{"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":["5833"],"full_dataset_link":["https://pax-db.org/dataset/5833/3453092459"],"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":["One of the critical gaps in malaria transmission biology and surveillance is our lack of knowledge about Plasmodium falciparum gametocyte biology, especially sexual dimorphic development and how sex ratios that may influence transmission from the human to the mosquito. Dissecting this process has been hampered by the lack of sex-specific protein markers for the circulating, mature stage V gametocytes. The current evidence suggests a high degree of conservation in gametocyte gene complement across Plasmodium, and therefore presumably for sex-specific genes as well. To better our understanding of gametocyte development and subsequent infectiousness to mosquitoes, we undertook a Systematic Subtractive Bioinformatic analysis (filtering) approach to identify sex-specific P. falciparum NF54 protein markers based on a comparison with the Dd2 strain, which is defective in producing males, and with syntenic male and female proteins from the reanalyzed and updated P. berghei (related rodent malaria parasite) gametocyte proteomes. This produced a short list of 174 male- and 258 female-enriched P. falciparum stage V proteins, some of which appear to be under strong diversifying selection, suggesting ongoing adaptation to mosquito vector species. We generated antibodies against three putative female-specific gametocyte stage V proteins in P. falciparum and confirmed either conserved sex-specificity or the lack of cross-species sex-partitioning. Finally, our study provides not only an additional resource for mass spectrometry-derived evidence for gametocyte proteins but also lays down the foundation for rational screening and development of novel sex-partitioned protein biomarkers and transmission-blocking vaccine candidates."],"pubmed_title":["Sex-partitioning of the Plasmodium falciparum stage V gametocyte proteome provides insight into falciparum-specific cell biology."],"pubmed_authors":["Tao Dingyin D, Ubaida-Mohien Ceereena C, Mathias Derrick K DK, King Jonas G JG, Pastrana-Mena Rebecca R, Tripathi Abhai A, Goldowitz Ilana I, Graham David R DR, Moss Eli E, Marti Matthias M, Dinglasan Rhoel R RR, Dinglasan Rhoel R RR"],"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":["DD, akr1c2, snRNP2, BcDNA:LD03002, 1.3.1.20, 2-diol dehydrogenase, MCDR2, srxy8, BABP, dD2, AKR1C-pseudo, 3-alpha-HSD3, TDD, Dihydrodiol dehydrogenase|bile acid-binding protein, CG1249, SRXY8, mcdr2, babp, hakrd, ddh2, Dihydrodiol dehydrogenase 2, HBAB., snRNP D2, DD|BABP, DmelCG1249, hbab, HAKRD, 1.-.-.-, Trans-1, Chlordecone reductase homolog HAKRD, DD2, dd2, DDH2, Type III 3-alpha-hydroxysteroid dehydrogenase, 2-dihydrobenzene-1, 1.1.1.357, DD-2"],"pubmed_title_synonyms":["Genotypic, Sex, sex, Genotypic Sex, Plasmodium (Laverania) falciparum, Biology, Phenotypic Sex, Cellular Biology, falciparums, developmental stage, Biologies, Plasmodium, Cellular, total expressed protein, Cell., stage, Cellular Biologies, malaria parasite P. falciparum, Plasmodium falciparums, Cell Biologies, Proteomes, Cell, Phenotypic"],"name_synonyms":["akr1c2, l(3)Ca, multi-cellular organism, BUERGER disease, Triacetyloleandomycin, mCRY, 2-diol dehydrogenase, srxy8, 26S protease, d-titin, inflammatory occlusive peripheral vascular disease, Mbh1, SLS, Sls, SRXY8, mcdr2, ingensin, Dihydrodiol dehydrogenase 2, large multicatalytic protease, DmelCG1249, HEL-S-66, HAKRD, DmelCG1915, Chlordecone reductase homolog HAKRD, Type III 3-alpha-hydroxysteroid dehydrogenase, Titin, Crry, multicatalytic endopeptidase complex, animal, DD-2, anon-CREST, Ket, CFU-Mast, l(3)j1D7, MARKK, AFCP, BcDNA:LD03002, 1.3.1.20, MCDR2, colony forming unit mast cell, tao-1, CG18857, ket, AAF48973, l(3)dre8, lens neutral proteinase, ddh2, Tao-1, KZ, polyhedral organelle, 1.-.-.-, l(3)rL182, DDH2, AHUS2, TRA2.10, Mcp, MCP, multicatalytic proteinase, DD, TAO, Oleandocetin, snRNP2, body, titin, AKR1C-pseudo, Oleandomycin, whole body, l(3)62Ca, 0020/01, threonine endopeptidase activity, Dihydrodiol dehydrogenase|bile acid-binding protein, CG1249, hakrd, tao, kettin, organism, CFU-MC, hbab, dTao-1, Trans-1, DD2, dd2, prosome, HBAB, tricorn proteinase, D-titin, CG14217, whole organism, TAO1, BABP, dD2, 3-alpha-HSD3, TDD, DmelCG14217, D-Titin, MIC10, sam, sal, TLX, babp, CG1915, snRNP D2, CT41299, triacetate (ester), DD|BABP, multicatalytic proteinase (complex), Koerper, proteasome endopeptidase complex., l(3)S002001, CG18242, tricorn protease, 2-dihydrobenzene-1, 1.1.1.357, tao1, occlusive peripheral vascular disease, alkaline protease, CG18245"],"pubmed_abstract_synonyms":["Biological Markers, Viral Marker, akr1c2, Materials, degree (angle), Surrogate Endpoints, single-organism developmental process, determination, Laboratory, selection process, postnatal development, 2-diol dehydrogenase, srxy8, Biochemical, Endpoint, growth and development, protein, sci, Serum, Foundation, Molecular Biologies, SRXY8, mcdr2, protein polypeptide chains, Readability, Laboratory Markers, DSmurf, Bio Informatics, Vectors, DmelCG1249, Biological, symptoms, HOW, How, HAKRD, Analysis, protein aggregate, DD-2, l(3)j5D5, male, 24B, Mass Spectrum Analysis, Sex, Man (Taxonomy), Biology, Analyses, Vaccine., BcDNA:LD03002, stru, MCDR2, proteins, l(3)S053606, CG10293, Bio-Informatic, Gaps, ecotype, Computational, Phenotypic, l(3)j5B5, Immune, sex, Markers, Smurf, Bio-Informatics, Viral Markers, Fever, falciparums, 1.-.-.-, stage, Strains, Marsh, Computational Molecular Biologies, CG4943, D-smurf, DD, screening, 0904/17, anatomical protrusion, Viral, Surrogate Endpoint, aberrant, rodents, frequency, Modern, Biologies, Plasmodium, Ratios, AKR1C-pseudo, Mosquito, Biochemical Markers, Lack, Dihydrodiol dehydrogenase|bile acid-binding protein, antibodies, Biologic Marker, female, Spectrum Analysis, Computational Molecular, CG1249, Dipodidae, Spectroscopy, Hydrochaeri, Screenings, Prgs, SZ1, hbab, Marker, Computational Molecular Biology, Genetic Materials, cultivar, HBAB, Genetic Material, Mosquitos, Genotypic, Epistemology, Bioinformatic, End Points, Plasmodium Infection, DmelCG4943, Plasmodium (Laverania) falciparum, Complement, maleate, Spectrometry, BABP, signs, 3-alpha-HSD3, INSDC_feature:gene, Immunologic, Beaver, Laboratory Marker, surveillance, morbidity, human, sex-specific, babp, Health, Parasite, Specificity and Sensitivity, spine, Material, DD|BABP, Biochemical Marker, Rodentias, Complement System, anon-EST:Liang-2.39, Cistron, 2-dihydrobenzene-1, 1.1.1.357, Strains and Sprains, Proteomes, atypia, human being, Health Resource, Mosquito Vector, Clinical Markers, P62, Clinical Marker, dSmurf1, developmental stage, Remittent, Gene, Capybara, rodent, Spectrum Analyses, protein-containing complex, Complement Protein, Vector, Human, protrusion, Surrogate End Points, Plasmodium Infections, Surrogate Markers, Dihydrodiol dehydrogenase 2, Homo sapiens, polypeptide chain, Gene Products, Mass, Screening, Chlordecone reductase homolog HAKRD, Type III 3-alpha-hydroxysteroid dehydrogenase, atypical, Sprains, Man, Resources, Plasmodium <Plasmodium>, Mass Spectroscopy, study, Biomarker, l(3)s2612, Genetic, Genotypic Sex, Clinical, Infections, occurrence, 1.3.1.20, Biological Marker, prevalence, Castor Beaver, Ratio, man, ddh2, Immunologic Markers, d-smurf, Plasmodiums, Jerboas, DmelCG10293, Sensitivity, Hemolytic, DDH2, species, Plasmodium falciparums, plasmodiosis, Immunologic Marker, Marsh Fever, Paludism, incidence, Biologic, Hydrochaeris, Molecular Biology, findings, snRNP2, female human body, clone 2.39, protein complex, Males, Proteins, Sprain, Serum Markers, End Point, defective, qkr, Dsmurf, l(3)S090417, Cistrons, Sex Ratios, Bioinformatics, Immune Marker, strain, dSmurf, development, hakrd, post-flowering stage, MS, native protein, Resource, natural protein, Mass Screenings, Surrogate End Point, Smurf ubiquitin ligase, KH93F, Protein, chemical analysis, Strain, Infection, Mosquitoes, Trans-1, DD2, dd2, Hemolytic Complement, outbreaks, Mass Spectrum Analyses, who, mature plant, Biologic Markers, Mass Spectrum, Serum Marker, Beavers, Surrogate, Endpoints, postnatal growth, Specificity, dD2, TDD, Rodents, Jerboa, Who/How, arc degree, Understanding, Capybaras, Rodent, endemics, Surrogate Marker, Protein Gene Products, male human body, Gene Proteins, Complement Proteins, snRNP D2, gender-specific anatomical structure, Phenotypic Sex, Modern Man, Remittent Fever, qkr[93F], gender-specific, epidemics, assay, malaria parasite P. falciparum, growth, Females, Immune Markers"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"P.falciparum - Whole organism, Dd2, SC (Tao,mcp,2014)","description":"abundance based on Spectral counting, Dd2, Interaction consistency score: 2.8, Coverage: 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