Expression Data Set 43 details

Information Item Value
Dataset Name SAGE transcript profiles from yeast grown on two different carbon sources
Dataset Number 43
Short Description SAGE analysis of wild type and mutant cells grown on oleate for
comparison with SAGE analysis of cells grown on glucose
Source URL
Reference Kal, AJ; et al (see LongDescrip for Complete Reference), Dynamics of Gene Expression
Revealed by Comparison of Serial Analysis of Gene Expression Transcript Profiles from Yeast Grown
on Two Different Carbon Sources, Mol. Biol. Cell 2000, 10(6):1859-1872
Strains Wild type strain BJ1991 (MATalpha, leu2, trp1, ura3-52, pip4-3, prb1-1122; Jones, 1977),
mutant strain BJ1991 pip2/oaf1 (MATalpha, leu2, trp1 ura3-52, pep4-3 prbl-1122, PIP2::KANMX4,OAF1::LEU2;
Rottenstein et al, 1997)
Conditions See LongDescrip
Date Added to ExpressDB Sep 15 2000 3:07:47:103PM
Number of Measures on ExpressDB 10 (here to download dataset and view measure details)
Long Description Abstract - We describe a genome-wide characterization
of mRNA transcript levels in yeast grown on the fatty acid oleate,
determined using Serial Analysis of Gene Expression (SAGE). Comparison
of this SAGE library with that reported for glucose grown cells
revealed the dramatic adaptive response of yeast to a change in carbon
source. A major fraction (>20%) of the 15,000 mRNA molecules in a
yeast cell comprised differentially expressed transcripts, which were
derived from only 2% of the total number of ~6300 yeast genes. Most of
the mRNAs that were differentially expressed code for enzymes or for
other proteins participating in metabolism (e.g., metabolite
transporters). In oleate-grown cells, this was exemplified by the huge
increase of mRNAs encoding the peroxisomal-oxidation enzymes required
for degradation of fatty acids. The data provide evidence for the
existence of redox shuttles across organellar membranes that involve
peroxisomal, cytoplasmic, and mitochondrial enzymes. We also analyzed
the mRNA profile of a mutant strain with deletions of the PIP2 and
OAF1 genes, encoding transcription factors required for induction of
genes encoding peroxisomal proteins. Induction of genes under the
immediate control of these factors was abolished; other genes were
up-regulated, indicating an adaptive response to the changed
metabolism imposed by the genetic impairment. We describe a
statistical method for analysis of data obtained by SAGE.

Data analysis methods

Initial data analysis was performed using the SAGE Software
package version 1.0 (Velculescu et al., 1995). The tag list from wild
type cells and pip2/oaf1 cells contained 10,943 and 3847 tags,
respectively, of which 577 and 234, respectively, were derived from
linker sequences. These tags were excluded from the analysis. The
resulting tag lists contained 10,366 total tags from wild type cells
and 3613 tags from pip2/oaf1 cells. We compiled a database of all
potential tags of the complete yeast genome (over 69,000 10-bp
sequences) and linked each tag to the gene annotations in the MIPS
database (as of 9th December 1998). Next, we merged this dataset with
the tags found with SAGE. Tag numbers can be converted to number of
mRNA transcripts per cell assuming a total of 15,000 mRNA molecules
per cell (see below). Classification in Functional Categories was done
according to the yeast protein functional catalogue (Goffeau, 1997;
Mewes et al., 1997); also available via the World Wide Web at

Usage of the SAGE data

Determine expression levels
To determine the expression level of a certain gene, follow the guidelines below.

1. Use the systematic name of the gene, e.g. YMR303C is the systematic
name for the ADH2 gene. For searches, always use the systematic names.
Not all synonyms are included in the descriptions, and sometimes the
same acronym is used for different genes (e.g. CTP1 = citrate
transport protein or copper transport protein).
2. Only consider tags that are within the 500 bp 3' of the ORF. If
multiple tags match a gene within the ORF or within the 500 bp 3' of
the ORF AND these tags have only one genome hit, tags can
be considered to originate from the same gene and can be added. If
tags match the genome at multiple places, all places should be
checked. Sometime the 11th bp of the tag can be identified using the
SAGE software, this sometimes resolves ambiguities.
3. Calculate the expression level (mRNA copies per cell) by dividing
the number of tags by the total number of tags for that condition, and
multiply the resulting number by 15,000 (total number of mRNA
molecules per cell). E.g. 100 tags from a gene in the wild type oleate
library equals an expression level of 100/10,366*15000=145 mRNA copies
per cell.

Note that a single tag can originate from multiple genes (e.g. tag
GGTGAAAACG can originate from ADH1, ADH2 or DYN1 genes), that a single
gene can give multiple tags and that tags that originate from
chromosome localizations far away (>500 bp) from annotated ORF can
originate from NORFs (Non-annotated ORFs).

Complete Reference - Kal, AJ; van Zonneveld, AJ; Benes, V; van den Berg, M; Koerkamp, G;
Albermann, K; Strack, N; Ruijter, J M; Richter, A; Dujon, B; Ansorge, W; Tabak, HF,
Dynamics of Gene Expression Revealed by Comparison of Serial Analysis of Gene
Expression Transcript Profiles from Yeast Grown on Two Different Carbon Sources,
Mol. Biol. Cell 2000, 10(6):1859-1872

Conditions - Strains were precultured 24 h on minimal medium
containing 0.3% glucose to obtain a derepressed culture. After a shift
to medium containing 0.12% oleate, 0.2% Tween 40, 0.3% yeast extract,
0.5% bacto-peptone, and 0.5% potassium phosphate buffer, pH 6.0, the
cells were cultured for 18 h at 280C. Cell growth was stopped by the
addition of an equal volume of ethanol (800C), and RNA was extracted
immediately. mRNA was isolated using the Poly-A-tract kit from Promega
(Madison, WI) according to the manufacturer's protocol.

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Copyright (c) 2006 by Wayne Rindone and the President and Fellows of Harvard University