2023
Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors
Shi G, Song C, Torres Robles J, Salichos L, Lou H, Lam T, Gerstein M, Turk B. Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors. Science Signaling 2023, 16: eabm5518. PMID: 36626580, PMCID: PMC9995140, DOI: 10.1126/scisignal.abm5518.Peer-Reviewed Original ResearchConceptsMitogen-activated protein kinaseDocking motifSequence motifsDocking sequenceShort linear sequence motifsLinear sequence motifsSubstrate recruitmentHuman proteomeProtein kinaseCatalytic cleftExchange mutantsEssential functionsCultured cellsScreening pipelineWide screeningInteractorsMotifSequenceLimited repertoireSelective bindingInteractomeCombinatorial librariesMKK6ProteomeMKK7
2021
The factors for the early and late development of midbrain dopaminergic neurons segregate into two distinct evolutionary clusters
Niu Y, Moghimyfiroozabad S, Moghimyfiroozabad A, Tierney T, Alavian K. The factors for the early and late development of midbrain dopaminergic neurons segregate into two distinct evolutionary clusters. Brain Disorders 2021, 1: 100002. DOI: 10.1016/j.dscb.2021.100002.Peer-Reviewed Original ResearchTranscription factorsNon-canonical functionsMidbrain dopaminergic neuronsDistinct evolutionary pathwaysEntire human proteomeNovel molecular connectionDopaminergic neuronsPotential novel linkPhylogenetic profilesEvolutionary pathwaysHuman proteomeEvolutionary scenarioMolecular connectionEvolutionary clustersDevelopmental pathwaysNovel linkNeuronal differentiationNovel linkageDevelopmental cascadeParkinson's diseasePathwayNeuronsMotor behaviorControl of emotionsProteome
2020
Comparative Proteomic Profiling of Unannotated Microproteins and Alternative Proteins in Human Cell Lines
Cao X, Khitun A, Na Z, Dumitrescu DG, Kubica M, Olatunji E, Slavoff SA. Comparative Proteomic Profiling of Unannotated Microproteins and Alternative Proteins in Human Cell Lines. Journal Of Proteome Research 2020, 19: 3418-3426. PMID: 32449352, PMCID: PMC7429271, DOI: 10.1021/acs.jproteome.0c00254.Peer-Reviewed Original ResearchConceptsRibosome profilingHuman cell linesQuantitative mass spectrometry-based proteomicsCell linesMass spectrometry-based proteomicsLabel-free quantitative proteomicsComplex human proteomeLabel-free comparative proteomicsAlternative open reading framesStress-dependent expressionSpectrometry-based proteomicsTissue-specific expressionOpen reading frameComparative proteomic profilingUnannotated ORFsComparative proteomicsUnannotated proteinsMammalian cellsHuman proteomeQuantitative proteomicsDifferential translationReading frameProteomic profilingHuman leukemia cell linesRegulated expressionComprehensive proteomic analysis of murine terminal erythroid differentiation
Gautier EF, Leduc M, Ladli M, Schulz VP, Lefèvre C, Boussaid I, Fontenay M, Lacombe C, Verdier F, Guillonneau F, Hillyer CD, Mohandas N, Gallagher PG, Mayeux P. Comprehensive proteomic analysis of murine terminal erythroid differentiation. Blood Advances 2020, 4: 1464-1477. PMID: 32282884, PMCID: PMC7160260, DOI: 10.1182/bloodadvances.2020001652.Peer-Reviewed Original ResearchConceptsTerminal erythroid differentiationErythroid differentiationProteomic dataMurine terminal erythroid differentiationTerminal differentiationOverall cellular contentComprehensive proteomic dataComprehensive proteomic analysisMurine erythroid cellsTerminal differentiation processMost biologic processesProteome levelComparison of murineHuman proteomeProteomic analysisTranscriptomic changesChromatin condensationProteomeErythroid cellsFundamental mechanismsRed cell disordersDifferentiation processErythroid progenitorsFriend erythroleukemiaCellular model
2017
Impact of Alternative Splicing on the Human Proteome
Liu Y, Gonzàlez-Porta M, Santos S, Brazma A, Marioni JC, Aebersold R, Venkitaraman AR, Wickramasinghe VO. Impact of Alternative Splicing on the Human Proteome. Cell Reports 2017, 20: 1229-1241. PMID: 28768205, PMCID: PMC5554779, DOI: 10.1016/j.celrep.2017.07.025.Peer-Reviewed Original ResearchConceptsProteomic diversityAlternative splicingAlternative splicing eventsDifferential transcript usageIntron retentionSplicing eventsHuman transcriptomeHuman proteomeTranscript usageRNA sequencingProtein abundanceTranscript levelsHuman diseasesProteomeSWATH-MSSplicingQuantitative snapshotIntegrative approachCritical determinantDiversityTranscriptomeSequencingAbundanceMRNAQuantitative manner
2015
Tissue-based map of the human proteome
Uhlén M, Fagerberg L, Hallström B, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson Å, Kampf C, Sjöstedt E, Asplund A, Olsson I, Edlund K, Lundberg E, Navani S, Szigyarto C, Odeberg J, Djureinovic D, Takanen J, Hober S, Alm T, Edqvist P, Berling H, Tegel H, Mulder J, Rockberg J, Nilsson P, Schwenk J, Hamsten M, von Feilitzen K, Forsberg M, Persson L, Johansson F, Zwahlen M, von Heijne G, Nielsen J, Pontén F. Tissue-based map of the human proteome. Science 2015, 347: 1260419. PMID: 25613900, DOI: 10.1126/science.1260419.Peer-Reviewed Original ResearchConceptsPutative protein-coding genesHuman tissue proteomesProtein-coding genesInteractive web-based databaseIntegrated omics approachDifferent tissuesGlobal expression patternsSingle-cell levelMembrane proteomeProteome variationDruggable proteomeOmics approachesHuman proteomeHuman secretomeMolecular detailsIndividual proteinsQuantitative transcriptomicsCancer proteomeTissue proteomeProteomeExpression patternsHuman biologyMetabolic functionsTissue microarray-based immunohistochemistryMajor tissues
2014
Glycoproteomic Analysis of Prostate Cancer Tissues by SWATH Mass Spectrometry Discovers N-acylethanolamine Acid Amidase and Protein Tyrosine Kinase 7 as Signatures for Tumor Aggressiveness*
Liu Y, Chen J, Sethi A, Li QK, Chen L, Collins B, Gillet LC, Wollscheid B, Zhang H, Aebersold R. Glycoproteomic Analysis of Prostate Cancer Tissues by SWATH Mass Spectrometry Discovers N-acylethanolamine Acid Amidase and Protein Tyrosine Kinase 7 as Signatures for Tumor Aggressiveness*. Molecular & Cellular Proteomics 2014, 13: 1753-1768. PMID: 24741114, PMCID: PMC4083113, DOI: 10.1074/mcp.m114.038273.Peer-Reviewed Original ResearchConceptsN-acylethanolamine acid amidaseProtein tyrosine kinase 7Non-aggressive prostate cancerTyrosine kinase 7Prostate cancerKinase 7N-glycositesDiverse biological processesPotential tissue biomarkersAggressive prostate cancerPCa tumor tissuesSWATH mass spectrometryTissue microarray analysisProstate cancer tissuesUrgent clinical needIdentification of biomarkersHuman proteomePCa aggressivenessMicroarray analysisBiological processesPCa casesTissue biomarkersTumor aggressivenessNormal prostateCancer tissues
2013
Chemoproteomic Discovery of Cysteine-Containing Human Short Open Reading Frames
Schwaid AG, Shannon DA, Ma J, Slavoff SA, Levin JZ, Weerapana E, Saghatelian A. Chemoproteomic Discovery of Cysteine-Containing Human Short Open Reading Frames. Journal Of The American Chemical Society 2013, 135: 16750-16753. PMID: 24152191, PMCID: PMC3868496, DOI: 10.1021/ja406606j.Peer-Reviewed Original ResearchConceptsShort open reading framesOpen reading frameReading frameProtein-coding genesProtein-coding potentialGene-finding algorithmsAffinity-based approachRibosome profilingNew genesHuman proteomeMass spectrometry technologyEndogenous RNASpectrometry technologyLabeling approachGenesHuman SEPsPotential importanceInvaluable insightsExperimental approachGenomeProteomeDiscoveryRNABiologyPolypeptideReceptor tyrosine kinases with intracellular pseudokinase domains
Mendrola JM, Shi F, Park JH, Lemmon MA. Receptor tyrosine kinases with intracellular pseudokinase domains. Biochemical Society Transactions 2013, 41: 1029-1036. PMID: 23863174, PMCID: PMC3777422, DOI: 10.1042/bst20130104.Peer-Reviewed Original ResearchConceptsWeak kinase activityKinase activitySignificant kinase activityReceptor tyrosine kinasesPseudokinase domainHuman proteomeProtein kinaseImportant residuesWnt receptorsTyrosine kinaseEGFR familyKinaseFunctional studiesRTKPseudokinasesPseudokinaseProteomeReceptorsWntNew lightErbB3MutationsResiduesActivityRecent work
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