The Interaction Section (left)

Search & Highlight

You can search for pathways, metabolites, enzymes, or BRENDA IDs in the Search & Highlight section by start typing your search term. Metabolite or reaction search starts when at least 3 characters are entered and support both, the shown label or common name (from tooltip).

It is also possible to show or hide different elements on the map. Buttons control whether inter-pathway links are shown or if the pathways are highlighted dependant on categories.

Plot Your Dataset

Example CSV files:

Download test EC file Download test metabolite file

You can plot your own data by loading a CSV file. It must contain any header (first row), which will be shown in tooltips, and identifiers in the first column. This identifier must be either a metabolite or an EC number. Please make sure that fields in the csv file are separated by semicolon. After uploading your data set, you must choose the type of identifier and select a plot type. Currently, three types of plots are supported:

• Circle indicators: colored circles are drawn beneath each node. The color of the circle indicates the value. This plot type is recommended because it needs less space and supports visualization of large data sets. If an identifier occurs multiple time in your data, the circles are plotted in rows.
• Label boxes: the node itself is colored to visualize the data. This is just recommended for simple data sets, where you have just one data point for each identifier (just one data column). More datasets or multiple identifiers will be ignored.
• Bar Chart: a bar chart is drawn beneath the node. It supports only positive data points and just one plot for each identifier. Multiple identifiers will be ignored. If you want all your bars to have the same color, please choose the same color for Zero and Max.

When you check highlight pathway, a border is added to each pathway.

Download Map

In this section, you can download either the whole map, or parts of it by selecting a pathway. Be aware that you download elements, which are shown on the map, meaning that the zoom level has an impact on your downloaded content. Additionally, all modifications to the map, including your graphs and visualizations are also downloaded. If a legend is available, it will be appended.

The Map Section (middle)

Zoom

You can zoom by scrolling or via double click on a pathway background.

Tooltips and links

You can hover over certain elements to get more information, e.g. molecule structures & common names, data labels... All the built-in SVG tooltips (everything except the molecular structure) will also be available after download.

You get to the BRENDA enzyme or compound page by clicking on the respective nodes.

Selecting pathways

When you double click on a pathway, it is selected automatically.

You can ctrl+click other pathways to add them to your selection. Selected pathways can be downloaded in the Download map area.

The Info Section (right)

Legends

If pathway categories are shown or the plotting function is used, a legend is drawn in the right column. Clicking on the close button will remove the map and the highlighting / plots.

Enzyme names

All enzymes in the currently selected pathway are shown here. You can use a switch at the top to toggle between enzyme names and EC numbers. When you hover over an enzyme, it is highlighted in the map.