SPIKE

Category Cross-Omics>Pathway Analysis/Tools

Abstract 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.

The goals of SPIKE are to help researchers integrate, visualize and interpret information related to biological networks, and to provide the research community with up-to-date, comprehensive, curated data on signal transduction pathways. SPIKE is also designed to enhance functional analysis of data generated by high-throughput functional genomics technologies.

Products features/capabilities include:

1) The SPIKE Data Model --

SPIKE's data model is general and can accommodate data on any signaling pathway from any organism. At present, the implemented database (DB) supports regulatory data obtained in human and contains extensive and highly curated data on signaling pathways induced by 'DNA damage', such as cell cycle checkpoints, apoptosis and other stress responses.

SPIKE's data model includes four (4) types of nodes:

and 2 types of edges -

Regulations (regulatory interactions) are divided into three (3) types:

In the SPIKE data model, regulations can also regulate other regulations. Associations are the links between a complex or a family and its members. Red and green dots within a node indicate that it has additional regulations and associations (respectively).

2) Superposition of Gene Expression Data on Signaling Networks --

SPIKE enables the user to superimpose functional genomics and proteomics data on the signaling maps, enhancing the interpretation of such data. SPIKE supports both absolute (e.g., Affymetrix chips) and relative (e.g., cDNA microarrays) gene expression data.

SPIKE also allows superimposition of clustering data: any partition of the genes into groups (e.g., according to Gene Ontology annotation, cellular compartment, clustering algorithms, or user-specific definitions) can be viewed on the pathway map.

3) Additional Viewing Features --

Further data about the entities in the pathway map can be viewed in a separate Properties Display dialog. SPIKE also provides links to external databases, such as EntrezGene for proteins, and PubMed for supporting references. To reduce clutter, users can hide nodes that they do Not want to view in the pathway (these nodes can later be restored if needed). The Bird's Eye View shows the "big picture", which is particularly useful for large pathways.

4) Data Filtering --

SPIKE DB includes data at diverse quality levels - from carefully curated data, through data supported by published articles to mass importation of data from public databases (such as Reactome and KEGG). Data items in SPIKE are assigned confidence levels, so that the software enables configuration of the quality of the data shown: users can set the minimum confidence level and see a map containing data from all sources, choose to see only curated data or data supported by a publication, include or exclude certain data sources, etc.

5) Data Submission --

The SPIKE client software includes an easy-to-use graphical interface for submission of new data to SPIKE DB or editing of existing data. Experimental or unpublished data can be labeled private, in which case it will only be accessible to the lab that submitted it. Published regulations must be accompanied by at least one supporting reference.

6) The SPIKE Community --

SPIKE DB is accessible to registered labs everywhere. Users can create pathway maps on their protein of interest and contribute new data to the database. In the current phase, a local database is installed at each research center and is synchronized periodically with the central DB.

In the next phase (SPIKE 2.0), a central database will serve all users through web-based software. Our vision is that SPIKE's DB will be populated by a distributed and highly collaborative effort taken by multiple groups of the DNA damage and cancer research community, where the quality of information submitted to the DB will be supervised by SPIKE's curators.

Expanding the collaborative effort will provide the research community with an integrated, comprehensive and constantly up-to-date Knowledge Base (KB) of the ever-growing DNA damage response (DDR) networks.

7) Conclusions --

a) SPIKE provides the community of DNA damage and cancer researchers with a comprehensive and curated knowledge base, which enables them to construct regulatory pathways dynamically and gain new insights with the aid of novel data submitted by the community.

b) SPIKE enables researchers to superimpose results of high- throughput experiments on pathway maps, thus enhancing the understanding of mechanisms underlying complex regulatory networks.

c) Population of SPIKE DB through submission of new data and mass importation of public data enables researchers interested in diverse regulatory networks to discover new links and instances of network cross-talk.

System Requirements

Java 1.5+, 100MB of free Disk Space, 523MB of Memory.

Manufacturer

SPIKE is developed jointly at the laboratories of Prof. Ron Shamir (School of Computer Sciences) and Prof. Yossi Shiloh (School of Medicine) in Tel Aviv University.

Manufacturer Web Site SPIKE

Price This software is provided free of charge to the research community as an academic software package with no commitment in terms of support or maintenance. More details appear in the license agreement.

Users interested in commercial applications should contact Prof. Ron Shamir (email rshamir AT post.tau.ac.il) or Prof. Yossi Shiloh (email yossih@post.tau.ac.il).

* Commercial users are also required to obtain a KEGG end-user license agreement from Pathway Solutions Inc. Please contact licensing@pathway.jp for information. Users of this product/service may not download large quantities of KEGG Data.

G6G Abstract Number 20127

G6G Manufacturer Number 102585