Supplementary material for Zirlinger et al. (2001) Proc. Natl. Acad. Sci. USA98 (9), 5270–5275. (10.1073/pnas.091094698)

Appendix B

EXAMPLE

Let's suppose we have four samples and six genes to compare with the following D values:

 

Sample 1

Sample 2

Sample 3

Sample 4

Gene 1

1000

1000

34

5

Gene 2

100

350

3

-8

Gene 3

-5

-100

-20

-50

Gene 4

150

350

-40

5

Gene 5

3

98

5

20

Gene 6

5

100

700

145

 The data matrix should thus be in this form:

1000

1000

34

5

100

350

3

-8

-5

-100

-20

-50

150

350

-40

5

3

98

5

20

5

100

700

145

Assume the program is run with the following settings:

THRESHOLD = 3

MINIMUM = 100

REF. SAMPLE = 2

OUTPUT FILE = test

The output file test.txt is created in C:/temp directory and contains the following (blue is the output file, explanations are in red):

Indices of enriched genes in reference sample compared to all other samples

1          2           This means gene # 2 is enriched

Indices of genes enriched with respect to all other samples but one

1          1          This means genes # 1 and # 4 are enriched with respect to all

2          4          but one sample

average difference values of enriched genes

            1          2          3          4

1          100      350      3          -8         These are the corresponding D values for gene # 2

average difference values of genes enriched with respect to all but one samples

            1          2          3          4         

1          1000    1000    34        5          These are the corresponding D values for genes # 1

2          150      350      -40       5          and # 4

Mean average difference value in each sample

                        1          2          3          4

                        208.83 299.67 113.67 19.50   These are the arythmetic means of D values

gene screen output

test       This is the name we gave to the output file

date and time

number of samples analyzed:     4

number of genes analyzed:         6

threshold ratio:  3.00

minimum:          100.00

reference sample:          2

percent enriched genes compared to all other samples:   16.67   (this is 1/6)

percent enriched genes compared to all but one samples:           33.33    (2/6)

To download this example dataset, go to http://www.its.caltech.edu/~mariela/example_data.txt. We recommend that you run the program with this dataset with different settings so that you get familiar with it first, before running it with your real data. (For example, try setting a lower ratio or a different reference sample.)