SPIKE – a database, visualization and analysis tool of cellular signaling pathways

Ran Elkon¹ , Rita Vesterman¹ , Nira Amit¹ , Igor Ulitsky² , Idan Zohar² , Mali Weisz¹ , Gilad Mass¹ , Nir Orlev¹ , Giora Sternberg¹ , Ran Blekhman¹^,3 , Jackie Assa² , Yosef Shiloh¹ and Ron Shamir²

¹The David and Inez Myers Laboratory for Genetic Research, Department of Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel

²School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel

³Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA

author email corresponding author email

BMC Bioinformatics 2008, 9:110doi:10.1186/1471-2105-9-110


Published:	20 February 2008

Abstract

Background

Biological signaling pathways that govern cellular physiology form an intricate web of tightly regulated interlocking processes. Data on these regulatory networks are accumulating at an unprecedented pace. The assimilation, visualization and interpretation of these data have become a major challenge in biological research, and once met, will greatly boost our ability to understand cell functioning on a systems level.

Results

To cope with this challenge, we are developing the SPIKE knowledge-base of signaling pathways. SPIKE contains three main software components: 1) A database (DB) of biological signaling pathways. Carefully curated information from the literature and data from large public sources constitute distinct tiers of the DB. 2) A visualization package that allows interactive graphic representations of regulatory interactions stored in the DB and superposition of functional genomic and proteomic data on the maps. 3) An algorithmic inference engine that analyzes the networks for novel functional interplays between network components.

SPIKE is designed and implemented as a community tool and therefore provides a user-friendly interface that allows registered users to upload data to SPIKE DB. Our vision is that the DB will be populated by a distributed and highly collaborative effort undertaken by multiple groups in the research community, where each group contributes data in its field of expertise.

Conclusion

The integrated capabilities of SPIKE make it a powerful platform for the analysis of signaling networks and the integration of knowledge on such networks with omics data.