Transcript CEPAS -Gene Expression Pattern Analysis Suite

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
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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