GEPAS -Gene Expression P attern Analysis Suite Hongli Li Computer Science Department UMASS Lowell http://www.cs.uml.edu/~hli/Courses/CompBio_files/ presentations.htm
GEPAS -Gene Expression Pattern Analysis Suite
Dec 30, 2015
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 - PowerPoint PPT Presentation
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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/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
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