SpinalCordLink

SpinalCordLink
Information Visualization for Spinal Cord Injury Microarray Experiments in Mouse and Rat

Project description

Traumatic spinal cord injury (SCI) is characterized by a primary mechanical insult, followed by widespread, coordinated changes in gene expression. These may be associated with pathogenic auto-destructive events such as hemorrhage, metabolic failure, inflammatory/immune activation, loss of ionic homeostasis, lipid degradation, production of free radicals, and neurotransmitter and growth factor imbalances. These changes may contribute to neuronal and oligodendroglial cell death, astrocyte proliferation (scarring) and demyelination. Alternatively, reactive expression changes that are neuroprotective and/or promote recovery (regeneration/plasticity) may also be induced. In addition, not all mechanisms following SCI are well known.

The NINDS recently supported the creation of a large database of quality-controlled Affymetrix profiles of spinal cord tissue taken from 1 hour to 6 months after mild, moderate or severe thoracic SCI (T9) in the rat. Spinal cord samples were also profiled from 30 minutes to 28 days after moderate thoracic injury (T9) in the mouse. Sampled regions included areas above (rostral), at (epicenter) and below (caudal) the site of impact. The goal of this project is provide a large scale analysis of expression events after SCI.

To promote the utility of the project, we developed an information visualization tool, named "SpinalCordLink." SpinalCordLink also integrates "biological pathways" from WikiPathways.org. We used a new data processing framework to integrate relevant pathway information into the analysis process.

Support

This work was supported by NIH NINDS-01 (NS-1-2339) and by NIH NCMRR/NINDS 5R24 HD 050846 (Integrated Molecular Core for Rehabilitation Medicine).

SpinalCordLink Participants

Jinwook Seo, Children's Research Institute, Children's National Medical Center

Eric Hoffman, Children's Research Institute, Children's National Medical Center

Josephine Chen, Children's Research Institute, Children's National Medical Center

Susan Knoblach, Children's Research Institute, Children's National Medical Center

Availability

SpinalCordLink is a Java application built on Piccolo toolkit.

SpinalCordLink User Manual

Launch using Java Web Start

Launch as a Java Applet

Download SpinalCordLink to your computer and run it: [zip], [tar.gz]

NOTE: If you do not have Java installed on your computer, you have to install Java (Java SE Runtime Environment 6 or higher) first to launch SpinalCordLink. If you are prompted to install a new Java after clicking on one of the links above, you have to install it first. To properly run SpinalCordLink, Sun's Java Virtual machine is necessary. You can down load it from the Java SE Downloads page.

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