SPEED: (S)ignaling (P)athway (E)nrichment using (E)xperimental (D)atasets

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SPEED is a signaling pathway annotation enrichment analysis tool with annotations based on evidences from pathway perturbation experiments. Thus, genes are annotated based on causal influences of pathway perturbations as opposed to pathway memberships alone. Identifying modulated pathways upstream of differentially expressed genes can facilitate the understanding of involved regulatory mechanisms. Currently only human genes and pathways are supported.


The project is part of PhD student summer research conducted by Jignesh Parikh from the Boston University Bioinformatics Program and Bertram Klinger from the Group of Systems Biology of Molecular Networks.

The SPEED project is hosted by the Group of Systems Biology of Molecular Network at the Laboratory of Molecular Tumor Pathology (Charite) and the Institute of Theoretical Biology (HU Berlin).

Please contact Nils Blüthgen at nils.bluethgen@charite.de for more information.