GEPAS -Gene Expression Pattern Analysis Suite

Hongli Li

Computer Science Department

UMASS Lowell

http://www.cs.uml.edu/~hli/Courses/CompBio_files/presentations.htm

Features

• Preprocessing– Log-transformation, replication handling, missing

value imputation, filtering and normalization

• Analysis Tools– Viewer– Unsupervised Clustering– Differential Gene Expression– Supervised Classification– Data Mining with Gene Ontology (GO)

http://gepas.bioinfo.cnio.es/tools.html

Pre-Analyses & Preprocessing

• Pre-analyses• Preprocessing the

data– Transform– Deal with replication

and missing value– Filter patterns,

standardize patterns– Filter genes

After Preprocess

PlotCorr

SOM

Cluster

EPCLUST

• Steps – Send to EPCLUST

from GEPAS– Proceed– Go to respective page,

remember the file name

– Select the data interested

– Use the interested tools to analysis

•http://ep.ebi.ac.uk/EP/EPCLUST/

Conclusion

• Easy to use

• Preprocessing is quite powerful

• Connected to gene database