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Exercises Protomics I. Exercise 1

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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.