{"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":["5811"],"full_dataset_link":["https://pax-db.org/dataset/5811/2851512285"],"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":["Toxoplasma gondii has a complex life cycle that is typified by asexual development that takes place in vertebrates, and sexual reproduction, which occurs exclusively in felids and is therefore less studied. The developmental transitions rely on changes in the patterns of gene expression, and recent studies have assigned roles for chromatin shapers, including histone modifications, in establishing specific epigenetic programs for each given stage. Here, we identified the T. gondii microrchidia (MORC) protein as an upstream transcriptional repressor of sexual commitment. MORC, in a complex with Apetala 2 (AP2) transcription factors, was shown to recruit the histone deacetylase HDAC3, thereby impeding the accessibility of chromatin at the genes that are exclusively expressed during sexual stages. We found that MORC-depleted cells underwent marked transcriptional changes, resulting in the expression of a specific repertoire of genes, and revealing a shift from asexual proliferation to sexual differentiation. MORC acts as a master regulator that directs the hierarchical expression of secondary AP2 transcription factors, and these transcription factors potentially contribute to the unidirectionality of the life cycle. Thus, MORC plays a cardinal role in the T. gondii life cycle, and its conditional depletion offers a method to study the sexual development of the parasite in vitro, and is proposed as an alternative to the requirement of T. gondii infections in cats."],"pubmed_title":["A MORC-driven transcriptional switch controls Toxoplasma developmental trajectories and sexual commitment."],"pubmed_authors":["Farhat Dayana C DC, Swale Christopher C, Dard Céline C, Cannella Dominique D, Ortet Philippe P, Barakat Mohamed M, Sindikubwabo Fabien F, Belmudes Lucid L, De Bock Pieter-Jan PJ, Couté Yohann Y, Bougdour Alexandre A, Hakimi Mohamed-Ali MA"],"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":["12.1."],"pubmed_title_synonyms":["Toxoplasma, Toxoplasma gondius., gondius, Toxoplasma gondii, Toxoplasmas"],"name_synonyms":["Koerper., organism, whole body, multi-cellular organism, whole organism, animal, body"],"pubmed_abstract_synonyms":["aP2, Class I Histone Deacetylases, 422/aP2, sexual differentiation, Materials, Sex Development, single-organism developmental process, RCS1, AP-2, AI115087., postnatal development, Deacetylase, NDPP, Infestations and Infections, Domestic Cat, ATRPD3A, growth and development, protein, Stage, ATHD1, Life History, CG31654, RPD3A, Histone H2b, Histone H2a, protein polypeptide chains, Techniques, domestic cat, Roles, Domestic Cats, Sexual Differentiation, Method, HDA1, AW537363, AA959943, DHDAC3, Concepts, Life Cycle, alpha-adaptin, Sexual, Lbpl, protein aggregate, tcfap2a, Chromatins, hdac3, HDAC, Sex, Gene Expressions, CG4260, entire life cycle, xap2, proteins, Domestic, Hdac 3, Acts, Methodological Studies, Deacetylase Complexes, 422|aP2, chromosome scaffold, Role Concepts, Histone H5, Histone H4, Histone H7, Toxoplasmas, stage, Infections and Infestations, Histone H1, Histone H3, nuclear chromatin, Acta-2, Actsk-1, F20D10.250, sigma2, Procedure, XAP-2, Deacetylases, ada, Programs, Ap-2 (a), D-Ada, Role Concept, cardinal, dmHDA402, Felis domestica, F20D10_250, cg4260, Role, Ap2tf, Genetic Materials, dAP-2a, HD3, ATHDA19, regulator, Genetic Material, l(2)06694, MENE (2L)-A, ALBP|Ap2, Factors, life, Life Cycle Stage, NDPP1, History Stage, Infection and Infestation, alpha, Methodological, Toxoplasma gondius, AP-2alpha, Felis silvestris catus, Methodological Study, Felis sylvestris catus, DmelCG4260, Dromel_CG2128_FBtr0078767_hdac3_mORF, Life Cycles, metastatic, Parasite, Material, Complexes, Toxoplasma, Cistron, TFIIIA, cytoplasmic chromatin, alpha-Ada, lifespan, T1N24_9, Procedures, RPD3, developmental stage, CARDINAL, Gene, T1N24.9, Development, protein-containing complex, Transcription Factor, l(2)SH2 0460, gondius, alpha-ada, method, polypeptide chain, histone deacetylase 2, method used in an experiment, Cycle, histone deacetylase 1, Gene Products, Studies, CARD-inhibitor of NF-kappa-B-activating ligand, ARABIDOPSIS HISTONE DEACETYLASE 1, Histone Deacetylase Complexes, Life, HISTONE DEACETYLASE 19, Technique, Histone H3.3, Cycles, study, CATS, Transcription, 6720460F02Rik, Genetic, TUCAN, dHDAC3, entire lifespan, Tcfap2a, Alpha-Adaptin, Expressions, Class II Histone Deacetylases, Life History Stages, Study, Cats, Infestation and Infection, Stages, CG6056, Life History Stage, Toxoplasma gondii, cats, Expression, Differentiation, Apoptotic protein NDPP1, CG2128, HISTONE DEACETYLASE19, Tumor up-regulated CARD-containing antagonist of CASP9, cg6056, protein complex, Felis catus, Proteins, Factor, Cistrons, Histone, Cell, HISTONE DEACETYLASE, Concept, AP2alpha, development, ALBP, HEL-S-104, native protein, natural protein, AP-2 sigma, Felis domesticus, Protein, vertebrates, Infection, Vertebrata, MENE(2L)-A, Vertebrate, Cat, HDA19, DmelCG6056, AFABP, tfap2alpha, Ap2, HDAC3, DAKAR, History Stages, D-alphaAda, DmelCG2128, DACAR, Papilio pandora, ALBP/Ap2, Histone Deacetylase, A-FABP, postnatal growth, cat, Histone H1(s), Protein Gene Products, plan specification, Gene Proteins, ap2, AP2, RPD3-2, tfap2a, l(2)SH0460, HDAC Proteins, DmHDAC3, 2610008F03Rik, growth, ARABIDOPSIS HISTONE DEACETYLASE 19"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Tgondii - Whole organism, iBAQ (Farhatetal,natmicrobiol2020)","description":"abundance based on iBAQ, Interaction consistency score: 12.1, Coverage: 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