Kastenmayer: Data from Kastenmayer et al. 2006

In PCpheno: Phenotypes and cellular organizational units

Description

Kastenmayer et al. (2006) undertook the first functional studies of small open reading frames (sORFs) in any system, using the model eukaryote Saccharomyces cerevisiae. Phenotypic analyses of the new gene-deletion strains identified 22 sORFs required for haploid growth, growth at high temperature, growth in the presence of a non-fermentable carbon source, or growth in the presence of DNA damage and replication-arrest agents.

Usage

data(KastenmayerRaw)

Format

Kastenmayer is a 5 columns dataframe.

SYSTEMATIC

Systematic name of the sORF.

COMMUN

Commun name of the sORF.

Length

Length of the small ORF sequence in number of amino acids.

Evidence

Experimental source of the data

refHomology

Bibliographical evidence of reported homology.

Kocollection

Bibliographical evidence of reported homology.

ESSENTIAL

Indicates if the sORF knockout is essential. A blank in this column indicates that the knockout is not-essential, if available.

GFPTAP

"GFP" or "TAP" signifies that sORF was detected by the indicated technique. "both" indicates that sORF was detected both as a TAP-tagged and GFP-tagged protein. "None" indicates that sORF was not detected by either method. Empty field indicates that sORF was not tested

UPTAG

Sequence of the upstream primer.

DOWNTAG

Sequence of the downstream primer.

Author(s)

N. LeMeur

Source

Kastenmayer et al. (2006), supplementary information: http://www.genomeresearch.org or ftp://genome-ftp.stanford.edu/pub/yeast/systematic_results/phenotypes

References

Kastenmayer JP, Ni L, Chu A, Kitchen LE, Au WC, Yang H, Carter CD, Wheeler D, Davis RW, Boeke JD, Snyder MA, Basrai MA. (2006) Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae. Genome Res. 16(3):365-73. PMID: 16510898

Examples

data(KastenmayerRaw)
str(KastenmayerRaw)

PCpheno documentation built on Nov. 8, 2020, 5:10 p.m.