{"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":["10090"],"full_dataset_link":["https://pax-db.org/dataset/10090/748046481"],"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":["The phospholipid- and Ca(2+)-binding protein annexin A5 (ANXA5) is the most abundant membrane-associated protein of ~P23 mouse vestibular hair bundles, the inner ear's sensory organelle. Using quantitative mass spectrometry, we estimated that ANXA5 accounts for ~15,000 copies per stereocilium, or ~2% of the total protein there. Although seven other annexin genes are expressed in mouse utricles, mass spectrometry showed that none were present at levels near ANXA5 in bundles and none were upregulated in stereocilia of Anxa5(-/-) mice. Annexins have been proposed to mediate Ca(2+)-dependent repair of membrane lesions, which could be part of the repair mechanism in hair cells after noise damage. Nevertheless, mature Anxa5(-/-) mice not only have normal hearing and balance function, but following noise exposure, they are identical to wild-type mice in their temporary or permanent changes in hearing sensitivity. We suggest that despite the unusually high levels of ANXA5 in bundles, it does not play a role in the bundle's key function, mechanotransduction, at least until after two months of age in the cochlea and six months of age in the vestibular system. These results reinforce the lack of correlation between abundance of a protein in a specific compartment or cellular structure and its functional significance."],"pubmed_title":["Annexin A5 is the Most Abundant Membrane-Associated Protein in Stereocilia but is Dispensable for Hair-Bundle Development and Function."],"pubmed_authors":["Krey Jocelyn F JF, Drummond Meghan M, Foster Sarah S, Porsov Edward E, Vijayakumar Sarath S, Choi Dongseok D, Friderici Karen K, Jones Sherri M SM, Nuttall Alfred L AL, Barr-Gillespie Peter G PG"],"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":["16-178, 16-55, swb., Chp, Co, DmelCG3936, EG:163A10.2, anon-EST:Liang-1.12, dNotch, Ax, clone 1.12, co, spl, shd, 1.1, l(1)3Cb, nd, NICD, CG3936, n[fah], notch, fa, NECD, EG:140G11.1, CT13012, l(1)N, l(1)Ax"],"pubmed_title_synonyms":["Integral Membrane Proteins, fur, setulae, single-organism developmental process, postnatal development, Proteins, Surface Proteins, Stereocilium, Cell Surface, Cell Surface Protein, Hairs, growth and development, Membrane-Associated Proteins, Integral, Stereovilli, Cell, Hair, development, Membrane-Associated Protein, Protein, Membrane Proteins, PP4, Anchorin CII, Cell Surface Proteins, Placental Anticoagulant Protein I, Membrane Associated Protein, Lanugo, Cell Membrane, Cell Membrane Protein, Stereovillus, Fetal Hairs, whisker, Fetal Hair, function., coat/ hair, Surface, Membrane-Associated, vibrissa, postnatal growth, hair, ANX5, Cell Membrane Proteins, Endonexin II, Membrane, microchaeta, ENX2, Lipocortin-V, Integral Membrane Protein, Calphobindin I, quill, Fetal, Surface Protein, Membrane Associated Proteins, coat hair, Lipocortin V, Membrane Protein, growth, Annexin V, PAP-I, Integral Membrane"],"name_synonyms":["muscle, muscle element., musculus"],"pubmed_abstract_synonyms":["1110014C03Rik, Utricle and Saccule, Materials, phospholipids, Laboratory, Stereocilium, A4, Cochlear Organ, Integral, Chromobindins, House Mouse, Histamine-releasing factor, MAGE-E1 antigen, Hair, protein polypeptide chains, 2, P 23, Annexin IX, Analysis, Tau protein kinase II 23 kDa subunit, Otolithic Organ, average, Alpha(B)-crystallin, Fetal Hairs, vestibular organ, Analyses, Surface, vibrissa, Tissue, proteins, Otolithic, internal ear, hearing, Structures, allergic reaction, cochlear duct, cochlear part of bony labyrinth, Audition, Cellular Structure, Parmidine, Smurf, F14D7.2, Role Concepts, Fortilin, Surface Protein, Lipocortin V, HRF, vestibulomotor system, CG4943, AnxB9, Pollution, integral to membrane, Hairs, Phosphatides, Lack, Spectrum Analysis, mice C57BL/6xCBA/CaJ hybrid, cellular morphology, DmelCG9968, DmIKKgamma, Role Concept, Playthings and Play, dIKK, DAMAGE, Hepatocellular carcinoma-associated protein 1, Role, auris interna, Cellular, CG5730, Membranous Labyrinths, Cell Membrane Protein, Caspase-14 subunit p10, Membrane-Associated, Swiss Mouse, IKK-gamma, Spectrometry, Cell Membrane Proteins, Caspase-14 subunit p19, Component, CDK5 activator 1, Crya2, AGE, P24(DELTA), Cell Component, Calphobindin I, Material, Mouse, Binding Proteins, P-23, Utricle, 3.4.22.-, Carrier Protein, AnxB10, AnxB11, BcDNA:GH16395, Membranous Labyrinth, TCTP, 5730442A20Rik, mini-ICE, Vestibular Systems, protein-containing complex, equilibrioception system, dIKK-gamma, Calelectrins, Labyrinth, sensitive, Membrane-Associated Protein, DmIKK-gamma, Gene Products, Mus musculus domesticus, MAM, Cochlea, Toy, Cell Membrane, ANNEXIN A2, 6-Pyridinedimethanol, Playthings, ANNEXIN A1, Tissues, Calcimedin, AI847422, Structure, Calelectrin, ENX2, Puppets, quill, 21 kDa transmembrane-trafficking protein, Puppet, Organ, fur, Proteins, Cell Surface, Cell Surface Protein, Trt, function, Dsmurf, Stereovilli, cochlear organ, Cell, Cyclin-dependent kinase 5 activator 1, Concept, p24delta, dSmurf, ANNEXIN, IKKgamma, Tmp21, N-acetyl-D-glucosamine 2-epimerase, MS, native protein, Inner Ear, Smurf ubiquitin ligase, TMP21, Cell Surface Proteins, Mass Spectrum Analyses, Membrane Associated Protein, Ann, Anginin, DMDA1, RGD1560259, Dmikkgamma, Specificity, House Mice, CG16910, microchaeta, RPRGL3, CDK5P35, Gene Proteins, coat hair, Prodectin, Vestibular, DmelCG5730, Integral Membrane Proteins, setulae, Saccules, NCK5A, Inner, Mus domesticus, Surface Proteins, 21 kDa polypeptide, CG9968, CASP-14, Membrane-Associated Proteins, protein, Organelle, p35nck5a, Lipocortins, Membrane Tissues, DSmurf, Bony Labyrinth, Roles, Cellular., Ptges, Duaxol, Concepts, PP4, protein aggregate, S31I125, IKKg, Annexin, KEY, Key, Transport Proteins, Mass Spectrum Analysis, F14D7_2, Cochleas, MXK3.27, Cochlear, CALCIUM ION, cPGES, membrane region, bis(methylcarbamate) (ester), Swiss Mice, TEBP, Estimated, Gasparol, Movecil, Annexin X, Fetal, HCA1, cochleae, Membrane Associated Proteins, MXK3_27, p02, house mouse, Membranous, Membrane Protein, Annexin V, Annexin XI, D-smurf, OXY5, Membrane Tissue, Noise, annexin 1, PLATEST, annexin 2, Angioxine, P23, mouse, membranous organ component, Carrier, doubly charged positive ion, Spectroscopy, cellular aspects, RENBP, p21, Mini-ICE, Kenny, p23, Plaything, p25, Genetic Materials, Tebp, Binding Protein, Genetic Material, Placental Anticoagulant Protein I, Mus musculus, Lisator, whisker, membrane of organ, Annx, DmelCG4943, Tmp-21-I, mice, System, Toys, p35, Cyclin-dependent kinase 5 regulatory subunit 1, Ca(2+), MICE, domesticus, calcium, DMDA, Bony, DmelCG16910, Specificity and Sensitivity, Labyrinths, vestibular apparatus, Annexin VIII, Cistron, Noise Pollution, ATOXY5, Calcimedins, labyrinth, mMage-e1, cell morphology, inner ear, Platelets, PAP-I, Integral Membrane, Duvaline, Bony Labyrinths, Plays, Internal, dSmurf1, Components, Calpactins, Gene, Spectrum Analyses, TYPE, DAGA4, cellular structure, Ca2+, polypeptide chain, House, integral component of membrane, Mass, CG9579, dmIKKgamma, Ear, IKK[[gamma]], Mice, SCG3, Anchorin CII, sensitivity, Mass Spectroscopy, Annexin B9, Lanugo, 6-Pyridinedimethanol-bis-(N-methylcarbamate), Phospholipid, Fetal Hair, Genetic, R74653, S31III125, Swiss, coat/ hair, annexin, Annexin A8, perception of sound, d-smurf, IKK, Otolithic Organs, Saccule, Crya-2, region of membrane, Play, Sensitivity, Cell Components, Transmembrane protein Tmp21, membrane, Colesterinex, DmelCG9579, protein complex, RnBP, Annexin B10, Alpha-dystrobrevin-associated MAGE Protein, otocyst, Internal Ears, GlcNAc 2-epimerase, CDK5R, Utricles, cell structure, Cistrons, HEL-S-7, Internal Ear, Anx B9, Sospitan, Mus muscaris, LGMD2C, Pyricarbate, natural protein, Mus, Protein, lagenas, Membrane Proteins, whole membrane, HspB5, p24 family protein delta-1, TPKII regulatory subunit, p24delta1, sid3177, a phospholipid derivative, Mass Spectrum, Stereovillus, Transport Protein, transmembrane, Annexin A11, hair, ANX5, Anx5, Endonexin II, Lipocortin, Membrane, Ears, Noises, Laboratory Mice, Protein Gene Products, anxX, Lipocortin-V, Integral Membrane Protein, SCARMD2, renin-binding protein, Calpactin, Laboratory Mouse, Inner Ears"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"M.musculus - Utricle of membranous labyrinth, SC (Kreyetal.,scireport2016)","description":"abundance based on Spectral counting, Interaction consistency score: 1.1, Coverage: 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