{"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":["83332"],"full_dataset_link":["https://pax-db.org/dataset/83332/853879106"],"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":["Deciphering physiological changes that mediate transition of Mycobacterium tuberculosis between replicating and nonreplicating states is essential to understanding how the pathogen can persist in an individual host for decades. We have combined RNA sequencing (RNA-seq) of 5' triphosphate-enriched libraries with regular RNA-seq to characterize the architecture and expression of M. tuberculosis promoters. We identified over 4,000 transcriptional start sites (TSSs). Strikingly, for 26% of the genes with a primary TSS, the site of transcriptional initiation overlapped with the annotated start codon, generating leaderless transcripts lacking a 5' UTR and, hence, the Shine-Dalgarno sequence commonly used to initiate ribosomal engagement in eubacteria. Genes encoding proteins with active growth functions were markedly depleted from the leaderless transcriptome, and there was a significant increase in the overall representation of leaderless mRNAs in a starvation model of growth arrest. The high percentage of leaderless genes may have particular importance in the physiology of nonreplicating M. tuberculosis."],"pubmed_title":["Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis."],"pubmed_authors":["Cortes Teresa T, Schubert Olga T OT, Rose Graham G, Arnvig Kristine B KB, Comas Iñaki I, Aebersold Ruedi R, Young Douglas B DB"],"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"],"pubmed_title_synonyms":["Bacillus tuberculosis, Bacterium tuberculosis, Transcriptome, wide/broad, Mycobacterium tuberculosis (Zopf 1883) Lehmann and Neumann 1896 (Approved Lists 1980), Genomes, Transcriptome Profile, Profile, Expression Profiles, Gene Expression Profile, Gene, whole genome, Profiles, broad, Signatures, whole transcriptome, Gene Expression, Mycobacterium tuberculosis H37Rv., wide, Expression Signature, Gene Expression Profiles, Expression Signatures, Mycobacterium tuberculosis var. hominis, Gene Expression Signatures, Transcriptomes, Gene Expression Signature, Signature, Expression Profile, Mycobacterium tuberculosis typus humanus, Transcriptome Profiles"],"name_synonyms":["dTAF[[II]]230, TAF[[II]]250, d230, multi-cellular organism, Rab interactor activity, Rab escort protein, Kochs Disease, F5E6_13, body, TAF200, ADP-ribosylation factor binding, Ral GTPase binding, l(3)84Ab, whole body, dTAFII250, AthREP, drep, BG:DS00004.13, TAFII-250, TAF250/230, F5E6.13, ARF binding, EfW1, Tip48/Reptin, rep, Cell, dTAF230, dmTAF[[II]]230, organism, Rab escort protein activity, TAFII250, dmTAF1, Taf230, p230, Ras interactor activity, Infection, TAF[[II]]250/230, Rept, TFIID, Tuberculosis, GTP-Rho binding, Tuberculoses, dRep, Ran GTPase binding, animal, DmelCG8432, TAF250, Koch's Disease, dReptin, Taf[[II]]250, l(3)06945, Koch Disease, Taf200, dTAF[[II]]250, TAF[[II]]230, whole organism, anon-WO0142479.1., TFIID TAF250, Infections, CG9750, cel, cell, Reptin, REPT, Taf1p, TAF[II]250, Ran-binding protein, Mycobacterium tuberculosis Infections, DmelCG9750, Rho GTPase binding, CG17603, TAF[[II]], Ran protein binding, dTAF250, DmelCG17603, Rac GTPase binding, CG8432, Taf250, GTP-Ral binding, SR3-5, Koerper, Tip48, Mycobacterium tuberculosis, Ras GTPase binding, Mycobacterium tuberculosis Infection, TAF, Rab GTPase binding, active tuberculosis, REP, TAF230, TAF1"],"pubmed_abstract_synonyms":["host organism, Ribonucleic, Materials, Transcriptome Profile, P62, postnatal development, Gene Expression Profile, Gene, growth and development, eubacteria, Profiles, sci, Mendosicutes, Readability, Rbt, Sense Codon, Mycobacterium tuberculosis var. hominis, Gene Products, HOW, How, Whole Transcriptome Shotgun Sequencing, Tuberculosis, Bacteriobiota, Non Polyadenylated, l(3)j5D5, RNA Gene Products, 24B, Koch's Disease, Bacillus tuberculosis, Bacterium tuberculosis, Koch Disease, Eubacteria, l(3)s2612, Genetic, Infections, Metabacteria, Profile, Sense, stru, proteins, l(3)S053606, Mycobacterium tuberculosis Infections, CG10293, Monera, Signatures, Non-Polyadenylated RNA, Bacteria Woese et al. 2024, Bacteria (ex Cavalier-Smith 1987), l(3)j5B5, INSDC_feature:misc_feature, GPR14, reaction, Expression Signature, Prokaryotae, DmelCG10293, Transcriptomes, Gpr14, site, Mycobacterium tuberculosis, Procaryotae, Archaebiota, 0904/17, RNA, bacteria, Archaebacteria, Transcriptome, Mycobacterium tuberculosis (Zopf 1883) Lehmann and Neumann 1896 (Approved Lists 1980), Kochs Disease, ribose nucleic acid, clone 2.39, Proteins, Expression Profiles, ribonucleic acids, UTR, RNA-seq, RNS, function, qkr, l(3)S090417, Cistrons, Ts, whole transcriptome, development, Gene Expression, native protein, untranslated region, SZ1, yeast nucleic acid, KH93F, Ribonukleinsaeure, Expression Signatures, Protein, Gene Expression Signatures, Infection, sequence, pentosenucleic acids, Genetic Materials, Sense Codons, prokaryotes, Ribonucleic acids, Tss, Gene Expression Signature, Tuberculoses, Expression Profile, Library, Genetic Material, region, Codons, Mycobacterium tuberculosis., who, Transcriptome Profiles, ribonucleic acid, Acid, growth pattern, not Bacteria Haeckel 1894, non-developmental growth, Mycobacterium tuberculosis H37Rv, Non Polyadenylated RNA, archaea, postnatal growth, Non-Polyadenylated, initiation, Codon, Who/How, Ribonucleic Acid, Understanding, UTR2, 0610025G13Rik, primary structure of sequence macromolecule, Protein Gene Products, Gene Proteins, UR-2-R, Material, prokaryote, Gene Expression Profiles, qkr[93F], anon-EST:Liang-2.39, Cistron, Mycobacterium tuberculosis Infection, Signature, growth, active tuberculosis, Prokaryota, Mycobacterium tuberculosis typus humanus"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"M.tuberculosis - Whole organism, Pepxml, SC (Cortes,cell_rep,2013)","description":"abundance based on Spectral counting, pepxml, Interaction consistency score: 5.2, Coverage: 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