{"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":["10090"],"full_dataset_link":["https://pax-db.org/dataset/10090/2795042795"],"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"],"pubmed_title_synonyms":["Membrane Tissue, fur, setulae, membrane, single-organism developmental process, protein complex, postnatal development, Proteins, Stereocilium, integral to membrane, Gene, Hairs, growth and development, protein, membranous organ component, protein-containing complex, Stereovilli, Hair, development, Membrane Tissues, protein polypeptide chains, native protein, natural protein, polypeptide chain, integral component of membrane, Protein, whole membrane, Gene Products, PP4, protein aggregate, Anchorin CII, Placental Anticoagulant Protein I, Lanugo, Stereovillus, transmembrane, membrane of organ, Fetal Hairs, whisker, Fetal Hair, function., Tissues, coat/ hair, membrane region, vibrissa, Tissue, postnatal growth, hair, ANX5, proteins, Endonexin II, Membrane, microchaeta, Protein Gene Products, Gene Proteins, ENX2, Lipocortin-V, Calphobindin I, quill, Fetal, region of membrane, associated, coat hair, Lipocortin V, growth, Annexin V, PAP-I"],"name_synonyms":["muscle, Vestibular Hair Cells, vestibular receptor cell, Vestibular Hair Cell., Hair Cell, musculus, muscle element, Vestibular"],"pubmed_abstract_synonyms":["DmelCG5730, setulae, 1110014C03Rik, Materials, NCK5A, phospholipids, Laboratory, Inner, Mus domesticus, 21 kDa polypeptide, CG9968, Stereocilium, A4, CASP-14, protein, Organelle, Cochlear Organ, Chromobindins, House Mouse, p35nck5a, Histamine-releasing factor, MAGE-E1 antigen, Hair, Membrane Tissues, Lipocortins, protein polypeptide chains, DSmurf, Bony Labyrinth, Roles, Ptges, Duaxol, Concepts, 2, PP4, P 23, Annexin IX, Analysis, protein aggregate, S31I125, Tau protein kinase II 23 kDa subunit, IKKg, Annexin, KEY, Key, Mass Spectrum Analysis, F14D7_2, average, Cochleas, MXK3.27, Cochlear, Alpha(B)-crystallin, Fetal Hairs, vestibular organ, Analyses, CALCIUM ION, membrane region, cPGES, vibrissa, Tissue, bis(methylcarbamate) (ester), Swiss Mice, proteins, internal ear, TEBP, hearing, Estimated, Gasparol, allergic reaction, Movecil, cochlear duct, cochlear part of bony labyrinth, Annexin X, Audition, Fetal, HCA1, Parmidine, Smurf, cochleae, F14D7.2, Role Concepts, Fortilin, MXK3_27, p02, house mouse, associated, Membranous, Lipocortin V, Annexin V, Annexin XI, HRF, vestibulomotor system, CG4943, D-smurf, OXY5, Membrane Tissue, AnxB9, Noise, annexin 1, PLATEST, annexin 2, Angioxine, P23, mouse, Pollution, integral to membrane, Hairs, Phosphatides, membranous organ component, Lack, Spectrum Analysis, results, mice C57BL/6xCBA/CaJ hybrid, doubly charged positive ion, Spectroscopy, DmelCG9968, DmIKKgamma, Role Concept, dIKK, RENBP, p21, Mini-ICE, DAMAGE, Hepatocellular carcinoma-associated protein 1, Kenny, p23, Role, auris interna, p25, Genetic Materials, CG5730, Tebp, Membranous Labyrinths, Genetic Material, Placental Anticoagulant Protein I, relational structural quality., Mus musculus, Lisator, membrane of organ, whisker, Annx, Caspase-14 subunit p10, DmelCG4943, Tmp-21-I, mice, System, Swiss Mouse, IKK-gamma, Spectrometry, p35, Cyclin-dependent kinase 5 regulatory subunit 1, Caspase-14 subunit p19, Ca(2+), MICE, CDK5 activator 1, Crya2, domesticus, AGE, calcium, P24(DELTA), DMDA, Bony, DmelCG16910, Calphobindin I, Specificity and Sensitivity, Material, Labyrinths, vestibular apparatus, Annexin VIII, Cistron, Mouse, Noise Pollution, ATOXY5, Calcimedins, labyrinth, mMage-e1, P-23, inner ear, Platelets, PAP-I, Duvaline, 3.4.22.-, Bony Labyrinths, AnxB10, Internal, AnxB11, BcDNA:GH16395, conformation, Membranous Labyrinth, TCTP, dSmurf1, number, Calpactins, Gene, 5730442A20Rik, mini-ICE, Vestibular Systems, Spectrum Analyses, protein-containing complex, equilibrioception system, presence, TYPE, dIKK-gamma, Calelectrins, DAGA4, Ca2+, Labyrinth, polypeptide chain, House, sensitive, integral component of membrane, DmIKK-gamma, Gene Products, Mass, Mus musculus domesticus, CG9579, dmIKKgamma, Ear, MAM, IKK[[gamma]], Cochlea, Mice, SCG3, Anchorin CII, sensitivity, Mass Spectroscopy, Annexin B9, Lanugo, ANNEXIN A2, 6-Pyridinedimethanol-bis-(N-methylcarbamate), 6-Pyridinedimethanol, Phospholipid, Fetal Hair, Genetic, R74653, S31III125, ANNEXIN A1, Tissues, Swiss, coat/ hair, ligand, annexin, Calcimedin, AI847422, Annexin A8, Calelectrin, perception of sound, ENX2, d-smurf, IKK, quill, 21 kDa transmembrane-trafficking protein, Crya-2, region of membrane, Sensitivity, Transmembrane protein Tmp21, fur, membrane, Colesterinex, DmelCG9579, protein complex, RnBP, Annexin B10, Proteins, Alpha-dystrobrevin-associated MAGE Protein, otocyst, Internal Ears, GlcNAc 2-epimerase, Trt, CDK5R, function, Dsmurf, Cistrons, HEL-S-7, Internal Ear, Stereovilli, Anx B9, cochlear organ, Cell, Cyclin-dependent kinase 5 activator 1, Sospitan, Mus muscaris, LGMD2C, Concept, p24delta, Pyricarbate, dSmurf, ANNEXIN, IKKgamma, Tmp21, count in organism, N-acetyl-D-glucosamine 2-epimerase, MS, native protein, natural protein, Mus, Inner Ear, Smurf ubiquitin ligase, Protein, lagenas, whole membrane, HspB5, TMP21, p24 family protein delta-1, TPKII regulatory subunit, Mass Spectrum Analyses, p24delta1, sid3177, Ann, a phospholipid derivative, Anginin, Mass Spectrum, Stereovillus, transmembrane, DMDA1, RGD1560259, Dmikkgamma, Annexin A11, hair, Specificity, ANX5, Anx5, House Mice, Endonexin II, Lipocortin, Membrane, CG16910, microchaeta, Ears, Noises, Laboratory Mice, Protein Gene Products, anxX, RPRGL3, Gene Proteins, CDK5P35, Lipocortin-V, SCARMD2, renin-binding protein, Calpactin, coat hair, Prodectin, Laboratory Mouse, Inner Ears, Vestibular"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"M.musculus - Vestibular hair cell, SC (Kreyetal.,scireport2016)","description":"abundance based on Spectral counting, Interaction consistency score: 6.2, Coverage: 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