Visualize: Gene Expression

On the Gene Expression tab of the Visualizations page you can inspect the gene expression patterns in the samples you have selected from the Search page.

The Gene Expression tab contains two cards:

  • Box Plot

  • Bar Chart

In order to populate both plots you’ll need to include at least one gene in the Gene Basket. For further information about how to do that see the Gene Basket article.

The cards are placed one below the other and their height depends on the amount of genes you have in the Gene Basket. However you can easily collapse and expand both cards by clicking the ‘Collapse’/’Expand icon in the upper right corner of each card.

../_images/Gene-Expressions.png

Box Plot card

The Tukey box plot, or box-and-whisker plot, is a familiar way to display non-parametric data without making assumptions on the underlying distribution. The normalized expression values (typically TMP, could be different in your particular flavor of Expressions product) across all samples in the basket (y-axis) are shown for each selected gene (x-axis). The horizontal line bisecting the box marks the median value whereas the bottom and top of the box denote the 1st and 3rd quartiles, respectively. The whiskers represent the lowest datum within the 1.5 interquartile range (IQR) of the 1st quartile, and the highest datum within 1.5 IQR of the 3rd quartile.

When an individual gene is selected in the Gene Basket, the corresponding box is highlighted blue. Mouse hover over boxes reveals a tooltip with additional quantitative details. You can toggle log2 transformation of the y-axis expression values. Further, you can use the Group by menu to organize the expressions by meta data and annotations in order to visualize the distribution of various sample groupings.

Bar Plot card

The bar plot enables a deep dive to see how selected genes are expressed in each individual sample in the basket. You may consider known biomarkers, novel genes of interest, or look more closely at differentially expressed genes identified in the Differential Expression tab. Normalized expression values (TPM) are shown, but the actual value displayed may be different in your particular flavor of Genialis Expressions product.

When an individual gene is selected in the Gene Basket, the corresponding bars are highlighted blue. Mouse hover reveals a tooltip with additional quantitative details. You can toggle log2 transformation of the y-axis expression values, or toggle between an extended view with sample names displayed within the bars or a more simplified view without the sample names. Further, you can use the Group by or Color by menus to organize or mark the bars by sample meta data and annotations to provide more insightful visual clues.

Download gene expression results

If you are interested in downloading your gene expression results, click on the ‘Export’ icon button in the top right of your screen (in the top bar). A modal window will appear where you can put down an optional prefix for the exported file and start the download by clicking the ‘EXPORT’ button.

../_images/Export.jpg

This will download a zipped report file that contains:

  • Bar Plot folder

    • A suggested caption text (.txt)

    • Expressions table (.tsv*)

    • Raster and vector plot image (.png and .svg)

  • Box Plot folder

    • A suggested caption text (.txt)

    • Expressions table (.tsv*)

    • Raster and vector plot image (.png and .svg)

  • Gene Basket folder

    • Information about the highlighted and selected genes in the Gene Basket (.tsv*)

  • Sample Basket folder

    • A list of selected samples in the Sample Basket (.tsv*)

*TSV (tab-separated-value) format files are plain-text tabular files that can be imported into any spreadsheet program.