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


CONCLUSIONS
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.
Elkon
Ran
R
The 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. ranel@post.tau.ac.il
Vesterman
Rita
R
Amit
Nira
N
Ulitsky
Igor
I
Zohar
Idan
I
Weisz
Mali
M
Mass
Gilad
G
Orlev
Nir
N
Sternberg
Giora
G
Blekhman
Ran
R
Assa
Jackie
J
Shiloh
Yosef
Y
Shamir
Ron
R
D002468:Cell Physiological Phenomena; D003628:Database Management Systems / Q000639:trends; D030541:Databases, Genetic / Q000639:trends; D053858:Metabolic Networks and Pathways / Q000502:physiology; D015398:Signal Transduction / Q000502:physiology*; D012984:Software / Q000639:trends