Table of contents

  1. General Notes
  2. Working with tables
  3. Working with charts
  4. Changing brightness/contrast in ImageJ

General notes

Important Note: since this component is currently in development things may have changed since this tutorial was last updated. Furthermore, internal MPI-CBG users may have some additional options available.

Start Page

You will see an abstract of the paper on the start page. Above it, there is a big search box which can be made even bigger by dragging it by the thick lower border.

This seach box has some useful features:

Working with tables

Typical Grid

Sorting, Filtering and changing column order

All tables used on this site have the same basic functionality:

Control bar buttons

There is a control bar at the top and at the bottom of each table.
The following buttons can eb found at the control button area at the left side:

The pagination area in the middle of the control bar allows you to select the page size in the drop down menu and navigate between pages either by typing a number or using the arrows.
Finally, there is a 'minimize table' button at the very left and some numbers, indicating which rows you are currently viewing and how many rows there are in this table, below it.

Links in data columns

Links to Profiles and to external data sources in the table.

Each row contains several links for the gene. The Profiles column links will lead you to either the profile of the specific gene or to all siRNA profiles of this gene. The links in the External links column will lead you to different websites with further information on that gene.
Additionally, there is a small preview of the gene profile in the column in between.

Compare Genes

Links to gene profiles below the table.


You can also resize the table by dragging either the lower right corner or the lower or right sides of the table.

Working with charts

Sample Gene Profiles

When viewing profiles you will see the graph above and a table with the respective data below. The legend on the right side tells you what the background colors mean and which graph is plotted in which color.
The plotted graphs can't be manipulated. You can see the name of the parameter and the specific value if you mouse over the graph.
Select a subset of genes to plot and export .csv
To view only a subset of the graphs simply select them in the table and click "plot selected profiles".


Additionally there is the option to export the data as a .csv file (comma-separated, can be opened by most office programs like Microsoft Excel or LibreOffice Calc) for further use.

Viewing Images

As Java 1.7 have stronger security policy, to run ImageJA inside your browser, you have to change security level to Medium (Details)

When you open the siRNA or siRNA profiles of a specific gene, you will see some representative Images at the bottom of the page.
You can either click on the Thumbnail to view a larger version of the image as .jpg or view the image as a .tif directly in your browser using ImageJ, which is an Java Applet (and therefore requires Java to be installed).

The .tif files have a higher quality and they are split by colour channel. This gives you much more insight since you have far more control options.

If you use the ImageJ Applet there is one specific functionality which will be of great help:
Go to: Image -> Adjust -> Color Balance... . This will open an popup window which looks like this:

Color adjustment dialog of ImageJ

You can select the color channel (red, blue or green) in the dropdown menu below. If you select any of the other options like cyan, they will affect multiple color channels.
Once you have selected your color channel you can move the 3 sliders and look at the effect. Above the sliders you will see a representation of the slider positions in a mathematical way.
At this point it is helpful to play around with the sliders a bit and see what they do. If you mess up, use the reset button. Alternatively, use the Auto Button to let the program decide how to improve the settings, but note that if use the auto function to often on one channel the picture will get worse again.
The 'Set' button will allow you to fiddle around with some parameters of the sliders and the 'Apply' button will apply the settings to the picture so that you can edit a different color channel.

If you want to learn more about ImageJ, visit their documentation pages at: