PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering265311https://pax-db.org/dataset/265311/3767265120mering@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 near-minimal bacterium Mesoplasma florum is an interesting model for synthetic genomics and systems biology due to its small genome (~ 800 kb), fast growth rate, and lack of pathogenic potential. However, fundamental aspects of its biology remain largely unexplored. Here, we report a broad yet remarkably detailed characterization of M. florum by combining a wide variety of experimental approaches. We investigated several physical and physiological parameters of this bacterium, including cell size, growth kinetics, and biomass composition of the cell. We also performed the first genome-wide analysis of its transcriptome and proteome, notably revealing a conserved promoter motif, the organization of transcription units, and the transcription and protein expression levels of all protein-coding sequences. We converted gene transcription and expression levels into absolute molecular abundances using biomass quantification results, generating an unprecedented view of the M. florum cellular composition and functions. These characterization efforts provide a strong experimental foundation for the development of a genome-scale model for M. florum and will guide future genome engineering endeavors in this simple organism.Integrative characterization of the near-minimal bacterium Mesoplasma florum.Matteau Dominick D, Lachance Jean-Christophe JC, Grenier Frédéric F, Gauthier Samuel S, Daubenspeck James M JM, Dybvig Kevin K, Garneau Daniel D, Knight Thomas F TF, Jacques Pierre-Étienne PÉ, Rodrigue Sébastien SAdd, 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, ratioAcholeplasma florum.Koerper., organism, whole body, multi-cellular organism, whole organism, animal, bodyscale tissue, Acholeplasma florum, Size, artificial sequence, Materials, single-organism developmental process, determination, postnatal development, Gene Expression Profile, Non-Governmental Organizations, growth and development, Progress Reports, Profiles, protein, Foundation, dmTAF[[II]]230, protein polypeptide chains, DSmurf, Summary Report, Volume, protein aggregate, animal, Summary Reports, strong, TFIID TAF250, Biology, Genomes, Progress Report, cel, Comparative Genomics, plant peltate hair, hypoplasia, proteins, Futurology, Signatures, Fast, Progress, Field Reports, Expression Signature, Smurf, Transcriptomes, Organizations, transcription from bacterial-type RNA polymerase promoter, SIMPLE, FAST, CG4943, D-smurf, size of cell, Predictions and Projections, close to, dTAF[[II]]230, Genomics, wide/broad, organisation, Comparative, Expression Profiles, TAF200, Volumes, FASTK, Functional Genomics, Lack, TAFII-250, TAF250/230, results, Gene Expression, organism, TAFII250, Investigative Report, PIG7, Expression Signatures, Sizes, Genetic Materials, Expression Profile, Genetic Material, Transcriptome Profiles, Koerper., whole organism, DmelCG4943, growth pattern, Nongovernmental, Engineerings, non-developmental growth, administrative structure, Field, INSDC_feature:gene, whole genome, CG17603, TAF[[II]], SYNTHETIC CONSTRUCT sequences, wide, Report, Taf250, Material, SR3-5, bacterial transcription, artificial, Cistron, Proteomes, TAF230, d230, multi-cellular organism, Transcriptome Profile, dSmurf1, peltate hair, STK10, Cell Volume, Gene, organization and administration, dTAFII250, Coding, broad, protein-containing complex, EfW1, Structural, Investigative, reduced, polypeptide chain, resilient, dmTAF1, Taf230, tough, Functional, Gene Products, Projections and Predictions, Non-Governmental, tiny, synthetic genetic interaction (sensu inequality), Medical, TAF250, Organization, Taf200, dTAF[[II]]250, Clinical, Genetic, cell, Medical Coding, Profile, synthetic genetic interaction defined by inequality, Taf1p, dTAF250, d-smurf, Non-Governmental Organization, ATP:Fas-activated serine/threonine protein phosphotransferase activity, species, organization, Investigative Reports, Cell Volumes, TAF, TP53I7, small, TAF[[II]]250, Transcriptome, organizational structure, protein complex, body, Proteins, total expressed protein, l(3)84Ab, artificial gene, whole body, BG:DS00004.13, synthetic DNA, Dsmurf, motif, Cistrons, Cell, dTAF230, near to, whole transcriptome, dSmurf, development, native protein, natural protein, p230, Smurf ubiquitin ligase, Systems, Research Reports, chemical analysis, Gene Expression Signatures, Protein, synthetic, TAF[[II]]250/230, TFIID, Gene Expression Signature, scales, Nongovernmental Organizations, INSDC_feature:regulatory, administrative management, Taf[[II]]250, TAF[[II]]230, scale, underdeveloped, postnatal growth, TAF[II]250, synthetic constructs, Protein Gene Products, Cell Sizes, Gene Proteins, Non Governmental Organizations, DmelCG17603, Reports, Biomasses, approaches, Gene Expression Profiles, vicinity of, organizational management, Structural Genomics, assay, Signature, Summary, Future, growth, Nongovernmental Organization, Field Report, TAF10falseMflorum L - Whole organism, SC (Matteauetal,molsystbiol2020)abundance based on Spectral counting, Interaction consistency score: 3.3, Coverage: 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