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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/presentations.htm – PowerPoint PPT presentation

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Title: GEPAS -Gene Expression Pattern Analysis Suite


1
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
2
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
3
Pre-Analyses Preprocessing
  • Pre-analyses
  • Preprocessing the data
  • Transform
  • Deal with replication and missing value
  • Filter patterns, standardize patterns
  • Filter genes

4
After Preprocess
5
PlotCorr
6
SOM
7
Cluster
8
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/

9
Conclusion
  • Easy to use
  • Preprocessing is quite powerful
  • Connected to gene database
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