{"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":["9606"],"full_dataset_link":["https://pax-db.org/dataset/9606/2206792627"],"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":["An essential question in human biology is how cells and tissues differ in gene and protein expression and how these differences delineate specific biological function. Here, we have performed a global analysis of both mRNA and protein levels based on sequence-based transcriptome analysis (RNA-seq), SILAC-based mass spectrometry analysis and antibody-based confocal microscopy. The study was performed in three functionally different human cell lines and based on the global analysis, we estimated the fractions of mRNA and protein that are cell specific or expressed at similar/different levels in the cell lines. A highly ubiquitous RNA expression was found with >60% of the gene products detected in all cells. The changes of mRNA and protein levels in the cell lines using SILAC and RNA ratios show high correlations, even though the genome-wide dynamic range is substantially higher for the proteins as compared with the transcripts. Large general differences in abundance for proteins from various functional classes are observed and, in general, the cell-type specific proteins are low abundant and highly enriched for cell-surface proteins. Thus, this study shows a path to characterize the transcriptome and proteome in human cells from different origins."],"pubmed_title":["Defining the transcriptome and proteome in three functionally different human cell lines."],"pubmed_authors":["Lundberg Emma E, Fagerberg Linn L, Klevebring Daniel D, Matic Ivan I, Geiger Tamar T, Cox Juergen J, Algenäs Cajsa C, Lundeberg Joakim J, Mann Matthias M, Uhlen Mathias M"],"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":["dTAF[[II]]230, TAF[[II]]250, d230, Transcriptome, human being, Transcriptome Profile, Modern, Expression Profiles, TAF200, Gene Expression Profile, total expressed protein, Gene, l(3)84Ab, dTAFII250, Profiles, BG:DS00004.13, TAFII-250, TAF250/230, EfW1, Cell, Human, dTAF230, whole transcriptome, Gene Expression, dmTAF[[II]]230, TAFII250, Homo sapiens, dmTAF1, Taf230, p230, Expression Signatures, Gene Expression Signatures, TAF[[II]]250/230, TFIID, Gene Expression Signature, Expression Profile, Man, Transcriptome Profiles, TAF250, Taf[[II]]250, Taf200, dTAF[[II]]250, TAF[[II]]230, Man (Taxonomy), TFIID TAF250, cel, cell, Profile, Taf1p, TAF[II]250, CG17603, man, TAF[[II]], Signatures, human, dTAF250, DmelCG17603, TAF1., Taf250, Expression Signature, Gene Expression Profiles, SR3-5, Modern Man, Transcriptomes, Signature, TAF, Proteomes, TAF230"],"name_synonyms":["Line, Cell Lines, multi-synapse, multisynapse, multiple synapse., Cell, Lines"],"pubmed_abstract_synonyms":["Ribonucleic, Materials, determination, Mbp1, Gene Expression Profile, A4, protein, Profiles, B-cell receptor complex, sci, dmTAF[[II]]230, protein polypeptide chains, DmelCG3424, Light Microscopy, HOW, How, 10.5, protein aggregate, myd, Non Polyadenylated, l(3)j5D5, RNA Gene Products, 10.9, integumentum commune, 24B, me75, F, Man (Taxonomy), TFIID TAF250, DmelCG2328, Genomes, cel, membrane bound, Polyadenylated Messenger, Simple, Tissue, stru, Mbp-1, proteins, V, l(3)S053606, Hand-Held Microscopy, Estimated, CG10293, Signatures, D17Mit170, T1, l(3)j5B5, Expression Signature, Hand-Held, Transcriptomes, B-lymphocyte receptor complex, 0904/17, dTAF[[II]]230, wide/broad, PLATEST, external covering of organism, Polyadenylated, ribose nucleic acid, gyltl1b-b, Modern, Expression Profiles, ribonucleic acids, TAF200, CG3424, RNA-seq, Light, organism surface, TAFII-250, antibodies, TAF250/230, Tl3, Tl2, Optical Microscopy, Gene Expression, TAFII250, SZ1, MDDGA6, Expression Signatures, Ribonukleinsaeure, mKIAA0609, Genetic Materials, pentosenucleic acids, VI, Ribonucleic acids, KIAA0609, Expression Profile, Genetic Material, Transcriptome Profiles, Polyadenylated Messenger RNA, fg, Acid, 20.35, Non Polyadenylated mRNA, gyltl1b, protein_coding_transcript, mdc1d, expanded, INSDC_feature:gene, whole genome, CG17603, TAF[[II]], human, Non-Polyadenylated mRNA, Hand Held Microscopy, MDC1D, immunoglobulin, wide, pth, DMDA, B cell receptor accessory molecule complex, enr, Taf250, enlarged, Material, integumentary system, SR3-5, B lymphocyte receptor complex, eve2, anon-EST:Liang-2.39, Cistron, Microscopy, dermal system, Poly(A) RNA, anon-WO0118547.271, Proteomes, Platelets, TAF230, CG2328, 14.10, big, protein levels, d230, human being, Transcriptome Profile, P62, Gene, dTAFII250, broad, protein-containing complex, EfW1, TYPE, froggy, Gyltl1a, Human, DAGA4, antibody, large, surface, BCR complex, Homo sapiens, polypeptide chain, dmTAF1, Messenger, Taf230, Gene Products, Whole Transcriptome Shotgun Sequencing, Cell., even, Low, MAM, immunoglobulin complex, SCG3, Man, anon-WO0118547.370, TAF250, study, Taf200, dTAF[[II]]250, l(3)s2612, Genetic, cell, MDDGB6, Profile, messenger RNA, Taf1p, LARGE, man, Non-Polyadenylated RNA, dTAF250, BPFD#36, template RNA, Optical, great, DmelCG10293, TAF, RNA, TAF[[II]]250, biological function, Transcriptome, cou, clone 2.39, protein complex, Proteins, Messenger RNA, total expressed protein, l(3)84Ab, RNS, BG:DS00004.13, qkr, l(3)S090417, Cistrons, Cell, LGMD2C, dTAF230, whole transcriptome, Lr, native protein, natural protein, Poly(A)+ mRNA, p230, yeast nucleic acid, KH93F, Simple Microscopy, Protein, chemical analysis, Gene Expression Signatures, INSDC_feature:mRNA, sequence, TAF[[II]]250/230, TFIID, Gene Expression Signature, Eve, EVE, Polyadenylated RNA, who, opsonin activity, Taf[[II]]250, ribonucleic acid, Poly(A)+ RNA, TAF[[II]]230, DMDA1, mRNA, Poly(A) Tail, Compound Microscopy, body surface, Non Polyadenylated RNA, Non-Polyadenylated, l(2)46Ce, TAF[II]250, Who/How, Ribonucleic Acid, primary structure of sequence macromolecule, l(2)46Cg, Protein Gene Products, l(2)46CFj, Gene Proteins, l(2)46CFh, DmelCG17603, Compound, l(2)46CFp, Gene Expression Profiles, Modern Man, SCARMD2, B cell receptor activity, Bra, qkr[93F], assay, Signature, Polyadenylated mRNA, E(eve), l(2)46CFg, TAF1"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"H.sapiens - Cell line, U251mg 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