PT  - JOURNAL ARTICLE
AU  - Sofia Triantafillou
AU  - Vincenzo Lagani
AU  - Christina Heinze-Deml
AU  - Angelika Schmidt
AU  - Jesper Tegner
AU  - Ioannis Tsamardinos
TI  - Predicting Causal Relationships from Biological Data: Applying Automated Casual Discovery on Mass Cytometry Data of Human Immune Cells
AID  - 10.1101/122572
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 122572
4099  - http://biorxiv.org/content/early/2017/03/30/122572.short
4100  - http://biorxiv.org/content/early/2017/03/30/122572.full
AB  - Learning the causal relationships that define a molecular system allows us to predict how the system will respond to different interventions. Distinguishing causality from mere association typically requires randomized experiments. Methods for automated causal discovery from limited experiments exist, but have so far rarely been tested in systems biology applications. In this work, we apply state-of-the art causal discovery methods on a large collection of public mass cytometry data sets, measuring intra-cellular signaling proteins of the human immune system and their response to several perturbations. We show how different experimental conditions can be used to facilitate causal discovery, and apply two fundamental methods that produce context-specific causal predictions. Causal predictions were reproducible across independent data sets from two different studies, but often disagree with the KEGG pathway databases. Within this context, we discuss the caveats we need to overcome for automated causal discovery to become a part of the routine data analysis in systems biology.