{"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"},"statusCode":"OK","statusCodeValue":200}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Christian von Mering"],"species":["4932"],"full_dataset_link":["https://pax-db.org/dataset/4932/2226156413"],"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":["Complete genome sequences together with high throughput technologies have made comprehensive characterizations of gene expression patterns possible. While genome-wide measurement of mRNA levels was one of the first applications of these advances, other important aspects of gene expression are also amenable to a genomic approach, for example, the translation of message into protein. Earlier we reported a high throughput technology for simultaneously studying mRNA level and translation, which we termed translation state array analysis, or TSAA. The current studies test the proposition that TSAA can identify novel instances of translation regulation at the genome-wide level. As a biological model, cultures of Saccharomyces cerevisiae were cell cycle-arrested using either alpha-factor or the temperature-sensitive cdc15-2 allele. Forty-eight mRNAs were found to change significantly in translation state following release from alpha-factor arrest, including genes involved in pheromone response and cell cycle arrest such as BAR1, SST2, and FAR1. After the shift of the cdc15-2 strain from 37 degrees C to 25 degrees C, 54 mRNAs were altered in translation state, including the products of the stress genes HSP82, HSC82, and SSA2. Thus, regulation at the translational level seems to play a significant role in the response of yeast cells to external physical or biological cues. In contrast, surprisingly few genes were found to be translationally controlled as cells progressed through the cell cycle. Additional refinements of TSAA should allow characterization of both transcriptional and translational regulatory networks on a genomic scale, providing an additional layer of information that can be integrated into models of system biology and function."],"pubmed_title":["The transcriptome and its translation during recovery from cell cycle arrest in Saccharomyces cerevisiae."],"pubmed_authors":["Serikawa Kyle A KA, Xu Xie Lillian XL, MacKay Vivian L VL, Law G Lynn GL, Zong Qin Q, Zhao Lue Ping LP, Bumgarner Roger R, Morris David R DR"],"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":["protein translation, protein anabolism, Transcriptome, protein biosynthetic process, lager beer yeast., tumor suppressor, Cell Cycle-Transition Point, Transcriptome Profile, Saccharomyces cerevisiae 'var. diastaticus', cell cycle arrest, Cell Cycle Control, Expression Profiles, Brewer's, Gene Expression Profile, Gene, baker's yeast, arrest of cell cycle progression, Profiles, Cell, Arrests, Saccharomyces italicus, Saccaromyces cerevisiae, whole transcriptome, Gene Expression, Baker's Yeasts, Sccharomyces cerevisiae, Cell Cycle-Transition Points, positive regulation of cell cycle arrest, cell cycle regulator, Checkpoints, Saccharomyces diastaticus, arrest of mitotic cell cycle progression, termination of cell cycle, Expression Signatures, Gene Expression Signatures, yeast, protein formation, protein biosynthesis, Cell Cycle Transition Points, Gene Expression Signature, Cell Cycle Arrests, Expression Profile, Transcriptome Profiles, Saccharomyces oviformis, Arrest, Yeast, Cell Cycle Controls, Profile, cessation of cell cycle, Control, Saccharomyes cerevisiae, Baker, Controls, Saccharomyces uvarum var. melibiosus, Signatures, Cell Cycle Checkpoint, mitotic cell cycle arrest, S. cerevisiae, Cycle-Transition Point, Saccharomyces cerevisiae (Desm.) Meyen ex E.C. Hansen, S cerevisiae, Candida robusta, protein synthesis, Expression Signature, Saccharomyces capensis, Gene Expression Profiles, Point, Transcriptomes, regulation of cell cycle arrest, Baker's, Checkpoint, Cell Cycle, Mycoderma cerevisiae, Cell Cycle-Transition, 1883, Signature, Baker's Yeast, brewer's yeast, Cell Cycle Arrest, Brewer's Yeast, negative regulation of cell cycle arrest, Baker Yeast"],"name_synonyms":["l(3)Ca, multi-cellular organism, body, mCRY, titin, whole body, 26S protease, l(3)62Ca, d-titin, 0020/01, threonine endopeptidase activity, Mbh1, SLS, Sls, ingensin, kettin, organism, large multicatalytic protease, CFU-MC, HEL-S-66, DmelCG1915, Titin, prosome, Crry, multicatalytic endopeptidase complex, animal, anon-CREST, Ket, CFU-Mast, tricorn proteinase, D-titin, l(3)j1D7, whole organism, AFCP, colony forming unit mast cell, D-Titin, CG18857, MIC10, ket, sam, sal, TLX, l(3)dre8, lens neutral proteinase, CG1915, CT41299, multicatalytic proteinase (complex), Koerper, proteasome endopeptidase complex., KZ, polyhedral organelle, l(3)S002001, l(3)rL182, CG18242, tricorn protease, AHUS2, TRA2.10, Mcp, MCP, alkaline protease, multicatalytic proteinase, CG18245"],"pubmed_abstract_synonyms":["protein translation, scale tissue, Hsp86-1, BamF, Materials, tumor suppressor, determination, BamC, AP-2, hspca, alpha-Spe, Cue, protein, E(sev)3A, alpha-Spc, CG31654, Arrests, C81438, Social Controls, DmelCG1242, stc, protein polypeptide chains, l(3)04276, Cell Cycle-Transition Points, cell cycle regulator, AL024080, Roles, LAP-2, responsivity, Concepts, alpha-adaptin, Cell Cycle Transition Points, LAP2, DmelCG10422, protein aggregate, Non Polyadenylated, Formal Social Controls, alpha-spec, hsp4, Cell Division Cycles, HSP82, Smstr2, anon-WO0068693, Gene Expressions, CG4260, reference sample, Genomes, Hsp89, Hsp84, Polyadenylated Messenger, plant peltate hair, Hsp86, Hsp90, Saccharomyes cerevisiae, FCAALL.134, cell sheath, proteins, Baker, Ssa2, E(sina)2, SSA2, Saccharomyces uvarum var. melibiosus, ecotype, hspc1, alpha-spectrin, l(3)j5C2, Social, allergic reaction, HSP90, HSPN, Saccharomyces capensis, Smstr-2, Cell Cycles, Role Concepts, Baker's, Hsp82, Mycoderma cerevisiae, Cell Cycle, Strains, brewer's yeast, Cell Cycle Arrest, hspn, A530054J02Rik, HSP83, HSP86, HSPCAL1, HSPCAL4, protein anabolism, protein biosynthetic process, Hsp84-1, wide/broad, LYT1, Polyadenylated, Arts, lamina, ham, 89kDa, CG1242, SST1, Division Cycles, ada, RORNP, 83K HSP, Baker's Yeasts, alphaSpec, en(lz)3C/4C, D-Ada, Role Concept, sst2, Saccharomyces diastaticus, arrest of mitotic cell cycle progression, git10, cg4260, protein formation, Role, Genetic Materials, dAP-2a, cultivar, spectrin, Genetic Material, Polyadenylated Messenger RNA, l(2)06694, MENE (2L)-A, HSP90N, Yeast, Arrest, Industrial, Non Polyadenylated mRNA, protein_coding_transcript, Industrial Arts, 1810007I17Rik, function., Division Cycle, anon-EST:Liang-2.53, cessation of cell cycle, Control, HSP90A, whole genome, alpha, AP-2alpha, Controls, Non-Polyadenylated mRNA, DmelCG4260, organ system, Saccharomyces cerevisiae (Desm.) Meyen ex E.C. Hansen, Cycle-Transition Point, wide, protein synthesis, Material, pheromone response, 90kDa, regulation of cell cycle arrest, microarray, Cistron, Regulation, Strains and Sprains, Poly(A) RNA, Brewer's Yeast, 83, Regulations, alpha-Ada, anon-EST:fe2E2, l(3)alpha-Spec, HSP89A, Cell Cycle Control, peltate hair, alpha-Spect, Brewer's, Gene, baker's yeast, arrest of cell cycle progression, MLSTD2, AL022974, broad, protein-containing complex, body system, Saccharomyces italicus, l(2)SH2 0460, fs(3)neo61, YG102, CG10422, alpha-ada, polypeptide chain, Messenger, sensitive, termination of cell cycle, yeast, Cycle, klo, Gene Products, swo1, system, alpha-Sp, CG1977, Sprains, sensitivity, lager beer yeast, Cycles, reactivity, hsp90a, anatomical systems, Genetic, DL3590W, layer, ms(3)08445, Cell Division Cycle, cell-division cycle, dre3, messenger RNA, Cell Division, SSTR-2, Alpha-Adaptin, Expressions, S. cerevisiae, template RNA, S cerevisiae, Candida robusta, hsp89, hsp86, hsp84, hsp83, Checkpoint, hsp90, Expression, 1883, Cell Cycle-Transition, negative regulation of cell cycle arrest, l(3)dre3, Controlled, RNA, Controlling, alpha-Spectrin, Cell Cycle-Transition Point, AI646302, Formal Social Control, Saccharomyces cerevisiae 'var. diastaticus', 3A9, protein complex, cell cycle arrest, DmelCG1977, Proteins, Sprain, hsp82, RO60, Messenger RNA, Cistrons, Saccaromyces cerevisiae, Cell, strain, Concept, Sccharomyces cerevisiae, positive regulation of cell cycle arrest, EL52, 86kDa, SS-A|Ro, Checkpoints, FAR-RED IMPAIRED RESPONSE 1, native protein, Temperatures, natural protein, Social Control, Poly(A)+ mRNA, Protein, chemical analysis, HSPC1, Strain, INSDC_feature:mRNA, protein biosynthesis, MENE(2L)-A, clone 2.53, Polyadenylated RNA, scales, connected anatomical system, Cell Cycle Arrests, alphaSp, 143198_at, Saccharomyces oviformis, anon-WO0140519.209, Poly(A)+ RNA, SDR10E1, lap2, D-alphaAda, mating_type_alpha, scale, mRNA, Poly(A) Tail, Cell Cycle Controls, Non-Polyadenylated, FCP-B, DMHSP82, HSPCA, Cell Cycle Checkpoint, mitotic cell cycle arrest, Protein Gene Products, Su(Raf)3A, Ssa, Gene Proteins, AP2, Hspcb, l(3)62Bd, AL024147, Bam-C, Point, ORF1, BAM, Bam, alpha mating type (yeast), Hspca, sheath of cells, l(2)SH0460, layer of cells, alfa-Spec, regulation, assay, response, Baker's Yeast, Polyadenylated mRNA, Spec, Baker Yeast"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"S.cerevisiae - Whole organism, SC (Serikawa,mcp,2003)","description":"abundance based on Spectral counting, Interaction consistency score: 1.6, Coverage: 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