PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering9823https://pax-db.org/dataset/9823/2274773369mering@imls.uzh.chUniversity of ZurichPAXDBFor the rescaling, the datasets are first parsed or processed such that the data reflect proportional abundances of whole protein molecules (i.e. proportionality to counts of complete, individual protein molecules, not to molecular weights, protein volumes, or digested peptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up to one million; this means the abundance of each protein of interest is finally expressed in (parts per million,) relative to all other proteins in a sample. For a given protein abundance dataset, we then compute the absolute log abundance ratios of all pairs of proteins annotated to be functionally linked. The median of these absolute log abundance ratios represents an indirect quality metric: the closer it is to zero, the better (i.e. the more there is consistency between abundance values and functional annotations such as protein complexes or pathways). We then compute a background expectation for this metric, by permuting the abundance values in a given dataset randomly, and recomputing the median log abundance ratios. The permutation is repeated several times, yielding a distribution of medians. The actually observed median is then expressed as a Z-score distance to the random distribution ofmedians—this distance is termed the interaction consistency score.Synovial fluid in an articulating joint contains proteins derived from the blood plasma and proteins that are produced by cells within the joint tissues, such as synovium, cartilage, ligament, and meniscus. The proteome composition of healthy synovial fluid and the cellular origins of many synovial fluid components are not fully understood. Here, we present a normative proteomics study using porcine synovial fluid. Using our optimized method, we identified 267 proteins with high confidence in healthy synovial fluid. We also evaluated mRNA expression data from tissues that can contribute to the synovial fluid proteome, including synovium, cartilage, blood, and liver, to better estimate the relative contributions from these sources to specific synovial fluid components. We identified 113 proteins in healthy synovial fluid that appear to be primarily derived from plasma transudates, 37 proteins primarily derived from synovium, and 11 proteins primarily derived from cartilage. Finally, we compared the identified synovial fluid proteome to the proteome of human plasma, and we found that the two body fluids share many similarities, underlining the detected plasma derived nature of many synovial fluid components. Knowing the synovial fluid proteome of a healthy joint will help to identify mechanisms that cause joint disease and pathways involved in disease progression.A normative study of the synovial fluid proteome from healthy porcine knee joints.Bennike Tue T, Ayturk Ugur U, Haslauer Carla M CM, Froehlich John W JW, Proffen Benedikt L BL, Barnaby Omar O, Birkelund Svend S, Murray Martha M MM, Warman Matthew L ML, Stensballe Allan A, Steen Hanno HAdd, 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, ratioSynovial Fluids, study, joint, Synovia, joints, Fluid, articulation, articular joint., Joint, joint fluid, knee, Fluids, total expressed protein, synovial fluid, Synovial, knee region, ProteomesSynovial Fluids, Fluids, Synovia, synovial fluid, Fluid, Synovial, joint fluid.Synovial Fluids, Fresh, synovial layer of articular capsule of synovial joint, true ligament, joints, human being, Fresh Frozen Plasma, Procedures, membrana synovialis capsulae articularis, Joint ankylosis of the forearm, Peptidomics, Blood, Synovium, Transudates and Exudates, Gene, Interosseous, Arthropathies, chondrogenic tissue, Menisci, jecur, Human, ankylosis of ankle and foot joint, method, Techniques, infectious arthropathy, Interosseous Ligament, ankylosis of joint of shoulder region, Homo sapiens, stratum synoviale, Method, Messenger, Joint, cartilages, method used in an experiment, Gene Products, Studies, Clinical Progression, Exudates, ankylosis of upper arm joint, Arthropathy, synovial membrane, Technique, Non Polyadenylated, Man, Joint ankylosis of the shoulder region, Cartilages, portion of blood, Progression, study, Fresh Frozen Plasmas, Fresh Frozen, Blood Plasma, synovium of articular capsule of synovial joint, portion of cartilage tissue, Man (Taxonomy), Clinical, Joint ankylosis of the hand, membrana synovialis (capsula articularis), Polyadenylated Messenger, ligament, articular ligament, Tissue, iecur, messenger RNA, proteins, cartilage tissue, man, stratum synoviale (capsula articularis), Study, template RNA, Methodological Studies, Joint ankylosis of the upper arm, Clinical Course, Disease., Blood Plasmas, articular joint, Exacerbation, ankylosis of joint of pelvic region and thigh, plasma, cartilaginous tissue, Ligament, joint, ankylosis of lower leg joint, Interosseal, RNA, data, Disease, Synovia, Frozen Plasma, whole blood, Transudates, Polyadenylated, vertebrate blood, Modern, Proteins, synovial layer, Disease Exacerbation, Fluids, ligament organ, total expressed protein, Messenger RNA, Interosseal Ligaments, ankylosis of forearm joint, Procedure, Plasmas, Joint ankylosis of the ankle and foot, Cell, Synovial Membranes, Frozen Plasmas, ankylosis of hand joint, Fluid, native protein, Poly(A)+ mRNA, Protein, joint fluid, ankylosis of multiple joints, INSDC_feature:mRNA, synovium, Transudate, Polyadenylated RNA, Interosseous Ligaments, Synovial, synovial membrane of articular capsule of synovial joint, Polyadenylated Messenger RNA, Plasma, Membranes, Exudate, portion of blood plasma, Poly(A)+ RNA, Joint ankylosis of the pelvic region and thigh, synovial tissue, Non Polyadenylated mRNA, ankylosis of joint of multiple sites, articulation, Body Fluid, protein_coding_transcript, mRNA, Poly(A) Tail, Non-Polyadenylated, Membrana Synovialis Capsulae Articularis, portion of plasma, Interosseal Ligament, Joint ankylosis of the lower leg, Methodological, articular larua, Membrane, Methodological Study, Non-Polyadenylated mRNA, human, Body, Protein Gene Products, plan specification, Gene Proteins, Livers, blood plasm, Joint Disease, cartilage, Modern Man, synovial fluid, Polyadenylated mRNA, Proteomes, Poly(A) RNA0falseS.scrofa - Synovial fluid, iBAQ (Bennikeetal,jproteomeres2014)abundance based on iBAQ, Interaction consistency score: 4.7, Coverage: 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