Glossary

A

B

C

Confidence

A rating of the quality of the data. Values can be excellent (Excl), good (Good), medium (Med), low (Low), and not applicable (#N/A) because the gene was not scored. The following are explanations of the confidence ratings.

Excellent: the particular message level was called "present" in both wild-type and both mutant experiments.

Good: The message level changed in the same direction in the duplicate mutant to wild-type comparisons, and was called "present" in both wild-type or both mutant experiments.

Medium: the message level changed in the same direction, but did not fulfill the "Good" or "Low" criteria.

Low: the message level changed in the same direction, but the message level was called "absent" for both wild-type and mutant experiments.

Not applicable: none of these criteria could be met.

C-terminal truncation

The rap1-17 mutant is a C-terminal truncation which deletes the carboxy-terminal 165 amino acids of Rap1. This mutation has been shown to abolish the silencing of reporter genes placed in close proximity to a yeast telomere (9).

D

Deletion mutation:

A deletion is the complete removal of the gene of interest from the yeast genome. In preparing RNA, we grow the strain at 30°C until the culture reaches an OD of about 0.6, and then harvest the cells.

E

F

Fold Change:

The fold change of the gene. This number is an average of two experiments. Positive numbers indicate increases in gene expression, whereas negative numbers indicate decreases in gene expression. A value of #N/A means that the gene was not scored for this experiment. (more details)

Fold Down:

The fold decrease in gene expression when the mutant is compared to the wild type. The genes reported in the lists of "Genes 3 fold down or more" are only those which are down two fold in both experiments. e.g. If gene X is down 4.0 fold and 3.2 fold in each experiment, gene X will be reported to be down 3.6 fold; however, if gene Y is down 3.8 fold and 2.4 fold in each experiment, gene Y will not be represented in the list.

Fold Up:

The fold increase in gene expression when the mutant is compared to the wild type. The genes reported in the lists of "Genes 3 fold up or more" are only those which are up two fold in both experiments. e.g. If gene X is up 4.0 fold and 3.2 fold in each experiment, gene X will be reported to be up 3.6 fold; however, if gene Y is up 3.8 fold and 2.4 fold in each experiment, gene Y will not be represented in the list.

G

GAL shutdown:

For essential components of the apparatus such as histone H4, we used a strain where the sole source of histone H4 protein is produced from a histone H4 driven by the GAL promoter. In the presence of galactose, this strain produces histone H4 and is viable. In the presence of glucose, this promoter is repressed, and consequently no new histone H4 is produced.

Gene:

Gene whose expression level is affected by a mutation in a given chromatin factor.

Gene Family:

An 'X' in this column indicates that the particular gene is a member of a gene family, as determined by Affymetrix (these genes are indicated with an "_f" qualifier).

Genetic Background:

The genetic background of the strain. e.g. S288C, W303.

H

I

J

K

L

M

Mutant Type:

We use mutations in transcription factors to assess their contribution toward the expression of every gene in the S. cerevisiae genome. Two different types of mutations have been used. For nonessential components we have used mutants which are a deletion of the entire gene. For essential components, we have used GAL shutdown mutants.

N

O

P

Q

R

S

Scored:

How many genes were scored for this experiment. A maximum of 6219 genes can be scored. (more details)

Subunit:

The data set for the listed transcription factor from which the search gene was found.

T

U

V

W

X

Y

YPD Title Line™:

A short description of a protein.
The descriptions are YPD Title Lines™ from the YPD Database. © Proteome, Inc. 2000, used with permission.

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Z