1. What is SPIKE
  2. Browsing and Downloading
  3. Standard Version vs. Stand Alone Version

1. What is SPIKE

SPIKE (Signaling Pathway Integrated Knowledge Engine) is an interactive software environment that graphically displays biological signaling networks, allows dynamic layout and navigation through these networks, and enables the superposition of DNA microarray and other functional genomics data on interaction maps.

SPIKE is composed of two main software components:

  1. A DB of signaling pathways.

    SPIKE stores a central DB containing carefully ascertained information uploaded by SPIKE users and supervised by the curators, data from external signaling DBs (e.g., KEGG, Reactome, IntAct), and wide-scale human protein-protein interaction datasets.

    Each research lab that installs SPIKE (a.k.a. site) uses its own, local, database. During SPIKE's installation each site's database is populated with data from the central DB. Each site's database is periodically updated by the central DB. At any time, a site may choose to share parts of its data with the rest of the SPIKE community by uploading its private database to the central database.

  2. A Java-based visualization package that allows interactive graphic representations of regulatory interactions stored in the DB.

    The different types of biological entities are represented in SPIKE maps by nodes of different colors: violet nodes correspond to protein-coding genes, turquoise nodes to non protein-coding genes (e.g., micro-RNAs, rRNAs, tRNAs), green nodes to protein complexes, and yellow nodes to protein families. Small molecules are displayed in orange (not included in this map). Blue directed edges represent regulations: arrows correspond to activation, T shape edges to inhibition, and open circles denote regulations whose effect is still not clear (e.g., ATM was reported to phosphorylate MCM2, but the effect of this modification is not known yet). Blue undirected edges represent protein-protein interactions (not included in this map). Green edges represent containment relations between nodes (e.g., a complex and its components). Red and green dots within a node indicate that not all regulation and containment relations stored in the DB for the node are displayed in the map. This map represents the ATM-regulated network which is set off by the cell in response to double-strand breaks in the DNA.

    Other features of the visualization software include:



2. Browsing and Downloading

SPIKE website offers basic searching utilities over SPIKE DB. Users can search the DB for each of the basic building blocks of SPIKE data model (namely, the five types of biological entities and three types of relationships). For each entity, pertinent information is displayed and a list of the maps that contain the inquired entity is shown.

The SPIKE database is freely available for download in several formats. The full database as well as individual maps can be downloaded. Download in the XML format allows use of the data in the SPIKE software with full functionality. Download in other formats (BioPax and SIF) allows import of the maps or the full database into other software tools. As different tools may use different data models, some information may be lost in the transfer. For example, the SIF format allows one to load simplified maps into the Cytoscape tool.

3. Standard Version vs. Stand Alone Version

SPIKE was designed as a tool for a research lab: All lab members use a single installation which insures sharing of data. To simplify the installation SPIKE also has a stand alone version which is designed for a single user. However, this is a limited version that does not allow sharing of data with other lab members and does not support sharing of data added by the user with the rest of the SPIKE community.

Contact

Questions? Please e-mail us at spike@post.tau.ac.il.