{"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/89462/1933059366"],"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":["Maternal-effect genes are especially critical for early embryonic development after fertilization and until massive activation of the embryonic genome occurs. By applying a tandem mass tag (TMT)-labeled quantitative proteomics combined with RNA sequencing approach, the proteome of the buffalo was quantitatively analyzed during parthenogenesis of mature oocytes and the two-cell stage embryo. Of 1908 quantified proteins, 123 differed significantly. The transcriptome was analyzed eight stages (GV, MII, 2-cell, 4-cell, 8-cell, 16-cell, morula, blastocyst) of Buffalo using the RNA sequencing approach, and a total of 3567 unique genes were identified to be differently expressed between all consecutive stages of pre-implantation development. Validation of proteomics results (TUBB3, CTNNA1, CDH3, MAP2K1), which are involved in tight junction and gap junction, revealing that the maternal expression of the proteins possibly plays a role in the formation of cellular junctions firstly after parthenogenetic activation. Correlation and hierarchical analyses of transcriptional profiles and the expression of NPM2 and NLRP5 mRNA of buffalo <i>in vitro</i> developed oocytes and parthenogenetic embryos indicated that the \"maternal-to-zygotic transition\" (MZT) process might exist in the model of parthenogenesis, which is similar to a normally fertilized embryo, and may occur between the 8-cell to 16-cell stage. These data provide a rich resource for further studies on maternal proteins and genes and are conducive to improving nuclear transfer technology."],"pubmed_title":["Integrated Analysis of Quantitative Proteome and Transcriptional Profiles Reveals the Dynamic Function of Maternally Expressed Proteins After Parthenogenetic Activation of Buffalo Oocyte."],"pubmed_authors":["Chen Fumei F, Fu Qiang Q, Pu Liping L, Zhang Pengfei P, Huang Yulin Y, Hou Zhen Z, Xu Zhuangzhuang Z, Chen Dongrong D, Huang Fengling F, Deng Tingxian T, Liang Xianwei X, Lu Yangqing Y, 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":["Protein Gene Products, Gene Proteins, count in organism, Oocyte., native protein, determination, chemical analysis, Protein, Gene Products, Proteins, number, oogonium, total expressed protein, Gene, assay, Ovocytes, proteins, function, Proteomes, presence, activation, Ovocyte"],"name_synonyms":["egg cell, mature oocyte, ovum, 2018."],"pubmed_abstract_synonyms":["N Cadherin, CPD photolyase activity, P Cadherins, Postnidation Embryo, Ribonucleic, Nalp5, Materials, Polyspermic Fertilization, PhrB photolyase activity, plant germ, Liver Cell Adhesion Molecules, Post-implantation, growth and development, Profiles, E-Cadherin, CDCBM, Delayed Fertilizations, dmTAF[[II]]230, zonula communicans, Thelytoky, Tight, CG9063, 3, NUP96, CDCBM1, Fs(3)Hor, epithelium, intercellular gap junction channel, Non Polyadenylated, WMS, MZT, TFIID TAF250, Genomes, cel, anabolism, proteins, NTef2, BcDNA:GH03694, Signatures, SUPPRESSOR OF AUXIN RESISTANCE 3, Expression Signature, Parthenogeneses, Role Concepts, stage, SGS, dTAF[[II]]230, anatomical protrusion, Polyspermic Fertilizations, Polyadenylated, TAF200, mek-2, E Cadherin, Fs(3)Sz11, ACMICD, TPSG1, Role Concept, Cadherin, Expression Signatures, Role, dipyrimidine photolyase (photosensitive), Ribonucleic acids, Cadherins, Expression Profile, activation, Polyadenylated Messenger RNA, Acid, Neural Cadherins, Non Polyadenylated mRNA, protein_coding_transcript, Industrial Arts, AA517462, Occluden, Epithelial Cadherin, N Cadherins, electrical synapse, BcDNAGH03694, whole genome, occluding junction, 3200002H15Rik, CFEOM3, Non-Polyadenylated mRNA, 3L6, N-Cadherins, Epithelial Cadherins, Fertilization, Taf250, rich, Material, PRSS31, CG2684, CLR19.8, NALP5, TMT, Mek1, MEK1, Poly(A) RNA, Embryonic Programmings, TAF230, zonula occludens, occluding cell junction, Zonula Occluden, P-cadherin, Peptidomics, developmental stage, number, CDH3, TUBB4, biosynthesis, Epithelial-Cadherins, deoxyribodipyrimidine photolyase activity, Occluding Junctions, Prenidation Embryo Development, Gene Products, CDHP, Polyspermic, Tight Junction, P-Cadherin, dTAF[[II]]250, cell, Profile, Postnidation Embryo Development, F23A5.3, Pcad, primitive ectoderm, messenger RNA, Cdhp, Pre-implantation, Structure, fetal development, synthesis, dTAF250, template RNA, P-Cadherins, embryonic organism, Presumptive Structure, Embryonic Structure, PCAD, RNA, Mater, communicating junction, Proteins, Post implantation Embryo Development, Post-implantation Embryo Development, Preimplantation, Messenger RNA, Cadp, RNS, BG:DS00004.13, Occludens, Cell, dTAF230, Concept, whole transcriptome, E-Cadherins, native protein, Epithelial-Cadherin, Preimplantation Embryos, Poly(A)+ mRNA, Gene Expression Signatures, TAF[[II]]250/230, INSDC_feature:mRNA, MFS1, Zonula, MATER, Placental Cadherins, Postimplantation Embryo Development, Embryonic, Taf[[II]]250, covalent modifier, RPE, mRNA, postnatal growth, Prkmk1, Ribonucleic Acid, Lds, p. pigmentosa retinae, Gene Proteins, embryonic development, developmental tissue, Gene Expression Profiles, Fertilizations, deoxyribonucleate pyrimidine dimer lyase (photosensitive), Industrial., Polyadenylated mRNA, PRKMK1, Conceptions, Prenatal Structures, Preimplantation Embryo, Pre-implantation Embryo Development, single-organism developmental process, Liver Cell Adhesion Molecule, postnatal development, Gene Expression Profile, Ovocytes, pigmented epithelium, Pre implantation Embryo Development, Ovocyte, Embryonic Programming, Embryo Development, Roles, Concepts, HJMD, RNA Gene Products, multicellular organismal biosynthetic process, blastocystis, single-organism biosynthetic process, DmelCG2684, cadherin-14, Polyadenylated Messenger, Op1, pigmented retina, DNA cyclobutane dipyrimidine photolyase activity, Preimplantation Embryo Development, PYPAF8, reaction, MEKK1, morula (2-16 cells), Transcriptomes, Neural Cadherin, GPHYSD2, DmelCG9063, Oocyte, Presumptive, PRE, embryo, Catna1, ribose nucleic acid, deoxyribonucleic cyclobutane dipyrimidine photolyase activity, Arts, Expression Profiles, Occluding, ribonucleic acids, beta-4, developing organism, TAFII-250, TAF250/230, cap102, results, Gene Expression, macula communicans, S-adenosyl-L-methionine:thiol S-methyltransferase activity, TAFII250, retinal pigment, Ribonukleinsaeure, Genetic Materials, pentosenucleic acids, Gap, retinal pigment layer, Occluding Junction, Genetic Material, Transcriptome Profiles, Cadherin-2, Cadherin-1, epiblast, Cadherin-3, Gap Junction, MASS, blastula, CG17603, Junction, TAF[[II]], Prenatal Structure, early, Morulas, Delayed, phr A photolyase activity, DNA-photoreactivating enzyme, spine, Horka, syngamy, SR3-5, gap junction macula, Fs(3)Horka, electrotonic synapse, Cistron, Postimplantation, Proteomes, Uvomorulin, d230, Transcriptome Profile, MAPKK1, FEOM3, CAP102, Prenatal, FBN, Gene, dTAFII250, Development, photoreactivating enzyme activity, AI385538, EfW1, presence, protrusion, Zonula Occludens, dmTAF1, ECTOL1, Taf230, Messenger, Embryonic Developments, Automixis, stratum pigmentosa retinae, DmF2, catna1, Animal, TAF250, Neural, lod, MKK1, Postnidation, Taf200, MOS3, deoxyribocyclobutadipyrimidine pyrimidine-lyase activity, Genetic, PRECOCIOUS, formation, Cadherin 1, Cadherin 3, Cadherin 2, Taf1p, AI988031, Junctions, OCTD, Non-Polyadenylated RNA, Delayed Fertilization, gap junction plaque, TAF, TAG, F23A5_3, thiol methyltransferase activity, Arrhenotoky, data, TAF[[II]]250, Transcriptome, Placental, parthenogenesis, total expressed protein, N-Cadherin, l(3)84Ab, ectoblast, Cistrons, npm-A, embryonic aspects, development, count in organism, MODIFIER OF SNC1, CFEOM3A, Conception, Blastocysts, yeast nucleic acid, p230, Embryos, Protein, deoxyribonucleic photolyase activity, TFIID, Gene Expression Signature, Polyadenylated RNA, 2010010M04Rik, blastocyst, CDH14, WMS2, Embryo, ribonucleic acid, Poly(A)+ RNA, TAF[[II]]230, Poly(A) Tail, photolyase activity, Non Polyadenylated RNA, Embryogenesis, Non-Polyadenylated, TAF[II]250, PAN11, P Cadherin, Presumptive Structures, Protein Gene Products, M(beta)3, DmelCG17603, prenatal development, M(beta)6, CFC3, SSKS, GRO:0005343, Signature, epiblastus, growth, E Cadherins, TAF1"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Bbubalis - 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