Exploring the Data Set :: Microarray Analysis (Bioinformatics Toolbox)

Bioinformatics Toolbox

Exploring the Data Set

The data for this procedure is available in the MAT-file yeastdata.mat. This file contains the VALUE data or LOG_RAT2N_MEAN, or log2 of ratio of CH2DN_MEAN and CH1DN_MEAN from the seven time steps in the experiment, the names of the genes, and an array of the times at which the expression levels were measured.

Load data into MATLAB.
```
load yeastdata.mat
```
Get the size of the data by typing
```
numel(genes)
```
MATLAB displays the number of genes in the data set. The MATLAB variable genes is a cell array of the gene names.
```
ans =
        6400
```
Access the entries using MATLAB cell array indexing.
```
genes{15}
```
MATLAB displays the 15th row of the variable yeastvalues, which contains expression levels for the open reading frame (ORF) YAL054C.
```
ans =
  YAL054C
```

Use the function web to access information about this ORF in the Saccharomyces Genome Database (SGD).

url = sprintf(...
        'http://genome-www4.stanford.edu/cgi-bin/SGD/
         locus.pl?locus=%s',...
        genes{15});
web(url);

A simple plot can be used to show the expression profile for this ORF.
```
plot(times, yeastvalues(15,:))
xlabel('Time (Hours)');
ylabel('Log2 Relative Expression Level');
```
MATLAB plots the figure. The values are log2 ratios.
Plot the actual values.
```
plot(times, 2.^yeastvalues(15,:))
xlabel('Time (Hours)');
ylabel('Relative Expression Level');
```
MATLAB plots the figure. The gene associated with this ORF, ACS1, appears to be strongly up-regulated during the diauxic shift.

Compare other genes by plotting multiple lines on the same figure.

hold on
plot(times, 2.^yeastvalues(16:26,:)')
xlabel('Time (Hours)');
ylabel('Relative Expression Level');
title('Profile Expression Levels');

MATLAB plots the image.

Overview of the Yeast Example

Filtering Genes