{"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":["3702"],"full_dataset_link":["https://pax-db.org/dataset/3702/159169384"],"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":["Gene annotation underpins genome science. Most often protein coding sequence is inferred from the genome based on transcript evidence and computational predictions. While generally correct, gene models suffer from errors in reading frame, exon border definition, and exon identification. To ascertain the error rate of Arabidopsis thaliana gene models, we isolated proteins from a sample of Arabidopsis tissues and determined the amino acid sequences of 144,079 distinct peptides by tandem mass spectrometry. The peptides corresponded to 1 or more of 3 different translations of the genome: a 6-frame translation, an exon splice-graph, and the currently annotated proteome. The majority of the peptides (126,055) resided in existing gene models (12,769 confirmed proteins), comprising 40% of annotated genes. Surprisingly, 18,024 novel peptides were found that do not correspond to annotated genes. Using the gene finding program AUGUSTUS and 5,426 novel peptides that occurred in clusters, we discovered 778 new protein-coding genes and refined the annotation of an additional 695 gene models. The remaining 13,449 novel peptides provide high quality annotation (>99% correct) for thousands of additional genes. Our observation that 18,024 of 144,079 peptides did not match current gene models suggests that 13% of the Arabidopsis proteome was incomplete due to approximately equal numbers of missing and incorrect gene models."],"pubmed_title":["Discovery and revision of Arabidopsis genes by proteogenomics."],"pubmed_authors":["Castellana Natalie E NE, Payne Samuel H SH, Shen Zhouxin Z, Stanke Mario M, Bafna Vineet V, Briggs Steven P SP"],"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"],"description_synonyms":["data., MS/MS, tandem MS, MS2"],"pubmed_title_synonyms":["Profiling, Materials, Genetic, Cresses, Research, Researchs, A., Arabidopsis thaliana, Mouse-ear Cress, Proteogenomic Profiling, thaliana, Gene, A. thaliana, Mouse-ear Cresses, Proteogenomic Analysis., Cistrons, Mouse-ear, Cardaminopsis, Arabidopsis, Arabidopsis thalianas, Proteogenomic, Material, A. thalianas, thalianas, Genetic Materials, Cress, Cistron, Proteogenomic Research, Mouse ear, Analysis, Arabidopses, Genetic Material"],"name_synonyms":["organism, whole body, multi-cellular organism, whole organism, animal, data., body, MS/MS, tandem MS, MS2, Koerper"],"pubmed_abstract_synonyms":["protein translation, Materials, Tandem, Sequence Annotations, A., Aminosaeure, Aminocarbonsaeure, Annotations, Amino acid, Gene, Mini Exon, Coding, protein, alpha-amino acid, protein-containing complex, Mass Spectrometry Mass Spectrometry, Arabis thaliana, Protein Annotation, Symptoms and Signs, Molecular Sequence Annotations, Cardaminopsis, Polypeptides, protein polypeptide chains, Sequence Annotation, Arabidopsis thalianas, peptido, polypeptide chain, A. thalianas, Mini-Exon, Gene Products, thalianas, Finding, protein aggregate, Medical, amino acids, Clinical, Genetic, peptides, Genomes, Cresses, Molecular, Medical Coding, MS2, Mouse-ear Cress, Tissue, Sciences, proteins, Mass Spectrometry, Mouse-ear, thale-cress, Gene Annotation, sample, Annotation, Cress, peptidos, Mouse ear, Arabidopses, Diagnostic Findings, Molecular Sequence, SIGNS SYMPTOMS, protein anabolism, protein biosynthetic process, Arbisopsis thaliana, protein complex, Aminokarbonsaeure, DESC, Proteins, Arabidopsis thaliana, incomplete, total expressed protein, A. thaliana, alpha-amino acids, Cistrons, INSDC_feature:misc_RNA, alpha-amino carboxylic acids, Peptide, Programs, abolished, Signs and Symptoms, native protein, natural protein, Protein, protein formation, sequence, Genetic Materials, Arabidopsis thaliana (thale cress), protein biosynthesis, Genetic Material, tandem MS, thale cress, mouse-ear cress, Amino Acid, Acid, Amino acids, distinct, exonic region, MS/MS, Mini-Exons, Protein Annotations, Exon, thaliana, Gene Annotations, INSDC_feature:gene, whole genome, Mass Spectrometry-Mass Spectrometry, Amino, Mouse-ear Cresses, primary structure of sequence macromolecule, sample population, Protein Gene Products, Gene Proteins, Arabidopsis, protein synthesis, Material, Cistron, Peptid, Acids, Polypeptide, Genetic Material., Clinical Finding, Proteomes"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"A.thaliana - Whole organism,  ms/ms data, SC (Castellana,pnas,2008)","description":"abundance based on Spectral counting,  MS/MS data, Interaction consistency score: 16.7, Coverage: 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