Introduction

The PhenoDCC Procedural and Ontological Heatmap web application allows a user to systematically browse phenotype expressions for a given genotype. It also provides the user with a portal for accessing data visualisations that correspond to specific phenotype expressions.

The heatmap web application was designed primarily for phenotypers and scientists who are interested in the knockout effects on mouse phenotype. It is accessed using a standard web browser, such as Google Chrome, by visiting the appropriate web application server. It is very likely that the PhenoDCC heatmap has been embedded inside other web pages (e.g., the gene details page etc.).

Usage modes

The PhenoDCC heatmap provides the user with two browsing modes. These are:

Procedural mode

In procedural mode, the available categories are listed as pipeline procedures and measured parameters. This allows the user to visualise phenotype expressions in relation to experimental procedures carried out on the specimens. The following shows the PhenoDCC Heatmap in procedural mode:

Heatmap in procedural mode

Heatmap in procedural mode

Ontological mode

In ontological mode, the available categories are listed as ontology terms. These terms are determined by the associated meanings defined for specific variation in the knockout expressions as compared to wild type expressions. The following shows the PhenoDCC Heatmap in ontological mode:

Heatmap in ontological mode

Heatmap in ontological mode

The user interface

The user interface for the PhenoDCC Heatmap is organised as follows:

Organisation of the user interface

Organisation of the user interface

At the top, we have the toolbar. This consists of the mode selectors on the right hand side, and the breadcrum interface for hierarchical navigation on the left. Below the toolbar is the controls panel, with three components.

Legends

The first is the group of legends:

  1. Significant - Defines colour to highlight phenotype cells with significant phenotype expressions.

  2. Insignificant - Defines colour to highlight phenotype cells with no significant phenotype expressions.

  3. No data - Defines the appearance of cells with no phenotype data.

Hovering over the first two legends will show a colour picker pop-up. Clicking on a colour will set the colour for that legend.

The p-value gradient

The second component is the Show p-value gradient control. This allows a user to visualise the relative strength of the phenotype expressions of all of the visible categories, as shown below:

Relative strength of phenotype expressions as p-value gradient

Relative strength of phenotype expressions as p-value gradient

The p-value slider

Finally, the last control is the p-value slider. This allows a user to change the p-value threshold which determines whether a phenotype expression is significant or insignificant.

Components of the p-value slider

Components of the p-value slider

The value of the p-value slider can be altered in two ways:

  1. Set the threshold value by entering the value manually in the text input box. This is useful when the user knows the exact p-value threshold that they require.

  2. Drag the slider button to apply the required value. This is useful when a user wishes to see variations at various thresholds.

The reset button is used to set the p-value slider to its default threshold.

The phenotype cells

Depending on the chosen category, the lower part of the heatmap displays various cells. These cells are grouped into sections. In each section, the genotype identifier is displayed on the left hand side and cell columns display phenotype expressions.

The column header cell displays the phenotype category. If a category may be examined further, these cells are made clickable. For instance, in the following, we are examining the 'Behavior / neurological' ontology further.