Experimental Data


Key Files
Here is the key for the cel files.
Note: Some strains were remade during the course of the study. Remade strains are listed with chr0X rather than chrX in the key.

This file is used to determine the background intensity distribution.
It was drawn from the files {11_27_03.cel, 11_27_05.cel, 09_21_04.cel} using this key for background tags.
Intensities <3000 are kept for the distribution.

File Descriptions
The cutoff for significance in standard time=3(15 gen) conditions is 100.
The cutoff for significance in standard time=2(5 gen) conditions is 20.

Fitness scores are calculated by comparing the tag intensities for a strain measured under a perturbation condition to the intensity distributions for each of those tags estimated from replicates of a standard condition. The scores are a measure of the likelihood of observing the experimental condition measurements by given the estimated standard distribution. Thus, a fitness defect score of 100 under a given condition implies that the tag intensities would not likely be seen in many replicates of the control experiments. However, the score does not reveal whether the tags are more or less intense than expected in the standard. This is directly determined by comparison of the measured intensities to the estimated mean of the tag intensities from the standard replicates. Those strains whose tag intensities fall lower than the mean (implying they were dropping out of the population) are classified as sensitive to treatment and those strains whose tag intensities fall higher than the mean are classified as refractory to treatment. Though it seems relatively straitforward to understand the meaning of a significant sensitive score (the strain grows slower in the perturbed condition than in the standard), the significant refractory strains are often harder to explain. Experimentally, many of the strains that turn up as significantly refractory are slow growers. These strains have tag intensity distributions that are not much above background and are therefore unreliable. Although true resistant strains exist in these lists, they are likely to be only a small percentage of the total number of refractory strains.

Experimental Conditions
Experiment Standard Time Condition Concentration Raw Chip Exp File Sensitives Refractory
3 (2) 5 Gen ypg 5 generations B na [cel] [exp] [sen] [ref]
5 (2) 5 Gen ypg 5 generations A na [cel] [exp] [sen] [ref]
8 (2) 5 Gen 1.5M Sorbitol 5 generations A 1.5M [cel] [exp] [sen] [ref]
9 (2) 5 Gen minimal + his/leu/ura 5 generations B na [cel] [exp] [sen] [ref]
10 (2) 5 Gen 1M NaCl 5 generations B 1M [cel] [exp] [sen] [ref]
11 (2) 5 Gen pH 8 5 generations A na [cel] [exp] [sen] [ref]
12 (2) 5 Gen minimal + his/leu/ura 5 generations A na [cel] [exp] [sen] [ref]
13 (2) 5 Gen pH 8 5 generations B na [cel] [exp] [sen] [ref]
14 (2) 5 Gen 1M NaCl 5 generations A 1M [cel] [exp] [sen] [ref]
18 (3) 15 Gen ypg 15 generations B na [cel] [exp] [sen] [ref]
19 (3) 15 Gen ypg 15 generations A na [cel] [exp] [sen] [ref]
29 (4) 20 Gen 1.5M Sorbitol 15 generations A 1.5M [cel] [exp] [sen] [ref]
31 (4) 20 Gen pH 8 15 generations B na [cel] [exp] [sen] [ref]
45 (3) 15 Gen 1M NaCl 15 generations B 1M [cel] [exp] [sen] [ref]
46 (3) 15 Gen pH 8 15 generations A na [cel] [exp] [sen] [ref]
47 (3) 15 Gen minimal + his/leu/ura 15 generations A na [cel] [exp] [sen] [ref]
48 (3) 15 Gen 1M NaCl 15 generations A 1M [cel] [exp] [sen] [ref]
51 (2) 5 Gen 1.5M Sorbitol 5 generations B 1.5M [cel] [exp] [sen] [ref]
52 (3) 15 Gen 1.5M Sorbitol 15 generations B 1.5M [cel] [exp] [sen] [ref]
53 (3) 15 Gen minimal + his/leu/ura 15 generations B na [cel] [exp] [sen] [ref]
58 (2) 5 Gen Nystatin 10uM 5 generations B 10uM [cel] [exp] [sen] [ref]
59 (2) 5 Gen Nystatin 10uM 5 generations A 10uM [cel] [exp] [sen] [ref]
60 (3) 15 Gen Nystatin 10uM 15 generations B 10uM [cel] [exp] [sen] [ref]
61 (3) 15 Gen Nystatin 10uM 15 generations A 10uM [cel] [exp] [sen] [ref]
68 (2) 5 Gen minimal complete 5 generations A na [cel] [exp] [sen] [ref]
69 (2) 5 Gen lys minus 5 generations A na [cel] [exp] [sen] [ref]
70 (2) 5 Gen trp minus 5 generations A na [cel] [exp] [sen] [ref]
71 (2) 5 Gen thr minus 5 generations A na [cel] [exp] [sen] [ref]
73 (2) 5 Gen minimal complete 5 generations B na [cel] [exp] [sen] [ref]
74 (2) 5 Gen lys minus 5 generations B na [cel] [exp] [sen] [ref]
75 (2) 5 Gen trp minus 5 generations B na [cel] [exp] [sen] [ref]
Amino Acid Deficient Conditions
The cutoff for significance in all conditions is 15.
Experiment Number Control Number Condition Ratio File
7473Lysine[rat]
6973Lysine[rat]
7573Tryptophan[rat]
7073Tryptophan[rat]
7173Threonine[rat]
Control Conditions
(0)-70C (1)0 Gen (2)5 Gen (3)15 Gen (4)20 Gen
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The information after this line was added for further clarification after the publication date: July 25, 2002.

For correspondence specific to these files or the data analysis feel free to e-mail
Pat Flaherty{patrickf@eecs.berkeley.edu}
Adam Arkin{aparkin@lbl.gov}
Guri Giaever{ggiaever@cmgm.stanford.edu}

[09/06/2002] The file 05_24_02.exp and 05_24_02.cel is listed in both (-70C) and 0 generations control chip columns. It should only be listed in the 0 generations column. This does not affect any of the reported results because 0 generation data was not used for analysis, but please be aware of this if you use the data in your work.

[09/06/2002] The file 07_20_04.exp is missing from the set of 17 generations control files.