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GEPAS -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

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GEPAS -Gene Expression Pattern Analysis Suite

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  1. GEPAS -Gene Expression Pattern Analysis Suite Hongli Li Computer Science Department UMASS Lowell http://www.cs.uml.edu/~hli/Courses/CompBio_files/presentations.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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