Tutorial of Simple BL-SOM
Finding related genes

In this tutorial, we briefly illustrate how to search for related genes based on transcriptional expression data (Hirai et al. 2004[PubMed] ) using BL-SOM. Hirai et al. analyzed gene expression and metabolite accumulation profiles of leaves and roots under sulfur- and nitrogen-deficiency conditions using cDNA macroarrays and FT/MS, respectively. In this tutorial, we show how to find genes related to glucosinolate metabolism using only the gene-expression profile.

Preparation

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

  • Have you read the paper ?  If you have not read the paper recently, we recommend that you read it again to improve your understanding.
  • Have you installed the Java Runtime Environment ?  You must install this software on your computer before you can use the Simple BL-SOM software.
  • Have you downloaded 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_PNASdemo.txt.gz). This file includes the gene expression profile 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_PNASdemo.txt", which is formatted as tab-delimited text.
    3. Copy this file to the 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 program is running, select the data file in the program's main window (Fig. 1 - [1]).
    6. The 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 you cannot modify the vertical matrix size. In Hirai et al.'s paper, this number was set to 50. We feel that choosing a display that shows all elements will improve the quality of your analysis. However, you can enter any number that works well for you.
    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...!" when 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_PNASdemo.txt.txt(X=50Y=31).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 surrounded by a border (Fig. 3 - [1]) to display the relevant experimental data. The dataset includes 14 experimental conditions:
    hydoroponic / control, 3weeks / leaf
    hydoroponic / -S, 3weeks / leaf
    hydoroponic / -N, 3weeks / leaf
    hydoroponic / -SN, 3weeks / leaf
    hydoroponic / control, 3weeks / root
    hydoroponic / -S, 3weeks / root
    hydoroponic / -N, 3weeks / root
    hydoroponic / -SN, 3weeks / root
    plate / control, 3weeks -> control, 48h / leaf
    plate / control, 3weeks -> -S, 48h / leaf
    plate / control, 3weeks -> +OAS, 48h / leaf
    plate / control, 3weeks -> control, 48h / root
    plate / control, 3weeks -> -S, 48h / root
    plate / control, 3weeks -> +OAS, 48h / root
    where -S means sulfur-deficient, -N means nitrogen deficient, -SN means deficient in both sulfur and nitrogen, and +OAS means O-acetyl-L-serine.
  • 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 an expression profile graph for the genes included in the cell.
    15. To find specific genes in the data, enter the probe ID and press the Enter key to highlight the cell that contains the specified gene.
    16. The probe ID identifies the cDNA on the macroarray. You can convert between probe ID and gene name using the data in the file named probe_desc.txt.tar.gz.
  • Fig. 4
    17. Hirai et al. indicated that the rectangles in Figure 4 - [1], [2], and [3] contained the genes and metabolites involved in photosynthesis, the pentose-phosphate pathway, and glucosinolate metabolism, respectively.

    Glucosinolate biosynthesis in Fig.4 - [3]

    Locus ID Probe ID Description
    At1g24100 07011A, 13009E Encodes a UDP-glucose:thiohydroximate S-glucosyltransferase, involved in glucosinolate biosynthesis.
    At1g16400 06604F Encodes cytochrome P450 CYP79F2.
    At5g23010 05811F, 07501H Encodes a methylthioalkylmalate synthase, catalyzes the condensation reactions of the first two rounds of methionine chain elongation in the biosynthesis of methionine-derived glucosinolates.

Procedure (Point-to-point comparison)
  • Fig. 3
    1. Click a button with "Compare" at Fig.3 - [2] to compare between the two points.
  • Fig. 6
    2. New window is started up and buttons are displayed in lower of the window (Fig.6).
    3. Choose condition points by clicking two buttons in surrounded by border at Fig.6 - [1] that your sees fit. And click a button with "Compare" at Fig.6 - [2] then lattices are colored respectively with difference between the two points.
  • Fig. 3
    4. To compare two points, click the "Compare" button (Fig. 3 - [2]).
  • Fig. 6
    5. 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).
    6. 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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