{"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/89462/1439943622"],"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":["Subclinical mastitis by Staphylococcus aureus (SAU) and by non-aureus staphylococci (NAS) is a major issue in the water buffalo. To understand its impact on milk, 6 quarter samples with >3,000,000 cells/mL (3 SAU-positive and 3 NAS-positive) and 6 culture-negative quarter samples with <50,000 cells/mL were investigated by shotgun proteomics and label-free quantitation. A total of 1530 proteins were identified, of which 152 were significantly changed. SAU was more impacting, with 162 vs 127 differential proteins and higher abundance changes (P < 0.0005). The 119 increased proteins had mostly structural (n = 43, 28.29%) or innate immune defence functions (n = 39, 25.66%) and included vimentin, cathelicidins, histones, S100 and neutrophil granule proteins, haptoglobin, and lysozyme. The 33 decreased proteins were mainly involved in lipid metabolism (n = 13, 59.10%) and included butyrophilin, xanthine dehydrogenase/oxidase, and lipid biosynthetic enzymes. The same biological processes were significantly affected also upon STRING analysis. Cathelicidins were the most increased family, as confirmed by western immunoblotting, with a stronger reactivity in SAU mastitis. S100A8 and haptoglobin were also validated by western immunoblotting. In conclusion, we generated a detailed buffalo milk protein dataset and defined the changes occurring in SAU and NAS mastitis, with potential for improving detection (ProteomeXchange identifier PXD012355)."],"pubmed_title":["Proteomic changes in the milk of water buffaloes (Bubalus bubalis) with subclinical mastitis due to intramammary infection by Staphylococcus aureus and by non-aureus staphylococci."],"pubmed_authors":["Pisanu Salvatore S, Cacciotto Carla C, Pagnozzi Daniela D, Puggioni Giulia Maria Grazia GMG, Uzzau Sergio S, Ciaramella Paolo P, Guccione Jacopo J, Penati Martina M, Pollera Claudia C, Moroni Paolo P, Bronzo Valerio V, Addis Maria Filippa MF"],"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, Bubalus bubalus, Bos bubalis, Inflammatory disorder of breast (disorder), Bubalis bubalis, inflammation of breast, aqua, river buffalo, Infestations and Infections, BOUND WATER, Inflammatory disease of breast, Buffalo, Milk, agua, breast infection, HOH, Water Buffaloes, mammary gland milk, H2O, inflammatory disease of breast, Cow's Milk, Infection, Cow's, breast inflammation NOS, Staphlococcus pyogenes citreus, Hydrogen Oxide, Bubalus arnee, domestic water buffalo, Staphylococcus aureus subsp. anaerobius, Water Buffalo, Bubalis arnee bubalis, Staphilococcus aureus, Bubalus, Inflammatory breast disease, inflammatory breast disease, hydrogen hydroxide, Infection and Infestation, Micrococcus aureus, eau, clinical infection, Bubalus arnee bubalis, acqua, water buffalo, Mastitis, Infestation and Infection, mastitis, breast inflammation, Micrococcus pyogenes, Staphylococcus pyogenes aureus, Streptococcus aureus., Cow Milk, Cow, Syncerus, dihydridooxygen, breast inflammation NOS (disorder), Wasser, Infections and Infestations, Staphylococus aureus, dihydrogen oxide, [OH2]"],"name_synonyms":["Cow's., mammary gland milk, Cow Milk, Cow, Cow's Milk, Milk"],"pubmed_abstract_synonyms":["Water, Networks, Bubalus bubalus, Inflammatory disorder of breast (disorder), Reverse, Immunoelectroblotting, MA387, Kinship, Cathelicidin LL-37, determination, LL-37 Antibacterial, inflammation of breast, Antimicrobial Peptide, Inflammatory disease of breast, LL-37 Peptide, breast infection, Milk, Polymorphonuclear, Water Buffaloes, Histone H2b, Background, Histone H2a, neonatal withdrawal, Electroimmunoblotting, neutrophilic leucocyte, hCAP 18, MIF, neutrophil leukocyte, responsivity, Cultural, CAP-18, Life Cycle, Cow's, LE Cell, present in fewer numbers in organism, Staphlococcus pyogenes citreus, Cathelicidin Antimicrobial Peptide, AI266795, Family Life Cycle, Neutrophil Band Cells, increased, ethnicity, Kinship Network, L1Ag, enzymes, Immunoblottings, Staphilococcus aureus, Inflammatory breast disease, 371, Bubalus, inflammatory breast disease, Micrococcus aureus, proteins, 8D8.1, CATH-1 Protein, free, fs(1)A371, 60B8Ag, water buffalo, Cathelicidin-1, breast inflammation, decreased, Mrp8, MRP8, polymorphonuclear leukocyte, polynuclear neutrophilic leucocyte, Histone H5, Histone H4, breast infection., Histone H7, LL 37 Peptide, DmelCG11411, Family Life Cycles, CATH-1, Histone H1, Histone H3, 60B8AG, anatomical protrusion, Cathelin-Related Antimicrobial, Bubalis bubalis, Data Set, vimentin, type III intermediate filament associated protein, river buffalo, eCATH 1 protein, fs(1)K1540, CAP18, S100, S100-B, Buffalo, K9CATH, Antimicrobial Peptide LL 37, Neutrophil Band Cell, neutrophil granulocyte, neutrocyte, Cultural Background, LL-37 Antibacterial Peptide, LE Cells, Cultures, CP-10, peripherin, Bos taurus, 162, Lipid, Filiation, Milk Protein, glial fibrillary acidic protein, Reverse Immunoblottings, Polymorphonuclear Neutrophil, CGLA, Water Buffalo, Cultural Beliefs, neutrophilic granulocyte, Antibacterial, AI323541, Bubalus arnee bubalis, Mastitis, Life Cycles, B8Ag, mastitis, Staphylococcus pyogenes aureus, spine, Reverse Immunoblotting, label, Biocatalyst, Cathelicidin 1, Polymorphonuclear Leukocytes, Myeloid Cathelicidin 1 Protein, E430016J11Rik, Antibacterial Peptide LL 37, Cathelicidin LL 37, accessory, Nas, CATH 1 Protein, lipids, polynuclear neutrophilic leukocyte, Peptide LL-37, Band Cell, HP, Family Member, Immunoblotting, Cathelin-Like Protein, Peptidomics, ALL-38, Biocatalysts, Dot Immunoblotting, Gene, Network, Ximpact, supernumerary, FA-LL-37, hCAP-18, Butyrophilin, protrusion, CAP18 Lipopolysaccharide Binding Protein, Dot, reduced, subnumerary, Cow's Milk, Metabolism, EG:8D8.1, S100-alpha, Gene Products, LL 37 Antibacterial Peptide, Histone H3.3, Backgrounds, reactivity, eCATH-1 protein, domestic water buffalo, lipid metabolism, Antibacterial Peptide, Bubalis arnee bubalis, Research, Cathelin-Related, neutrophil leucocyte, Cultural Relativisms, fs(1)Nasrat, CAP 18, neutrophilic leukocyte, decreased number, Ropocamptide, fs(1)M6, CG11411, S100beta, Enzyme, desmin, Cow Milk, Cow, Syncerus, eCATH 1, NEF, Lipopolysaccharide-Binding Protein, Cathelicidin, Customs, Immunoelectroblottings, Staphylococus aureus, culture, CAP18 Lipopolysaccharide-Binding Protein, Kinship Networks, Cathelin-Like, LE, Family, Neutrophil, ALL 38 Peptide, Antimicrobial, LL-37, Leukocyte, Polymorphonuclear Neutrophils, Family Research, Leukocytes, Proteins, Haptoglobin, enzyme activity, Cultural Backgrounds, Histone, impact-a, Cell, Peptide, Polymorphonuclear Leukocyte, Fs(1)N, Family Members, mammary gland milk, Antibacterial Peptide LL-37, inflammatory disease of breast, Bac4 Protein, CAGA, native protein, Dot Immunoblottings, FA LL 37, Protein, chemical analysis, breast inflammation NOS, milk protein, Equus caballus, Bubalus arnee, Electroimmunoblottings, Cathelin-Related Antimicrobial Peptide, Staphylococcus aureus subsp. anaerobius, Caga, fs(1)[nas], p8, S100a, increased number, ALL-38 Peptide, CFAG, Histone H1(s), Streptococcus aureus, CAP18 Lipopolysaccharide-Binding, Protein Gene Products, fs(1)Nas, Gene Proteins, present in greater numbers in organism, Micrococcus pyogenes, P8, NIF, S100A, Families, PMN, Relativisms, polymorphonuclear leucocyte, breast inflammation NOS (disorder), assay, response, CFAg, Relativism, poly, Cultural Relativism, Relatives, RWDD5, polymorphonuclear neutrophil, eCATH-1, Antimicrobial Peptide LL-37"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Bbubalis - Milk, NSAF (Pisanuetal,scirep2019)","description":"abundance based on NSAF, Interaction consistency score: 4.3, Coverage: 1","dates":{"publication":"2019"},"accession":"1439943622","cross_references":{"pubmed":["31676851"],"uniprot":["89462.XP_006067540.1","89462.XP_006070778.1","89462.XP_006065006.1","89462.XP_006059233.1","89462.XP_006064330.1","89462.XP_006042170.1","89462.XP_006052740.1","89462.XP_006051368.1","89462.XP_006046651.1","89462.XP_006075893.1","89462.XP_006039931.1","89462.XP_006077719.1","89462.XP_006051721.1","89462.XP_006060946.1","89462.XP_006056351.1","89462.XP_006068845.1","89462.XP_006056942.1","89462.XP_006043742.1","89462.XP_006058686.1","89462.XP_006051590.1","89462.XP_006062764.1","89462.XP_006068348.1","89462.XP_006046104.1","89462.XP_006078135.1","89462.XP_006061844.1","89462.XP_006039905.1","89462.XP_006060813.1","89462.XP_006065017.1","89462.XP_006054204.1","89462.XP_006047571.1","89462.XP_006078693.1","89462.XP_006053322.1","89462.XP_006055596.1","89462.XP_006050183.1","89462.XP_006043256.1","89462.XP_006078910.1","89462.XP_006077060.1","89462.XP_006068398.1","89462.XP_006058253.1","89462.XP_006041720.1","89462.XP_006073358.1","89462.XP_006045222.1","89462.XP_006070027.1","89462.XP_006052221.1","89462.XP_006059042.1","89462.XP_006064569.1","89462.XP_006058374.1","89462.XP_006045944.1","89462.XP_006068982.1","89462.XP_006042699.1","89462.XP_006067524.1","89462.XP_006063431.1","89462.XP_006062918.1","89462.XP_006067029.1","89462.XP_006057898.1","89462.XP_006050302.1","89462.XP_006045267.1","89462.XP_006058445.1","89462.XP_006040835.1","89462.XP_006078136.1","89462.XP_006072612.1","89462.XP_006068627.1","89462.XP_006052615.1","89462.XP_006071702.1","89462.XP_006042626.1","89462.XP_006067153.1","89462.XP_006067130.1","89462.XP_006048032.1","89462.XP_006062752.1","89462.XP_006075623.1","89462.XP_006071576.1","89462.XP_006046781.1","89462.XP_006047223.1","89462.XP_006045337.1","89462.XP_006066976.1","89462.XP_006074763.1","89462.XP_006079592.1","89462.XP_006075732.1","89462.XP_006048080.1","89462.XP_006057537.1","89462.XP_006054263.1","89462.XP_006064716.1","89462.XP_006055812.1","89462.XP_006080796.1","89462.XP_006056409.1","89462.XP_006078186.1","89462.XP_006060333.1","89462.XP_006078140.1","89462.XP_006052124.1","89462.XP_006078543.1","89462.XP_006055508.1","89462.XP_006072360.1","89462.XP_006076454.1","89462.XP_006062208.1","89462.XP_006065874.1","89462.XP_006067328.1","89462.XP_006060962.1","89462.XP_006070893.1","89462.XP_006050320.1","89462.XP_006063582.1","89462.XP_006057755.1","89462.XP_006062102.1","89462.XP_006061077.1","89462.XP_006041590.1","89462.XP_006068757.1","89462.XP_006050667.1","89462.XP_006040040.1","89462.XP_006054791.1","89462.XP_006047480.1","89462.XP_006057333.1","89462.XP_006051427.1","89462.XP_006070234.1","89462.XP_006053589.1","89462.XP_006072686.1","89462.XP_006076733.1","89462.XP_006071637.1","89462.XP_006063725.1","89462.XP_006078020.1","89462.XP_006050985.1","89462.XP_006062675.1","89462.XP_006058587.1","89462.XP_006050936.1","89462.XP_006071988.1","89462.XP_006051052.1","89462.XP_006043687.1","89462.XP_006077038.1","89462.XP_006059944.1","89462.XP_006069410.1","89462.XP_006074852.1","89462.XP_006067733.1","89462.XP_006055851.1","89462.XP_006041162.1","89462.XP_006076453.1","89462.XP_006071379.1","89462.XP_006064386.1","89462.XP_006048261.1","89462.XP_006042246.1","89462.XP_006043917.1","89462.XP_006070283.1","89462.XP_006056111.1","89462.XP_006060963.1","89462.XP_006076075.1","89462.XP_006047782.1","89462.XP_006075671.1","89462.XP_006080552.1","89462.XP_006051480.1","89462.XP_006061745.1","89462.XP_006041551.1","89462.XP_006042163.1","89462.XP_006048053.1","89462.XP_006068504.1","89462.XP_006041112.1","89462.XP_006069846.1","89462.XP_006042855.1","89462.XP_006079472.1","89462.XP_006041937.1","89462.XP_006043089.1","89462.XP_006060829.1","89462.XP_006053085.1","89462.XP_006069701.1","89462.XP_006077971.1","89462.XP_006077764.1","89462.XP_006064877.1","89462.XP_006065232.1","89462.XP_006060953.1","89462.XP_006062820.1","89462.XP_006059855.1","89462.XP_006067461.1","89462.XP_006045987.1","89462.XP_006077557.1","89462.XP_006074456.1","89462.XP_006043264.1","89462.XP_006076530.1","89462.XP_006040190.1","89462.XP_006068114.1","89462.XP_006077267.1","89462.XP_006049744.1","89462.XP_006055167.1","89462.XP_006047104.1","89462.XP_006056961.1","89462.XP_006061632.1","89462.XP_006069818.1","89462.XP_006045083.1","89462.XP_006056283.1","89462.XP_006055529.1","89462.XP_006055170.1","89462.XP_006053992.1","89462.XP_006079689.1","89462.XP_006058003.1","89462.XP_006057227.1","89462.XP_006061196.1","89462.XP_006045914.1","89462.XP_006063448.1","89462.XP_006043252.1","89462.XP_006051231.1","89462.XP_006077824.1","89462.XP_006052952.1","89462.XP_006068426.1","89462.XP_006047640.1","89462.XP_006080932.1","89462.XP_006074139.1","89462.XP_006055456.1","89462.XP_006058536.1","89462.XP_006065638.1","89462.XP_006080872.1","89462.XP_006061979.1","89462.XP_006062483.1","89462.XP_006072022.1","89462.XP_006078007.1","89462.XP_006079133.1","89462.XP_006069281.1","89462.XP_006050307.1","89462.XP_00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