DTU Health Tech

Department of Health Technology

This site contains supplementary information and data sets from the paper

Dynamic Complex Formation During the Yeast Cell Cycle
Ulrik de Lichtenberg, Lars Juhl Jensen, Søren Brunak and Peer Bork
Science, 307 (5710), 724-727, 2005 [PubMed]

Interactive version of the cell cycle network

Interactive version of the cell cycle network. You can use the slider on the right to zoom in/out to explore on you own. Hovering the mouse over a node gives you the name of that protein (names adopted from SGD). You can move the nodes around yourself using the left mouse button. If it doesn't work, see below for a few tips that may help. Alternatively, you can inspect the PDF version of the network (see below). The interactive network is based on a special version of the NetView program by Sean Hooper.

3D virtual reality version of the cell cycle network

This 3D virtual reality version allows you to rotate the network and to zoom in/out to explore on you own. Clicking on the nodes with the left mouse button takes you to the corresponding protein page in SGD. To view this you need to have a VRML plugin installed. We recommend using Cortona.

PDF version of the cell cycle network

PDF version of the interaction network (Figure 1), complete with all protein names. Use your acrobat reader (or other viewer) to zoom in/out and move around to inspect the details of the network. An interactive Java version is also available (see above).

Interaction data set

This file contains all the binary interactions in the cell cycle network, each accompanied by a confidence score (a number between 0 and 1). A high number signifies high confidence in that particular interaction and the score combined evidence from multiple interaction data sets. The scoring scheme is explained in detail in the paper and is similar to that used in the STRING server. Names are reported as systematic yeast ORF names according to the annotation in SGD.

Re-annotated MIPS complexes

This file defines complex membership in the MIPS data set after our re-annotation of specific complexes, as described in the paper. First column gives the MIPS complex id and the second column contains the name of a protein belonging to that complex. Names are reported as systematic yeast ORF names according to the annotation in SGD.

Dynamic proteins

This file contains the systematic ORF names (according to SGD) of the 600 periodically expressed genes that encode the "dynamic proteins" (colored nodes) inside and outside the network. The number in the second column is the "peak time" describing where in the cell cycle that particular gene is maximally expressed. The numbers are given as percent of the cycle completed, with zero being the time of cell division. The identification and analysis of these 600 genes is described in the paper "Comparison of computational methods for the identification of cell cycle regulated genes".

If the interactive version of the network doesn't work:

  • your browser may not have the Java plug-in needed. If this is the case, the browser should automatically ask you if you want to download it. Do so, and try again. If that doesn't work, a suitable version of Java (choose J2SE version 1.4.2 or newer) can be downloaded for Windows, Linux and Solaris [here].

  • if you run windows XP and have installed service pack 2, internet explorer may block the applet with a message in the top of the window saying something like "to help protects your security, Internet Explorer has restricted this file from showing active content that could access your computer. Click here for options...". Move the mouse to this message and click on it. A small menu will appear in which you select "Allow blocked content".
  • Correspondance: Ulrik Nicolai de Lichtenberg