{"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":["7955"],"full_dataset_link":["https://pax-db.org/dataset/7955/2197486425"],"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":["Accurate annotation of protein-coding genes is one of the primary tasks upon the completion of whole genome sequencing of any organism. In this study, we used an integrated transcriptomic and proteomic strategy to validate and improve the existing zebrafish genome annotation. We undertook high-resolution mass-spectrometry-based proteomic profiling of 10 adult organs, whole adult fish body, and two developmental stages of zebrafish (SAT line), in addition to transcriptomic profiling of six organs. More than 7,000 proteins were identified from proteomic analyses, and ∼ 69,000 high-confidence transcripts were assembled from the RNA sequencing data. Approximately 15% of the transcripts mapped to intergenic regions, the majority of which are likely long non-coding RNAs. These high-quality transcriptomic and proteomic data were used to manually reannotate the zebrafish genome. We report the identification of 157 novel protein-coding genes. In addition, our data led to modification of existing gene structures including novel exons, changes in exon coordinates, changes in frame of translation, translation in annotated UTRs, and joining of genes. Finally, we discovered four instances of genome assembly errors that were supported by both proteomic and transcriptomic data. Our study shows how an integrative analysis of the transcriptome and the proteome can extend our understanding of even well-annotated genomes."],"pubmed_title":["Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis."],"pubmed_authors":["Kelkar Dhanashree S DS, Provost Elayne E, Chaerkady Raghothama R, Muthusamy Babylakshmi B, Manda Srikanth S SS, Subbannayya Tejaswini T, Selvan Lakshmi Dhevi N LD, Wang Chieh-Huei CH, Datta Keshava K KK, Woo Sunghee S, Dwivedi Sutopa B SB, Renuse Santosh S, Getnet Derese D, Huang Tai-Chung TC, Kim Min-Sik MS, Pinto Sneha M SM, Mitchell Christopher J CJ, Madugundu Anil K AK, Kumar Praveen P, Sharma Jyoti J, Advani Jayshree J, Dey Gourav G, Balakrishnan Lavanya L, Syed Nazia N, Nanjappa Vishalakshi V, Subbannayya Yashwanth Y, Goel Renu R, Prasad T S Keshava TS, Bafna Vineet V, Sirdeshmukh Ravi R, Gowda Harsha H, Wang Charles C, Leach Steven D SD, Pandey Akhilesh A"],"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":["zebra fish, Danio rerio (Hamilton, Zebra, leopard danio, Danio rerio, Zebra Fish, Genomes, Danio frankei, Zebrafishes, proteomic analysis., Fishes, whole genome, Cyprinus rerio Hamilton, danio, Zebra danios, Zebra danio, zebra danio, B. rerio, Danio rerio frankei, 1822), Zebra Fishes, 1822, D. rerio, Brachydanio rerio, Cyprinus rerio, Brachidanio rerio, zebrafish, D. rerios, Brachydanio rerio frankei"],"name_synonyms":["l(3)Ca, testicle, mCRY, titin, 26S protease, l(3)62Ca, d-titin, 0020/01, threonine endopeptidase activity, Mbh1, SLS, Sls, gonad of male reproductive system, ingensin, kettin, large multicatalytic protease, CFU-MC, HEL-S-66, gonad of male genitalia, DmelCG1915, Titin, prosome, testiculus, Crry, multicatalytic endopeptidase complex, anon-CREST, Ket, CFU-Mast, tricorn proteinase, D-titin, l(3)j1D7, Testicle, AFCP, colony forming unit mast cell, male gonad, D-Titin, CG18857, MIC10, ket, sam, sal, TLX, l(3)dre8, lens neutral proteinase, CG1915, CT41299, orchis, multicatalytic proteinase (complex), Testicles, proteasome endopeptidase complex., KZ, polyhedral organelle, l(3)S002001, l(3)rL182, CG18242, tricorn protease, testes, AHUS2, TRA2.10, Mcp, MCP, alkaline protease, Testes, multicatalytic proteinase, CG18245"],"pubmed_abstract_synonyms":["protein translation, Intergenic Region, Materials, l(3)LG9, RNA Sequence Determination, determination, Junk DNAs, Sequence Determination, Intercistronic Regions, adult stage, RNA Sequence, Sry-rDM33, Sry-rDM36, Gene Expression Profile, Mini Exon, protein, Progress Reports, Profiles, sci, PAPSS 2, PAPSS 1, protein polypeptide chains, Readability, Sulfate adenylate transferase, C230050L11, Regions, Summary Report, TSK5, Sry-rDM23, HOW, How, 10.5, Analysis, protein aggregate, animal, Spacer DNAs, Summary Reports, D. rerios, WMS, adult, l(3)j5D5, 10.9, Gm5098, 24B, bony fishes, F, DM10, Genomes, Analyses, Progress Report, DmelCG2328, Determination, Junk, SK 2, Zebrafishes, SK 1, stru, Sulfate adenylyltransferase, proteins, Fishes, V, l(3)S053606, Fish, Sequence Determinations, CG10293, APS kinase, Intergenic Sequence, Signatures, Sry-rDM10, 2.7.1.25, Progress, l(3)j5B5, Field Reports, Expression Signature, Zebra Fishes, Transcriptomes, fish, FISH, GPHYSD2, Sox70D, DNAs, SGS, Sulfurylase kinase 1, Danio rerio (Hamilton, Sulfurylase kinase 2, PAPS synthase 2, Intercistronic Sequences, protein anabolism, 0904/17, leopard danio, PAPS synthase 1, protein biosynthetic process, 3'-phosphoadenosine-5'-phosphosulfate synthase, DM33, DM36, Expression Profiles, Genome Sequencing, Cyprinus rerio Hamilton, Determinations, ACMICD, Spectroscopy, Gene Expression, organism, Complete Genome, ray-finned fishes, Investigative Report, DM23, SZ1, Cephalaspidomorphi, KFSDX, Expression Signatures, 1822), 1822, protein formation, Genetic Materials, Brachydanio rerio, VI, Intergenic, SSAT, AI413738, Region, Adults, Expression Profile, Genetic Material, Sry-rDM63, Transcriptome Profiles, Untranslated Region, Monorhina, 20.35, Danio rerio, Junk DNA, whole organism, KFSD, Field, Spectrometry, INSDC_feature:gene, whole genome, MASS, SK1, SK2, Intercistronic Sequence, TKS5, Tks5, DC21, Report, Spacer DNA, protein synthesis, Material, Koerper, D. rerio, eve2, Cistron, anon-EST:Liang-2.39, DNA, zebrafish, Adenylylsulfate 3'-phosphotransferase, Proteomes, CG2328, zebra fish, 14.10, SOXB2.1, multi-cellular organism, Transcriptome Profile, fishes, P62, 2310014D11Rik, FBN, Gene, Coding, protein-containing complex, Agnatha, loD, Protein Gm1141, Adenylyl-sulfate kinase, AA589508, SSAT-1, Intergenic Regions, DM63, zebra danio, Sh3md1, Investigative, polypeptide chain, ECTOL1, Intercistronic, Mini-Exon, Gene Products, even, CG5893, Cyprinus rerio, Medical, Genomes., study, Complete, Whole Genome, Clinical, Genetic, l(3)s2612, Medical Coding, Profile, Spectrum, Complete Genome Sequencing, Intergenic Sequences, EG329070, Sequencing, OCTD, UTRs, RNA Sequence Analyses, B. rerio, Whole, DmelCG10293, RNA Sequencing, species, Investigative Reports, Brachydanio rerio frankei, Sequence Analyses, DmelCG5893, AI256723, Sox B2-1, RNA, data, Zebra Fish, Transcriptome, protein complex, body, RNA Sequence Determinations, clone 2.39, SH3MD1, Proteins, Sox70, Novel protein, total expressed protein, whole body, qkr, Cistrons, l(3)S090417, Actinopterygi, whole transcriptome, Sequences, Adenosine-5'-phosphosulfate 3'-phosphotransferase, native protein, natural protein, SOX70D, Sequence, KH93F, Protein, Danio rerio frankei, Research Reports, chemical analysis, Gene Expression Signatures, protein biosynthesis, MFS1, Gene Expression Signature, Eve, EVE, Spacer, Intergenic DNAs, Brachidanio rerio, WMS2, SOXDP, who, Hyperotreti, Zebra, AA617398, SAT, Sat, Intercistronic Region, Danio frankei, exonic region, Mini-Exons, Untranslated, Exon, l(2)46Ce, Who/How, Understanding, danio, 2.7.7.4, Zebra danios, l(2)46Cg, Osteichthyes, Protein Gene Products, l(2)46CFj, Gene Proteins, 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