Large-scale Prediction of Yeast Gene Function Introduction to Bio-Informatics 236523Winter 2010-2011

Roi Adadi roia@csNaama Kraus nkraus@cs

Main QuestionPredict the function of

hypothetical proteins which are inferred by genome sequencing

Annotate proteins at one of possible three levels◦Function◦Biological process◦Cellular localization

ProcessCluster the gene expressions using EPCLUST

Two possible directions:

Direction 1◦ Choose some "nice" cluster (e.g. a tied cluster)◦ Identify a common function F using GO◦ Search for hypothetical proteins in the cluster ◦ Predict their function as F◦ Validate the prediction using other methods

Use Blast to search for homologous proteins, do they contain F ?

Use Meme/Pfam to identify a common Motif/Domain, does it relate to F ?

Process – cont’dDirection 2

◦Decide on some function of interest and search for a cluster where this function is common Identify a cluster with a significant

localization function Look for a significant motif/domain in the

mRNA UTRs of the sequences in the cluster using MEME/Pfam

Search the motif/domain in other proteins, do they localize at the same location ?