag that exceeded 8 h. A substantial proportion of the time-of-day proteome exhibited abrupt fluctuations at the anticipated light-to-dark and dark-to-light transitions, and was enriched for proteins involved in several key biological pathways, most notably, mitochondrial oxidative phosphorylation. Additionally, predicted targets of miR-133ab were enriched in specific hierarchical clusters and were inversely correlated with miR133ab expression in the SCN. These insights into the proteomic landscape of the SCN will facilitate a more integrative understanding of cellular control within the SCN clock.The proteomic landscape of the suprachiasmatic nucleus clock reveals large-scale coordination of key biological processes.Chiang Cheng-Kang CK, Mehta Neel N, Patel Abhilasha A, Zhang Peng P, Ning Zhibin Z, Mayne Janice J, Sun Warren Y L WY, Cheng Hai-Ying M HY, Figeys Daniel DAdd, 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, scale tissue, anatomical protrusion, nucleus suprachiasmaticus, gyltl1b-b, peltate hair, Mbp1, 5330400M04Rik, XClock, dIKK-gamma, froggy, Gyltl1a, protrusion, clk, IKKgamma, large, DmIKKgamma, dIKK, MDDGA6, mKIAA0609, DmIKK-gamma, Kenny, spine., dmIKKgamma, scales, IKK[[gamma]], Suprachiasmatic Nucleus, myd, KIAA0609, IKKg, KEY, Key, bHLHe8, fg, Hypothalamic, gyltl1b, scale, Dmikkgamma, MDDGB6, plant peltate hair, mdc1d, IKK-gamma, KAT13D, expanded, Mbp-1, LARGE, mKIAA0334, CG16910, Hypothalamic Suprachiasmatic Nuclei, BPFD#36, Xclk, MDC1D, DmelCG16910, enr, IKK, enlarged, Hypothalamic Suprachiasmatic Nucleus, great, nucleus suprachiasmaticus hypothalami, Suprachiasmatic Nuclei, suprachiasmatic nucleus (Spiegel-Zwieg), SCNnucleus suprachiasmaticus hypothalami, Suprachiasmatic Nuclei, SCN., muscle, Hypothalamic, Suprachiasmatic Nucleus, nucleus suprachiasmaticus, Hypothalamic Suprachiasmatic Nucleus, suprachiasmatic nucleus (Spiegel-Zwieg), musculus, muscle element, Hypothalamic Suprachiasmatic NucleiHac-1/Dark, PP17, PP19, DmelCG6829, fond, bar, Gene Expression Profile, Visible Light, Profiles, protein, sci, CycEI, Apaf-1, IDOL, Long Term, prevention, protein polypeptide chains, Readability, anon-WO0134654.19, Ccne, DmelCG4637, Oxidative, hnu, AA959943, HOW, How, Apaf1, Analysis, 1110025J15Rik, Mir, MIR, protein aggregate, Effect, ARK, prevention and control, foton, l(3)j5D5, IKKg, C1orf215, KEY, Key, 24B, Mass Spectrum Analysis, Miranda, average, Hypothalamic, Gene Expressions, hac-1, reference sample, Genomes, Analyses, proportionality to, KAT13D, stru, arc, proteins, l(3)S053606, mir, mKIAA0334, DmelCG7693, CG10293, ark, Signatures, 4624, T1, Acts, Pp17, Pp18, preventive measures, l(3)j5B5, TNFSF14, Expression Signature, Pp19, Transcriptomes, CP-22, dApaf1, P18, l(3)07551, P19, Idol, Long-Term Effects, gamma, single-organism behavior, Acta-2, 9430057C20Rik, 0904/17, preventive therapy, Radiation, wide/broad, nucleus suprachiasmaticus, Process, D-Apaf-1, UNQ391/PRO726, 6.3.2.-, Expression Profiles, anon-53Fa, Longterm Effect, Actsk-1, l(2)SH0173, RCB2758, Light, Cyc E, br37, XClock, Spectrum Analysis, INSDC_feature:misc_RNA, Acceptance Processes, predicted, CG4637, Spectroscopy, CG12249, Gene Expression, Menstruation, Acceptance Process, DmIKKgamma, LIGHT, BG:DS07108.3, neutropenia, ATP synthase D chain, SZ1, dIKK, Expression Signatures, bar3, LAP18, Kenny, l(2)05206, Expression Profile, CG6829, Lap18, Transcriptome Profiles, dark/hac-1/dapaf-1, Visible Radiations, dOSR1, Phosphorylation, Epistemology, Mitochondrial, Visible Radiation, l(3)neo56, HVEML, l(3)neo57, CG7693, Mira, proportionality, IKK-gamma, Spectrometry, rate, Inducible degrader of the LDL-receptor, whole genome, hac1, dapaf-1S, wide, apaf-1, light quantum, dapaf-1L, l35Dd, DmelCG16910, MIRA, anon-EST:Liang-2.39, Proteomes, V19, hg, HH, cycline, Dapaf-1/HAC-1, Transcriptome Profile, Effects, Processes, P62, DmcyclinE, number, Gene, cycE, broad, Spectrum Analyses, 5330400M04Rik, protein-containing complex, mitochondrial, presence, l(2)br37, dIKK-gamma, CYCLE, Ly113, Hh, cdi7, Dark/Hac-1/dApaf1, clk, Hac1, Dark/Hac-1/dApaf-1, cyclinE, polypeptide chain, DmIKK-gamma, Gene Products, Cdi7, CDI7, Mass, SMN, Smn, dmIKKgamma, IKK[[gamma]], Mass Spectroscopy, bHLHe8, 19k, proportion, CYCE, l(3)s2612, pattern, MONDOA, Longterm, distribution, DmelCG3938, dSTRAD, Lichtquant, Profile, CyclE, Mrt, dapaf-1, 3938, dapaf, Long-Term, Visible, dark, DmcycE, respiratory-chain phosphorylation, Expressions, l(2)k05007, dm-cycE, Oxidative Phosphorylations, Myosin regulatory light chain-interacting protein, IKK, DARK, bar-3, DmelCG10293, Pig, photon, CP22, Lag, LAG, Suprachiasmatic Nuclei, Long-Term Effect, Expression, TR2, bHLHe36, Behaviors, dArk, Dapaf-1, Controlled, dark/dapaf-1/hac-1, l(3)hh, Controlling, Transcriptome, Myosin regulatory light chain interacting protein, clone 2.39, protein complex, dApaf-1, Proteins, Phosphorylations, total expressed protein, lag, apaf1, function, qkr, l(3)S090417, CD258, whole transcriptome, AW228700, IKKgamma, count in organism, APAF1, MS, l(2)k02514, native protein, DmCycE, natural protein, Period, Hac-1, KH93F, Gene Expression Signatures, Protein, Long Term Effects, DmelCG12249, Gene Expression Signature, CyeE, STE20-like/SPAK, Dark, Suprachiasmatic Nucleus, Dark/Apaf-I, Mass Spectrum Analyses, who, Radiations, Acceptance, Mass Spectrum, severe congenital, Pr22, XClock., l(2)k02602, HVEM-L, Dmikkgamma, Op18, prophylaxis, l(2)35Dd, Photoradiation, Dark/Dapaf-1/HAC1, Who/How, Understanding, CG16910, dApaf-1/DARK/HAC-1, Longterm Effects, LTg, Hypothalamic Suprachiasmatic Nuclei, Protein Gene Products, Gene Proteins, D-CycE, Xclk, PR22, Photoradiations, anon-WO0182946.19, control, Hypothalamic Suprachiasmatic Nucleus, Gene Expression Profiles, OP18, quotient, qkr[93F], nucleus suprachiasmaticus hypothalami, Severe Chronic Neutropenia, Signature, CG3938, suprachiasmatic nucleus (Spiegel-Zwieg), dAPAF-1, SCN0falseM.musculus - Suprachiasmatic nucleus, iBAQ (Chiangetal,plosgenetics.2014)abundance based on iBAQ, Interaction consistency score: 15.5, Coverage: 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