1 / 1

Exercises Proteomics IV

Exercises Proteomics IV. Exercise 1

sheera
Download Presentation

Exercises Proteomics IV

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. ExercisesProteomicsIV Exercise 1 The web siteExPASymaintains a comprehensivelistoftoolsanddatabasesusefulforproteomicsresearch (http://www.expasy.org/proteomics). Have a lookat a fewdatabasesandtoolsandtryto find out whattheyaregoodfor. Pick onerandomtool (ordatabase) thathas not beencovered in thiscourseandbepreparedtogive a two-minutepresentation (withoutslides) on itspurpose: Whatkindofinputisrequired, whatkindofoutputisprovided, whatistheidea? Exercise2 Familiarizeyourselfwiththe GO databaseandtheQuickGO (orAmiGO) browser. Searchforcategoriesrelatedto 'apoptosis'. Whatareparentanddaughtercategories? Which human Genes are in theapoptosisset? Exercise 3 Assumeyouhaveperfomed a bioinformatical analysisofthe human proteomeandfoundthat an unusuallybigproportionof all proteins end withtheresidues K-D-E-L. Youwouldliketo find out whatthismotifisgoodfor. UseMyHits (seeExPASy) tosearchthe human proteomeforthemotif KDEL. Attention!! Have a lookatthesyntaxtomakesureyou pick onlyproteinsthat end withthemotif. Youshouldgetlessthan 15 hits. Get a listofUniprot-IDs (via MSA-Hub, Protein-Hub). Also get a filewith all Sequences in FASTA-format (via Protein-Hub, 'send tofasta'). UsethelistofUniprot-IDs toquerythe DAVID serverfor GO andpathwayenrichments. Follow theinstructions on the DAVID web page http://david.abcc.ncifcrf.gov UsetheSignalPserver (uses multi-sequence FASTA file) topredictwhichofthe KDEL proteinshavesignalsequences. Download fromthe 'data' sectionoftheSignalPserverinformation on howmany human proteinshavepredictedsignals (andhowmany human proteinsthereare). Calculatetheenrichmentfactorandthesignificance (Fisher) Exercise4 Searchproteinsets phosphorylated bythe kinases Cdk1, Jak2, Tbk1, mTOR. Whatprocesses do theyregulate?

More Related