Glossary

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A

B

C

Catalytically inactive mutation:

A catalytically inactive mutation is a point mutation in a gene whose protein product has a known enzymatic activity. The point mutation inactivates the enzyme, but does not effect its stability. 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.

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 data did not have to be corrected in any way, but not all were "present".
Medium: the message level changed two fold in both wild type to mutant comparisons, but did not fulfill the "Good" criteria.
Low: the message level changed in the same direction, but did not fulfill the "Medium" criteria.
Not applicable: none of these criteria could be met.

Copies/Cell

The numbers of copies of a given mRNA per yeast cell.

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 2 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 3.0 fold and 1.8 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 2 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 3.0 fold and 1.8 fold in each experiment, gene Y will not be represented in the list.

G

Gene:

Gene whose expression level is affected by a mutation in a given transcription factor, or whose copies/cell, half-life, and transcriptional frequency is being reported.

Genetic Background:

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

H

Half-life:

The calculated half-life of each mRNA. This calculation was performed using the rpb1-1 mutant, which is responsible for all class II transcription.

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 either catalytically inactive or are a deletion of the entire gene. For essential components, we have used temperature sensitive mutants.

N

O

P

Q

R

S

Scored:

How many genes were scored for this experiment. A maximum of 6217 genes can be scored. (more details)

Subunit:

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

T

Temperature sensitive mutation:

A temperature sensitive mutation is a point mutation in the gene of interest which has a minimal effect at the permissive temperature, but renders its protein product nonfunctional at the restrictive temperature. In preparing RNA, we grow a culture to an OD of about 0.6 at the permissive temperature (either 30°C or 24°C), shift the culture to the restrictive temperature (either 37°C or 38°C) for 45 minutes, and then harvest the cells. (their primary/secondary effects)

Transcriptional Frequency:

The number of polyadenylated (i.e. full length) transcripts for a given gene which are produced per minute.

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.

This material contains proprietary and copyrighted text of Proteome, Inc. (http://www.proteome.com) which is reprinted by the Young Lab with Proteome's permission. Provided that Proteome's copyright notice is not removed and the text is not modified in any manner, Protoeme's proprietary and copyrighted text may be used for a user's non-commercial research purposes only. Any other use, including any commercial use, reproduction, transmission, distribution, republication, or retransmission, or creation of derivative works without the express written consent of Proteome is prohibited. Information on licenses for commercial purposes or for distribution, republication, or retransmission of the text is available from Proteome (email: info@proteome.com)

Z

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