| 1. | What is SpinalCordLink? |
| We generated a world largest microarray dataset under a contract from NIH NINDS to query spinal cord injury. This dataset has multiple dimensions: animal model (mouse or rat), location relative to injury site (at, above and below), severity of injury (control, mild, moderate and severe), time after injury (7-10 time points). Applying information visualization technologies such as parallel coordinates and animations, we designed and developed an interactive web interface (SpinalCordLink) to this large dataset for researchers who are tackling spinal cord injuries. There are also considerations of the analysis methods, and the entire data set was converted into three probe set algorithms (Plier, GC-RMA, and dChip), leading to nearly 10,000 microarray data files. SpinalCordLink can provide researchers with a good resource to investigate interactively one of the world largest microarray datasets.
SpinalCordLink showing a relevant genetic pathway at the injury site (T9), 7 days after a severe spinal cord injury at a vertebral level T9. A gene "ywhah" is very active across all time points at the sham samples.
There are four visualization components in SpinalCordLink:
- grid display (A)
- parallel coordinates view (B)
- pathway view (C)
- gene list view (D)
The horizontal axis of the grid display (A) is for severity of spinal cord injuries induced (sham, mild, moderate, and severe). The vertical axis is for the sampling location relative to the injury site (T8:above, T9:at, and T10:below). Below the grid display is the parallel coordinates view (B) for time after injury. The current pathway is shown in the bottom left corner (C) and the gene names in the pathway are shown in the gene list view (D) at the bottom right. Brown horizontal and vertical lines indicate the condition where the current pathway is selected. The blue rectangle and the blue vertical line represent the conditions for the current gene expression patterns of the same selected pathway shown in the display.
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| 2. | How to run it |
| SpinalCordLink is a Java application built on Piccolo toolkit.
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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| 3. | Data Preprocessing |
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- Run three signal algorithms: Plier, GC-RMA, and dChip
- For each time point, compare it to "time 0" and " previous time point"
- For each comparison, generate a list of probe sets by running t-Test (p<0.01)
- For each probe set list, run through pathways at WikiPathways.org to choose top 10 ranked pathways (Fisher's Exact Test)
- Visualize user-selected pathways in SpinalCordLink
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| 4. | Fetch Data From Databases |
| The first thing you have to do is to fetch a pathway data from our databases. Click on the button that says "Fetch Data" at the top left corner of SpinalCordLink.
Please note that the data fetching can take about 10 - 15 seconds in a typical LAN environment.
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| 5. | Interaction |
| The condition under which the current pathway is selected as significant is highlighted with a horizontal and vertical brown lines (A). The condition under which users are looking at the genes in the selected pathway is highlighted with a blue rectangle and a vertical blue line (B).
As indicated by brown lines in the figure (A), users are looking at the expression patterns of the genes in a pathway that is significant at T8 (above injury site) at 28 days after severe injury. They can investigate the gene expression pattern of the selected genes at any condition. For example, as indicated by a blue line and a blue rectangle (B), users can look into the patterns of the same selected genes at T8 (above) at 4 hours after no injury (sham). Users can change it by clicking on any block of the grid display. The blue vertical line on the parallel coordinates view indicates (B) the current time point selected by users. Users can change it by clicking either on a time axis or on a time label at the parallel coordinates view. Any change of the current selected condition in one display triggers an instantaneous corresponding change in other display. When users click on a different block or on a different time axis, the blue selection marks moves to the selected block with a smooth animation.
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