OncoLand Case Study - Custom Query

From Array Suite Wiki

MTBP expression and copy number correlates with poor patient survival

A recent paper used TCGA data to show that cancer patients with higher expression/amplified copy number of MTBP had reduced survival.

We can use TCGALand to verify and explore these results, using Custom Queries and SampleSets.

Visualize MTBP expression in tumor vs. normal breast cancer tissue


Categorize breast tumor samples by MTBP expression quartiles

By categorizing different samples by MTBP levels, we can visualize how high- vs. low-expressing breast cancers differ in survival.




Categorize breast tumor samples by MTBP copy number

If you want to explore how amplification or deletion of a gene correlates with expression, mutation, or clinical metadata, you can perform a "custom query" on Copy Number Variation.



Create a SampleSet of Triple-Negative Breast Cancer samples

Triple-Negative Breast Cancers do not express the receptors that act as common targets for treatment, so are of special interest. 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.



Filter and Group per-sample gene expression by a SampleSet

When you create a SampleSet with at least one metadata column with multiple levels, you can separate gene expression data by those levels. For example, A gene's expression can be compared between breast cancer samples that were identified as "Triple-Negative" for ER, PR, and HER2, compared to samples that express at least one receptor.

Subgroup sample expression data by multiple variables

In OncoLand, each sample can be grouped by extensive metadata, including clinical metadata such as clinical calls of receptor expression by immunohistochemistry. You can quickly partition a gene's expression by each permutation of multiple clinical variables to identify combinations (such as triple-negative breast cancer samples) that are significantly different.


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