Tutorial of Simple BL-SOM
Finding related genes

In this tutorial, we briefly describe how to use BL-SOM to search transcriptional expression and metabolite accumulation data for related genes and metabolites, respectively, according to Hirai et al. 2005 [PubMed] . In their paper, they analyzed gene expression and metabolite accumulation profiles in leaves and roots under sulfur-deficiency conditions using Affymetrix Genechips and FT/MS, respectively. In this tutorial, we show how to find genes and metabolites related to glucosinolate metabolism using only leaf data.

Preparation

Please confirm that you have met the following criteria before you begin this tutorial.

  • Have you read the paper ?  If it has been some time since you read the paper, we recommend reading it again to improve your understanding.
  • Have you installed the Java Runtime Environment ?  You must install this software before you can use the Simple BL-SOM software.
  • Have you downloaded and installed the Simple BL-SOM  software? If not, please download and install the software before continuing.

Procedure
  • Fig. 1
    1. Download the sample data file DATA_JBCdemo.txt.gz. This file includes the gene expression and metabolite accumulation profiles used in Hirai et al.'s paper. Details of the data processing are described in this paper.
    2. Expand the downloaded file to provide access to the data file named "DATA_JBCdemo.txt", which is formatted as tab-delimited text.
    3. Copy this file to the data folder used by Simple BL-SOM, "SimpleSOM\Data\".
    4. Start the Simple BL-SOM software ("SimpleSOM\simpleSOM.jar") by double-clicking the program's icon.
    5. When the software is running, select the data file in the program's main window (Fig. 1 - [1]).
    6. he software will display a number (Fig. 1 - [2]). that represents the lateral matrix size of the two-dimensional classification map; you can change this number, but cannot change the vertical matrix size. In Hirai et al.'s paper, this number of columns was set 40. We feel that choosing a display that shows all elements will improve the quality of your analysis. Enter a number that meets your needs.
    7. Click the "Let's start...!" button (Fig. 1 - [3]).
    8. The software begins the calculations, and the button name changes to "Wow...SOM start!" until the calculations are complete. The button name will change back to "Let's start...!" once the calculations are complete.
    9. To display the results of the calculations, click the "SOM Viewer" button (Fig. 1 - [4]).
  • Fig. 2
    10. The calculation results are displayed in a file name list (Fig. 2 - [1]). To choose a given results file (e.g., CLSOMDATA_JBCdemo.txt.txt(X=40Y=29).txt), click to select its name. The viewer window will open automatically.
  • Fig. 3
    11. When the viewer window opens, cells are colored to reflect the number of elements included in each cell. Cells that include a relatively small number of the elements are colored dark blue, whereas those that include a relatively large number of elements are colored intermediate blue, and those that include an unusually large number of elements are colored light blue.
    12. Click a button in surrounded by a border (Fig. 3 - [1]) to display the relevant experimental data. The dataset include 6 stress conditions based on duration:
    3 h
    6 h
    12 h
    24 h
    48 h
    168 h
  • Fig. 4
    13. For each data set, cells with a greater than average value are colored red or pink, and those with a lower than average value are colored blue or light blue (Fig. 4). The darker the color, the greater the difference between the value and the mean.
  • Fig. 5
    14. When you click in a cell, a new window opens (Fig. 5). The window displays a list of names and profile graphs for the genes and metabolites included in that cell.
    15. To find specific genes and metabolites , enter the element name and press the Enter key to highlight the cell that contains the specified gene.
    16. The elements included in the data are identified as locus IDs, metabolite names or exact masses.
  • Fig. 4
    17. Hirai et al. indicated that the rectangles in Figure 4 - [1], [2], [3], and [4] contained, respectively, glucosinolates, isothiocyanates, glucosinolate biosynthesis genes, and the genes for degrading enzyme myrosinase genes, respectively.

Procedure (Point-to-point comparison)
  • Fig. 3
    1. To compare two points, click the "Compare" button (Fig. 3 - [2]).
  • Fig. 6
    2. In the new window that opens, the buttons displayed at the bottom of the window let you define the conditions for the comparison (Fig. 6).
    3. Choose the conditions by clicking the two buttons surrounded by a border (Fig. 6 - [1]). Then click the "Compare" button (Fig. 6 - [2]) to color the cells to illustrate the difference between the two points.
 
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