GenePattern is a freely available software package released in 2004 that provides access to over 250 genomic analysis tools. It allows users to design sophisticated analysis pipelines by chaining modules together to capture methods, parameters, and data used to produce results. Pipelines can be used to create, edit, share, and reproduce in silico genomic analysis results.

1. GENE PATTERN

2. GenePattern
• GenePattern is a freely available software
package that provides access to a wide range
of computational methods used to analyze
genomic data.
• It was first released in 2004.
• Designed to enable researchers to develop,
capture, and reproduce genomic analysis
methodologies,

3. USAGE
It provides access to more than 250 genomic
analysis tools.
 Use the analysis tools as building blocks to
design sophisticated analysis pipelines that
capture the methods, parameters and data used
to produce analysis results.
Pipelines can be used to create, edit and share
reproducible in silico results.

4. Features
• Regularly updated repository of computational analysis
modules that support data preprocessing, gene expression
analysis, proteomics, single nucleotide polymorphism (SNP)
analysis, flow cytometry, and next-generation sequencing
• Pipelines that allow you to chain modules together to create
analysis workflows
• Tools to support easy creation and integration of new analysis
modules
• Versioning of modules and pipelines to ensure reproducible
research
• Web browser, application, and programmatic interfaces to
make analysis modules and pipelines available to a broad
range of users

9. Run an Analysis in GenePattern
• Learn how to run an analysis in GenePattern
by preprocessing gene expression data and
visualizing the resulting data as a heat map.
• Step 1: PreprocessDataset(Preprocess gene
expression data to remove platform noise and
genes that have little variation.)
• Step 2: HeatMapViewer (Display a heat map
of the preprocessed gene expression data. )

10. Step 1: PreprocessDataset

17. Step 2: HeatMapViewer: it provides users with several
options for manipulating and visualizing array-based data

22. Samples
Name
Gene
Name

23. By Using GenePattern We Can Also
Find:
• ComparativeMarkerSelection analysis to
find marker genes the genes in the dataset
that are most closely correlated with the two
phenotypes (ALL and AML) in the dataset.
• ComparativeMarkerSelectionViewer to
examine the ComparativeMarkerSelection
analysis result
• ExtractComparativeResults analysis to
create a smaller dataset that contains only the
marker genes