{"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":["9606"],"full_dataset_link":["https://pax-db.org/dataset/9606/440404448"],"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":["<h4>Background</h4>The vitreous humor is a transparent, gelatinous mass whose main constituent is water. It plays an important role in providing metabolic nutrient requirements of the lens, coordinating eye growth and providing support to the retina. It is in close proximity to the retina and reflects many of the changes occurring in this tissue. The biochemical changes occurring in the vitreous could provide a better understanding about the pathophysiological processes that occur in vitreoretinopathy. In this study, we investigated the proteome of normal human vitreous humor using high resolution Fourier transform mass spectrometry.<h4>Results</h4>The vitreous humor was subjected to multiple fractionation techniques followed by LC-MS/MS analysis. We identified 1,205 proteins, 682 of which have not been described previously in the vitreous humor. Most proteins were localized to the extracellular space (24%), cytoplasm (20%) or plasma membrane (14%). Classification based on molecular function showed that 27% had catalytic activity, 10% structural activity, 10% binding activity, 4% cell and 4% transporter activity. Categorization for biological processes showed 28% participate in metabolism, 20% in cell communication and 13% in cell growth. The data have been deposited to the ProteomeXchange with identifier PXD000957.<h4>Conclusion</h4>This large catalog of vitreous proteins should facilitate biomedical research into pathological conditions of the eye including diabetic retinopathy, retinal detachment and cataract."],"pubmed_title":["Proteomic analysis of human vitreous humor."],"pubmed_authors":["Murthy Krishna R KR, Goel Renu R, Subbannayya Yashwanth Y, Jacob Harrys Kc HK, Murthy Praveen R PR, Manda Srikanth Srinivas SS, Patil Arun H AH, Sharma Rakesh R, Sahasrabuddhe Nandini A NA, Parashar Arun A, Nair Bipin G BG, Krishna Venkatarangaiah V, Prasad Ts Keshava TK, Gowda Harsha H, Pandey Akhilesh A"],"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":["humoral fluid, vitreous fluid, vitreous humour, Humor., ocular fluid"],"pubmed_title_synonyms":["Human, Vitreous, humoral fluid, Vitreous Humor, human being, Vitreous Humors, Man (Taxonomy), vitreous body, Homo sapiens, vitreous humour, Bodies, Modern Man, Humor, proteomic analysis, Modern, Humors, vitreous fluid, man, Man, human, Body, Vitreous Bodies, ocular fluid."],"name_synonyms":["Peptidomics., Vitreous, humoral fluid, Vitreous Humor, Vitreous Humors, vitreous body, vitreous humour, Bodies, ocular fluid, Humor, Line, Humors, Cell Lines, vitreous fluid, Cell, Body, Vitreous Bodies, Lines"],"pubmed_abstract_synonyms":["liquid chromatography tandem mass spectroscopy, biochemical pathways, Diabetic retinopathy, Intercellular, Plasma Membranes, Metabolic Process, Opacities, visual_system, Activity, determination, postnatal development, Metabolic Concepts, Mbp1, opacity of the lens, BOUND WATER, growth and development, Uniandra, Protoplasm, HOH, Space, Cell Interactions, lenses, Classifications, dmTAF[[II]]230, Readability, hierarchies, hierarchy, Communications, Roles, systematics, eye, Concepts, globe, Analysis, Cell-to-Cell, Metabolism Concept, Nutrient, Phenomenon, myd, WMS, Vitreoretinal degeneration, detached retina, Mass Spectrum Analysis, average, portion of tissue, Inner layer of eyeball, LCMSMS, Man (Taxonomy), TFIID TAF250, Analyses, cel, catabolism, eyes, Cell to Cell Interaction, non-developmental growth of a unicellular organism, visual system, Tissue, Cloudy lens, ocular lens, crystalline lens, Vitreoretinal abnormality, tunica interna of eyeball, Mbp-1, proteins, metabolic process resulting in cell growth, Extracellular Spaces, Opacity, Vitreous Bodies, inner endospore membrane, Communication, Intercellular Space, Cataract, plasma membrane lipid bilayer, cataract, Komplexauge, vitreous humour, plasmalemma, Role Concepts, Plasma Membrane, cellular growth, Medicine, dihydridooxygen, biotransformation, dihydrogen oxide, Membranous, GPHYSD2, Catabolism, SGS, Contradens, LC-MS2, eye globe, dTAF[[II]]230, anatomical protrusion, Process, gyltl1b-b, Cytoplasms, Modern, metabolism resulting in cell growth, aqua, LC-MS/MS, Systematics, TAF200, vertebrate eye, TAFII-250, TAF250/230, inner layer of eyeball, Spectrum Analysis, results, ACMICD, Spectroscopy, Vitreous, Eyes, Taxonomies, H2O, cellular membrane, TAFII250, Interaction, Experimental, Role Concept, juxtamembrane, MDDGA6, non-developmental cell growth, mKIAA0609, Role, Diabetic Retinopathies, tissue portion, secretion, simple tissue, bacterial inner membrane, zusammengesetztes Auge, KIAA0609, Hydrogen Oxide, eyeball, Retinal, Detachments, fg, Vitreous Humors, cell membrane, Cell Communications, gyltl1b, growth pattern, lens, non-developmental growth, Orbital part of face, mdc1d, hydrogen hydroxide, Spectrometry, expanded, Lens Opacities, MASS, CG17603, TAF[[II]], human, acqua, MDC1D, hyaline, enr, Lens opacity, Taf250, enlarged, orbital part of face, spine, liquid chromatography-tandem mass spectroscopy, SR3-5, Humor, Wasser, Proteomes, Lens <bivalves>, Intercellular Spaces, TAF230, big, d230, Retinopathies, human being, localised, vitreous body, compound eye, regio orbitalis, Bodies, taxonomy, Retinal Detachments, Processes, Cytoplasmic Membrane, adult compound eye, FBN, Lens <eudicots>, Gene, vitreous fluid, dTAFII250, Spectrum Analyses, Metabolic Processes, EfW1, lens crystallina, froggy, agua, LC-MS-MS, Gyltl1a, Biomedical, protrusion, Human, large, Investigative, camera-type eye plus associated structures, Homo sapiens, dmTAF1, ECTOL1, Taf230, Metabolism, Cell-to-Cell Interactions, LC-MSMS, Medical Research, Mass, Gene Products, detached, Detachment, camera-type eye lens, Membranous Cataract, Metabolism Phenomena, Medical, Lens, Man, Mass Spectroscopy, Catalogs, Netzhaut, TAF250, light-detecting organ, study, Orbital region, Taf200, Taxonomy, Lens opacities, dTAF[[II]]250, localized, Cell Interaction, growth of cell, retinas, retina of camera-type eye, Research, cell, MDDGB6, ligand, nutrients, Metabolic Concept, Cell-to-Cell Interaction, Taf1p, LARGE, eau, man, OCTD, Cytoplasmic, dTAF250, BPFD#36, Membranous Cataracts, Pseudoaphakias, Cytoplasmic Membranes, Extracellular, great, Ora Serrata, Investigational Medicine, Retinal Pigment Epithelial Detachment, TAF, molecular function, eye lens, integral to plasma membrane, Macronutrient, Cataracts, retinal abnormality - diabetes-related, molecular function unknown, humoral fluid, nutrient, Retinopathy, data, TAF[[II]]250, lens capsule, degradation, integral component of plasma membrane, Humors, Proteins, total expressed protein, bulbus oculi, l(3)84Ab, enzyme activity, BG:DS00004.13, Pseudoaphakia, Cell, retinal detachment, visual apparatus, Concept, dTAF230, Metabolic Phenomena, Macronutrients, development, Metabolism Concepts, cell expansion, Investigative Medicine, LC/MS/MS, MS, native protein, Facettenauge, p230, diabetic retinopathy, ocular fluid, chemical analysis, Protein, Phenomena, TAF[[II]]250/230, TFIID, MFS1, background, intercellular space, Spaces, Cell Membranes, metabolism, Mass Spectrum Analyses, Investigational, WMS2, Tunica interna of eyeball, Metabolic Phenomenon, Plasma, Taf[[II]]250, Mass Spectrum, Membranes, multicellular organism metabolic process, cataract (disease)., TAF[[II]]230, biodegradation, Metabolic, Experimental Medicine, postnatal growth, Clouding of the lens of the eye, retina, TAF[II]250, Diabetic, Understanding, small-molecule carrier or transporter, Membrane, Body, introduction, Protein Gene Products, requirements, Gene Proteins, single-organism metabolic process, Vitreous Humor, DmelCG17603, clear, orbital region, Modern Man, SSKS, Protoplasms, liquid chromatography tandem mass spectrometry, carrier, Lens Opacity, assay, cytoplasmic membrane, [OH2], growth, General activity, Interactions, TAF1, Anabolism"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"H.sapiens - Cell line, Vitreous humor, SC (Murthy,clin_proteomics,2014)","description":"abundance based on Spectral counting, vitreous_humor, Interaction consistency score: 7.3, Coverage: 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