OncoLand Case Study - SampleSets with Grouping

From Array Suite Wiki

Identify gene expression differences between Triple-Negative and other Breast Cancer samples

Breast cancers missing Estrogen Receptor, Progesterone Receptor, and EGF Receptor (HER2) cannot be targeted by many of the common treatments for breast cancer, so are of particular interest. We can use Land Analytics tools to identify genes that are significantly different between TNBC and other breast tumors.

Create a SampleSet of Triple-Negative Breast Cancer samples

Triple-Negative Breast Cancers can be identified in TCGALand by filtering for clinical variables indicating results of IHC assays. These samples can be sub-grouped within a SampleSet, and this SampleSet grouping can be used to compare samples for differences in expression, mutation frequency, clinical variables, etc.

Identify and Visualize Gene Expression Differences between TNBC and other Breast Tumors

SampleSets can be used to identify "signatures" that reflect differences between specified sub-groupings in the SampleSet. In this example, TCGALand is queried for genes that are differentially expressed between "Triple-Negative" vs other breast cancers samples, revealing gene signatures of these subtypes.

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