{"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":["89462"],"full_dataset_link":["https://pax-db.org/dataset/89462/562539239"],"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":["A comprehensive identification of the proteins of spermatozoa and seminal plasma enables the full characterization of sperm biology and is essential to understand how seminal plasma influences sperm fertility. In this study, proteomics of buffalo spermatozoa and seminal plasma were analyzed using a bottom-up approach. A total of 2147 and 864 proteins were identified from mature spermatozoa and seminal plasma, respectively. Of these, 371 proteins-42.9% in the seminal plasma set-were common to both spermatozoa and seminal plasma. ODF2, AKAP4, and TUBB were the most highly abundant proteins of spermatozoa whereas the three most highly abundant proteins in seminal plasma were ALB, CLU, and AZGP1. Gene Ontology (GO) analysis indicated that most sperm proteins were involved in transport, phosphorylation and macromolecule localization. More seminal plasma proteins were related to proteolysis, response to stimulus and homeostatic process. Pathways associated with energy metabolism, protein processing and RNA transport were significantly enriched in spermatozoa. In buffalo seminal plasma, three distinguishing GO pathways-proteasome activity, lysosomal activity, complement and coagulation cascades-were found to play important roles in sperm protection. Protein-protein interaction (PPI) network analysis indicated that 531 and 620 proteins participated in buffalo sperm and seminal plasma PPI networks, respectively. Sub-network mining elaborated detailed biological events. This study is the first to provide an in-depth proteomic analysis of buffalo spermatozoa and seminal plasma. The results extend our understanding of male buffalo reproduction and provide clues for determining the relationships between sperm biology and seminal plasma."],"pubmed_title":["Proteomic profiles of buffalo spermatozoa and seminal plasma."],"pubmed_authors":["Fu Qiang Q, Pan Limei L, Huang Delun D, Wang Zhiqiang Z, Hou Zhen Z, Zhang Ming 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":["Water, X-Chromosome-Bearing Sperm, Plasma, Y-Chromosome-Bearing, X-Chromosome-Bearing, male genital secretion, X-Bearing Sperm, Sperm, X-Bearing, Water Buffalo, prostate fluid, Bubalus, X-Bearing Sperms, milt, Y-Chromosome-Bearing Sperm, X Bearing Sperm, Buffalo, X-Chromosome-Bearing Sperms, Water Buffaloes, seminal fluid, Y Chromosome Bearing Sperm, prostatic fluid, Y-Bearing Sperms, Seminal Plasma, Y-Bearing Sperm, male genital fluid., sperm, X Chromosome Bearing Sperm, Sperms, Syncerus, Y-Chromosome-Bearing Sperms, Spermatozoon, Y-Bearing, Y Bearing Sperm, Seminal, ejaculate"],"name_synonyms":["X-Chromosome-Bearing Sperm, sperm cell, Y-Chromosome-Bearing, X-Chromosome-Bearing, X-Bearing Sperm, Sperm, X-Bearing, ejaculate., X-Bearing Sperms, Y-Chromosome-Bearing Sperm, spermatozoid, X Bearing Sperm, X-Chromosome-Bearing Sperms, spermatozoon, seminal fluid, Y Chromosome Bearing Sperm, Y-Bearing Sperms, Y-Bearing Sperm, sperm, X Chromosome Bearing Sperm, Sperms, Y-Chromosome-Bearing Sperms, Spermatozoon, SPERM, Y-Bearing, Y Bearing Sperm"],"pubmed_abstract_synonyms":["Water, ANALBA, APO-J, Ribonucleic, Product, prostate fluid, Metabolisms, milt, sci, DmelCG8443, phosphorylation, Water Buffaloes, 5730420M11Rik, solute:solute exchange, protein polypeptide chains, DmelCG12298, Below Replacement, Multicatalytic Endopeptidase Complex, Biological, HOW, How, AI325297, SCRAMBLED, Dmel_CG4807, Expenditure, Biological Product, CDCBM5, Reproductive Periods, CDCBM6, Fertility Surveys, Ab, sperm cell, male genital secretion, Fertility Incentives, SET, X-Bearing, Biologic Drugs, ODF2/2, hAKAP82, ODF2/1, stru, proteins, OK|SW-cl.56, l(3)S053606, inhibition of homeostatic process, Proteasome Endopeptidase, DmelCG4299, Y Chromosome Bearing Sperm, set, Biological Medicine, Role Concepts, Fertility Determinant, reproductive physiological process, Medicine, Fertility Preference, mAKAP82, CG43860, Periods, 26S proteasome, Biologic Drug, Differential Fertility, PRO1341, ejaculate, Y-Chromosome-Bearing, Degradations, AKAP 82, Indices, Biologic Products, Index, TRPM2B, STRUBBELIG, fs(1)K1540, Buffalo, peptidolysis during protein maturation, Sperm Tail, Tail Proteins, Seminal Plasma, Role Concept, Playthings and Play, Human Reproductive Indices, Role, Cellular, Ontology Projects, CLU2, CLU1, Sperm Specific, MMTEST29, X-Chromosome-Bearing, Ontology, HLA-DR-associated protein II, Projects, DI-2, Complement, maleate, Biological Medicines, I-2Dm, Biological Drug, Protein Digestions, PRKA4, protein maturation by proteolysis, Biologics, X Bearing Sperm, Preferences, I-2PP1, seminal fluid, TAF-IBETA, Sperms, Surveys, Complement System, AAG4, TAF-Ibeta, Fecundability, Nas, HI, CLI, Cli, Sperm, Biologic Pharmaceuticals, Peptidomics, TUBB5, Fertility, TUBB2, TUBB1, Acid Transport, Albza, Y-Chromosome-Bearing Sperm, Complement Protein, protein-containing complex, Gene Ontology Project, Gene Ontology, Human, Determinant, Ribonucleic Acid Transport, clu, EG:8D8.1, Gene Products, Spermatozoon, Sperm-Specific, Y Bearing Sperm, Transport, Fecundity, Toy, Biologicals, network topology analysis, FDAH, Playthings, Sperm Specific Proteins, RNA Localization Processes, mei-1794, 2pp2a, Energy, fs(1)Nasrat, Expenditures, CG10574, Reproductive Indices, CG11411, Tubb4, Spermatozoa Proteins, 2PP2A, Puppets, mRNA Sorting, Syncerus, dSET, dSet, negative regulation of homeostatic process, Macroxyproteinase, RATTRPM2B, SPERM, Fertility Incentive, Alb, Human Reproductive, Puppet, Biologic, DmelCG43860, Pharmaceuticals, Products, Reproductive, X-Bearing Sperm, RNA, Alb1, Biologic Medicines, Proteins, Reproductive Period, Phosphorylations, Sugp-2, Messenger RNA, PRO0903, AI848335, qkr, l(3)S090417, Digestions, Concept, native protein, Proteolyses, I-2PP2A, ZNGP1, KH93F, Dm I-2, chemical analysis, Biopharmaceutical, proteomic analysis, phosphorylation enrichment, Messenger RNA Sorting, Hemolytic Complement, AKAP82, regulation of homeostatic process, Y-Bearing, SP40, Energy Expenditure, Ontology Project, ensemble, mRNA, Prosome, Dub, Energy Expenditures, 20S, FBF-1, Ribonucleic Acid, Understanding, male human body, fs(1)Nas, Gene Proteins, Complement Proteins, Differential, Marital, AI893575, multicatalytic endopeptidase, Fsc1, FSC1, General activity, proteasome endopeptidase complex, ZAG, Zag, IPP2A2, Messenger RNA Localization Processes, Gene Ontology Projects, Activity, determination, Bioenergetics, Human Reproductive Indexes, protein, World Fertility Survey, SUB, Fertility Preferences, Readability, male genital fluid., Roles, Project, Concepts, dJ40E16.7, Sperm Tail Proteins, protein aggregate, KIF20A, l(3)j5D5, male, X-Chromosome-Bearing Sperm, 24B, Human Reproductive Index, PPI, ATP-dependent proteolysis, TAF-I, Macropain, Natural, Bubalus, 371, TRPM2, APOJ, ApoJ, Biological Drugs, CG10293, 8D8.1, 20S Proteasome, Protein Degradation, male genital fluid, fs(1)A371, l(3)j5B5, IGAAD, Y-Bearing Sperm, DmelCG10574, AKAP-4, X Chromosome Bearing Sperm, Y-Chromosome-Bearing Sperms, homeostasis, Trpmb, Medicines, DmelCG11411, RNA Sorting, l(2)k02807, phapii, Spermatozoa, 0904/17, Dmel_CG32830, Tubb, Proteinase, Endopeptidase Complex, CG8443, World Fertility Surveys, StF-IT-1, ODF2|2, ODF2|1, Alb-1, Trpm2, Reproductive Index, Ingensin, TUBB, positive regulation of homeostatic process, single-organism transport, SZ1, Digestion, Biopharmaceuticals, Plaything, Biologic Product, proteasome, Gene Ontologies, clotting, Water Buffalo, Ontologies, Toys, CG4299, spermatozoid, Fertility Determinants, ptd, Energy Metabolisms, small molecule transport, anon-EST:Liang-2.39, i2pp2a, Msgp-2, Marital Fertility, AT1G11140, Subfecundity, Plays, P62, SGP2, Degradation, Sgp2, Gene, anon-WO0118547.143, PHAPII, Specific Proteins, CG12298, Multicatalytic Proteinase, OK/SW-cl.56, polypeptide chain, Messenger, Metabolism, Survey, Preference, World Fertility, KUB1, NA1|NA2, Drugs, study, l(3)s2612, tubb5, CT99, Complex, ipp2a2, Natural Product, X-Bearing Sperms, SP-40, Protein Degradations, X-Chromosome-Bearing Sperms, fs(1)M6, PRO0883, prostatic fluid, Sperm-Specific Proteins, Multicatalytic Endopeptidase, sperm, taf-ibeta, p82, DAG, Multicatalytic, Below Replacement Fertility, DmelCG10293, Play, Hemolytic, SRF9, M40, clone 2.39, World, protein complex, Males, D14Ucla3, igaad, SGP-2, ZA2G, CT134, Protein Digestion, spermatozoon, group, Proteasome, Fs(1)N, STRUBBELIG-RECEPTOR FAMILY 9, natural protein, Period, Protein, I2PP2A, Natural Fertility, ODF84, physiological response to stimulus, Determinants, CG4807, CG32830, who, Plasma, fs(1)[nas], Who/How, Bioenergetic, mRNA Localization Processes, Protein Gene Products, TRPM-2, Drug, M(beta)4, dSET/TAF-Ibeta, Sgp-2, Y-Bearing Sperms, 2610030F17Rik, activation of homeostatic process, Indexes, Sorting, XLOT, qkr[93F], Natural Products, NA1/NA2, assay, AA407739, T19D16.8, Seminal, SCM, macromolecule localisation, Fertility Survey, B2149"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Bbubalis - Sperm, SC (Fuetal,theriogenology.2019)","description":"abundance based on Spectral counting, Interaction consistency score: 9.5, Coverage: 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