Supplementary Material

Automatically inferring causal networks linking growth factor stimuli to functional cell state changes

Carito Guziolowski¹², Aristotelis Kittas ¹², Florian Dittmann¹² and Niels Grabe¹²

¹ Medical Informatics Department, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, Im Neuenheimer Feld 305 and ² Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, University Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany

Supplementary Figures

• Supplementary Figures S1 and S2 and Table 1

Cytoscape files (v2.8.1)

Network of early events

• Cytoscape session file (EarlyEvents.cys)
• SIF file (EarlyEventsNet.sif)
• Node attributes (nodeAt.zip)
• Edge attributes (edgeAt.zip)
• Vizmap property file (netView.props)

Union network of all time points

• Cytoscape session file (allTimePoints.cys)
• SIF file (allTimePoints.sif)
• Node attributes (nodeAt.zip)
• Edge attributes (edgeAt.zip)
• Vizmap property file (netView.props)

Visualization file: Upload the Vizmap property file into Cytoscape in order to obtain the same visualization effects as in the figures of the article.

PIDXMLtoCytoscape converter (Java)

• Java executable file (PidFileConverter.jar)
• Jar file with sources. (PidFileConverter_src.jar)
• Usage instructions

Please Note: For troubleshooting regarding the usage of the PID converter java program please contact: carito.guziolowski at bioquant.uni-heidelberg.de

UML Package Diagram

• Package Description

Example PID XML File

IL-6 pathway downloaded from the PID database on 16.09.2011 (il6.xml). Many other xml files examples can be found in the PID database website.