Expression of a gene set in Lands

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Contents

Case

Biological questions:

Testing for a gene set or gene signature is a popular method for testing association with a specific phenotype, which allows noise reduction and can provide greater biological interpretability.

Method #1

Step #1: search multiple genes from interactive search bar

Define the list of genes that the user would like to summarize, and enter them into the multi-functional search bar.

SearchMultipleGenes.png

Afterwards, you can apply filters to customize the samples displayed by applying the metadata filters in the left side panel.

Step #2: Navigate to the "Average FPKM" view in Lands

After searching for the genes of interest, switch to the Average FPKM view from the "Select View" menu. This will switch to a visualization that summarizes the expression values and displays one mean value for each sample based on expression of all genes averaged together.

AverageFPKMView.png


You can modify the grouping of the samples using the Grouping option at the top of the screen, and other aspects of the chart using the Task tab.

ChangeChartGrouping.png

ChangeChartDetails.png

Method #2

Step #1: create a custom query to summarize multiple genes

If you would like more control over the summarization method used for the gene set's expression (i.e, median instead of average), then you can instead set up a custom query for multiple genes. To create a multiple gene custom query, click on the star icon with the plus symbol and choose Add Omic Data Query. Enter your genes of interest in the search field, select the data type (RnaSeq_FPKM), toggle the option “summarize multiple genes by”, then choose the desired summarization method (i.e. median).

GeneSetCustomQuery.png

Step #2: Grouping by Custom Query

The generated custom query will appear on the filter panel. This custom query can also be used as a Grouping method on any chart type within the Lands.

GroupByCustomQuery.png