{"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/9606/3333699990"],"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":["Patients with Alzheimer's disease (AD) and Parkinson's disease (PD) often have overlap in clinical presentation and brain neuropathology suggesting that these two diseases share common underlying mechanisms. Currently, the molecular pathways linking AD and PD are incompletely understood. Utilizing Tandem Mass Tag (TMT) isobaric labeling and synchronous precursor selection-based MS3 (SPS-MS3) mass spectrometry, we performed an unbiased quantitative proteomic analysis of post-mortem human brain tissues (n=80) from four different groups defined as controls, AD, PD, and co-morbid AD/PD cases across two brain regions (frontal cortex and anterior cingulate gyrus). In total, we identified 11 840 protein groups representing 10 230 gene symbols, which map to ~65% of the protein coding genes in brain. The utility of including two reference standards in each TMT 10-plex assay to assess intra- and inter-batch variance is also described. Ultimately, this comprehensive human brain proteomic dataset serves as a valuable resource for various research endeavors including, but not limited to, the identification of disease-specific protein signatures and molecular pathways that are common in AD and PD."],"pubmed_title":["Global quantitative analysis of the human brain proteome in Alzheimer's and Parkinson's Disease."],"pubmed_authors":["Ping Lingyan L, Duong Duc M DM, Yin Luming L, Gearing Marla M, Lah James J JJ, Levey Allan I AI, Seyfried Nicholas T NT"],"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":["the brain, Parkinson's syndrome, Parkinson's disease, Parkinsons, Primary Parkinsonism, suprasegmental structures, human being, determination, Parkinson's disease NOS, Lewy Body, Modern, number, total expressed protein, Paralysis agitans, Primary, presence, encephalon, Idiopathic Parkinson Disease, Human, count in organism, Idiopathic Parkinson's Disease, Homo sapiens, Paralysis Agitans, Parkinson's Disease, Lewy Body Parkinson Disease, chemical analysis, synganglion, Man, PD., Man (Taxonomy), Parkinson disease, Parkinson's disease (disorder), Encephalon, suprasegmental levels of nervous system, man, human, Idiopathic PD, Lewy Body Parkinson's Disease, Parkinsonian disorder, Idiopathic, Parkinson's disease NOS (disorder), paralysis agitans, Shaking palsy, Modern Man, Parkinson Disease, Parkinsonism, Parkinson syndrome, assay, Proteomes"],"name_synonyms":["Brodmann's, Brodmann Area 8, Lobe, Eye Fields, Lobus Frontalis., Area 8, Frontal Cortex, Cortex, Supplementary Eye Fields, Brodmann, Frontal region, Brodmann's Area 8, Brodmanns Area 8, frontal cortex, frontal neocortex, Frontal Eye Field, Eye Field, Frontal, Supplementary, Frontal Lobes, Supplementary Eye Field, Frontal Eye Fields, Frontal Cortices"],"pubmed_abstract_synonyms":["Presenile Alzheimer Dementia, Parkinson's disease, deceased, ALZHEIMERS DIS, Materials, Activity, methionine aminopeptidase activity, determination, Laboratory, Early Onset, Parkinson's disease NOS, selection process, protein, Cardiac Death, Early Onset Alzheimer Disease, progressive encephalomyelitis with rigidity, Alzheimer's disease, Lobus Frontalis, ischiocoxopodopatellar syndrome, Primary Senile Degenerative, Morsch Woltman syndrome, AD, DmelCG11081, protein polypeptide chains, unspecified, AW111620, Paralysis Agitans, diseases, Frontal region, DPlexA, congenital coxa vara, sucrose phosphate synthetase activity, 2, diseases and disorders, synganglion, Analysis, Research Activity, Frontal, protein aggregate, Laboratory Research, WMS, tarsal synostosis, peptidase M activity, AI505014, Mass Spectrum Analysis, adenomas, Priorities, rabGAPLP, LATE ONSET ALZHEIMER DIS, human disease, L-methionine aminopeptidase activity, Frontal Cortex, Familial Alzheimer Disease (FAD), Alzheimer Diseases, Parkinson disease, Man (Taxonomy), DAT - Dementia Alzheimer's type, Parkinson's disease (disorder), Analyses, UDP-glucose-fructose-phosphate glucosyltransferase activity, Tissue, RabGAP-5, Neuropathologists, proteins, Focal Onset Alzheimer's Disease, suprasegmental levels of nervous system, Late Onset Alzheimer Disease, Frontal Cortices, CG17245, Brodmann Area 8, AD - Alzheimer's disease, RUSC3, scientific observation, Shaking palsy, Alzheimer Type Dementia, Homo sapiens disease, ALZHEIMER DIS EARLY ONSET, Parkinson syndrome, Research Priority, Presenile, GPHYSD2, Reference Standard, Alzheimers disease, SGS, AA589574, 1110046B24Rik, sucrose phosphate-uridine diphosphate glucosyltransferase activity, Parkinson's syndrome, Brodmann's, Senile, Parkinsons, Standard Preparation, Standard Preparations, Alzheimer disease, suprasegmental structures, Standardization, Data Set, Acute Confusional Senile Dementia, Modern, familial, MYH-associated polyposis, autosomal recessive familial adenomatous polyposis, Maps, Research Priorities, Neuropathologist, Spectrum Analysis, Frontal Eye Fields, Alzheimer's Dementia, ACMICD, Alzheimer Type, Spectroscopy, TPSG1, S-adenosyl-L-methionine:thiol S-methyltransferase activity, Idiopathic Parkinson's Disease, batch, Lewy Body Parkinson Disease, Diseases, Genetic Materials, NOS, overlap, PlexA1, uridine diphosphoglucose-fructose phosphate glucosyltransferase activity, Genetic Material, BcDNA:GM05237, autosomal recessive, Dementia, parent ion, Research and Development, RUTBC3, Alzheimers, Standard, PlexB, PlexA, Alzheimer, Encephalon, Brodmanns Area 8, Spectrometry, frontal neocortex, common, Dementias, INSDC_feature:gene, MASS, Alzheimer-Type (ATD), Supplementary, Plex1, ICPPS, human, RABGAP5, MRSR, Activities, disease, Area 8, Senile Dementia, precursor ion, Patient, Supplementary Eye Fields, paralysis agitans, Material, Neuropathologies, Acute Confusional, PRSS31, multiple colorectal, Alzheimer-Type Dementia (ATD), Cistron, Alzheimer's Disease, PLEXB, TMT, Alzheimer Type Dementia (ATD), Dementia of the Alzheimer's type, the brain, Lobe, other disease, common., sucrose 6-phosphate synthase activity, human being, Alzheimers Diseases, Lewy Body, Sclerosis, Stiff-trunk syndrome, number, FBN, Gene, Coding, CG11081, precursor, Spectrum Analyses, Focal Onset, protein-containing complex, presence, unspecified (disorder), Human, ALZHEIMER DIS, UDPglucose-fructose-phosphate glucosyltransferase activity, [X]Dementia in Alzheimer's disease, Homo sapiens, polypeptide chain, UDP-glucose:D-fructose-6-phosphate 2-alpha-D-glucosyltransferase activity, ECTOL1, Brodmann's Area 8, Mass, Gene Products, disease or disorder, Coxo-podo-patellar syndrome, D-Plex A, SMS, Medical, Man, familial adenomatous polyposis, Mass Spectroscopy, MAP, SPMSY, patella aplasia, Genetic, Clinical, sucrosephosphate-UDP glucosyltransferase activity, Research, MS3, Medical Coding, familial adenomatous polyposis 2, plex A, plex B, frontal cortex, Frontal Eye Field, labeling, Eye Field, man, Idiopathic PD, FOCAL ONSET ALZHEIMERS DIS, Presenile Dementia, non-neoplastic, OCTD, autosomal recessive multiple colorectal adenomas, DmelCG17245, UDPglucose:D-fructose-6-phosphate 2-alpha-D-glucosyltransferase activity, Reference, Idiopathic, Clients, Alzheimer Disease, SELD, Parkinson Disease, Parkinsonism, disorder, Alzheimer's disease (disorder), Development and Research, Preparation, SpS, Alzheimers Dementia, TAG, Supplementary Eye Field, thiol methyltransferase activity, SPS1, coxa vara, Alzheimer Senile Dementia, Stiff person syndrome and related disorders, measuring, Disease, Primary Parkinsonism, STIFF-PERSON syndrome, MUTYH-Associated Polyposis, Alzheimer Syndrome, protein complex, Proteins, disorders, Paralysis agitans, Primary, medical condition, SPS, Cistrons, plex, Client, encephalon, Primary Senile Degenerative Dementia, Idiopathic Parkinson Disease, [X]Dementia in Alzheimer's disease (disorder), Alzheimer Dementias, count in organism, MS, Priority, Cortex, native protein, natural protein, Parkinson's Disease, Brodmann, Alzheimer's Diseases, Protein, chemical analysis, proteomic analysis, post-mortem, Research Activities, condition, MFS1, Death, Mass Spectrum Analyses, WMS2, Stiff-Man syndrome, covalent modifier, Mass Spectrum, Dementia in Alzheimer's disease, Alzheimer's Disease Pathway, Alzheimer Type Senile Dementia, SRS, MYH-Associated Polyposis, Alzheimer Dementia, Alzheimer Sclerosis, Lewy Body Parkinson's Disease, Parkinsonian disorder, Protein Gene Products, Gene Proteins, Eye Fields, Preparations, Late Onset, Parkinson's disease NOS (disorder), Familial (FAD), Modern Man, Dementia in Alzheimer's disease (disorder), SSKS, Standards, MAP syndrome, PD, patella aplasia and tarsal synostosis, assay, Familial Alzheimer Diseases (FAD), Frontal Lobes, FAP2, colorectal adenomatous polyposis"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"H.sapiens - Frontal cortex, SC (Pingetal,scidata2018)","description":"abundance based on Spectral counting, Interaction consistency score: 15.9, Coverage: 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