GEPAS -Gene Expression Pattern Analysis Suite

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GEPAS -Gene Expression Pattern Analysis Suite

• Hongli Li
• Computer Science Department
• UMASS Lowell

http//www.cs.uml.edu/hli/Courses/CompBio_files/p
resentations.htm
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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
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Pre-Analyses Preprocessing

• Pre-analyses
• Preprocessing the data
• Transform
• Deal with replication and missing value
• Filter patterns, standardize patterns
• Filter genes

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After Preprocess
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PlotCorr
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SOM
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Cluster
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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/

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Conclusion

• Easy to use
• Preprocessing is quite powerful
• Connected to gene database