Gene Expression Analysis  Print-icon

GenePattern provides support for 4 broad categories of gene expression analysis:

GenePattern also supports several data conversion tasks, such as filtering and normalizing, which are standard prerequisites for genomic data analysis.

Differential Analysis/Marker Selection

Differential analysis, also known as marker selection, is the search for genes that are differentially expressed in distinct phenotypes. GenePattern can assess differential expression using either the signal-to-noise ratio or t-test statistic.

GenePattern provides the following support for differential analysis:

View all current GenePattern marker selection modules

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Class Prediction (Supervised Learning)

Supervised learning, also known as class prediction, is the search for a gene expression signature that predicts class (phenotype) membership. The basic methodology for class prediction is to start with two data sets, a training set and test set; use your training data set to build a classifier (class predictor) based on your chosen classification method; and use your test data set to test the classifier.

GenePattern provides the following support for class prediction:

View all current GenePattern class prediction modules

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Class Discovery (Unsupervised Learning)

Unsupervised learning, also known as class discovery, is the search for a biologically relevant unknown taxonomy identified by a gene expression signature or a biologically relevant set of co-expressed genes.

The basic methodology for class discovery is clustering: you cluster the data based on your chosen clustering method and then validate the clusters through gene annotations, enrichment analysis (are the clusters enriched by genes from functionally important categories, pathways, or processes), or by replicating the results in other data sets. GenePattern provides the following support for clustering:

Clustering is the traditional method for class discovery. GenePattern also supports the following less traditional methods:

View all current GenePattern clustering modules

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Pathway Analysis

Pathway analysis is the search for sets of genes differentially expressed in distinct phenotypes. GenePattern provides the following support for pathway analysis:

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Data Formats

Gene expression analysis modules are designed for easy access:

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Modules

View all current GenePattern modules

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Updated on July 22, 2012 13:52