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Proteomics Exercises: Analysis of Gene Expression and Protein Localization

Exercise 1 involves searching for specific genes and their protein products in kidney and skin tissues, comparing RNA and protein expression levels, identifying cell types expressing proteins, and checking antibody specificity. Exercise 2 focuses on querying databases for abundant proteins in human blood, brain, and lung tissues, and examining differences in gene expression and protein localization.

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Proteomics Exercises: Analysis of Gene Expression and Protein Localization

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  1. ExercisesProtomics I Exercise 1 Searchthe ArrayExpress database (orsimilar) forthree genes withspecificexpression in kidneyandthreeother genes withskin-specificexpression. Ifpossible, selectforeachtissueoneexamplewithhighexpressionlevel, onewith intermediate levelandonewithlowexpressionlevel. Go totheUniprotdatabaseandsearchtheaccessionnumbersforthe 6 genes. Also write down thecalculatedmolecularweightforeachprotein. Look upthesix genes in the Human Proteome Atlas. Do theproteinsshowthe same expressionpropertiesasthemRNAs? Can youidentify in whatcelltypestheproteinsareexpressed? Save representativefigures UsetheProteome Atlas tolookupthesubcellularlocalizationandnotetheresultsandrepresentativefigures. Check thespecificityoftheantibodies. Do theproteinexpressiondata (histology, subcellular) rely on onlyoneantibody? Doesthisantibodyrecognize a single band oftheexpectedmolecularweight? Iftherearedifferences, cantheybeexplained? Exercise2 Thereis a publiclyaccessibledatabaseforproteinabundance in multipeorganisms (and multiple tissuesforsomeofthem). Try to find the web pageofthedatabase. Query thedatabaseforthe top 5 most abundant proteins in human bloodplasmaandbloodserum. Are these different genes? Whatisthedifferencebetween Plasma and Serum anyway? Query the ArrayExpress database (orBioGPS) toseewherethemRNAsofthese genes areexpressed. Whatarethe top 5 most abundant genes in brainandlung? Are theseresultsrealistic? (UseUniprotorWikipediato find out more on the genes ifnecessary) In thelistofhighlyexpressedbrainproteins, identifyonegenewith neuronal expressionandonewithglialexpression. Check the Human Proteomeatlasifthesedifferencesarevisible in theimmunohistologyslides.

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