High-resolution transcription atlas of the mitotic cell cycle in budding yeast

Query

Enter a gene symbol (e.g., RPS16A, GIM3, GCN4)
or chromosomal coordinate as chr:bp (e.g., 13:552000)
(For interpretation of the plots, please see Figure 3 in the paper. mtDNA is treated as chromosome 17)

Data

Data are available from ArrayExpress, accession number E-TABM-587. Average expression levels for each time point are also provided as a text file, [Whole genome - cdc28 and alpha factor], and for convenience, two subtables: [ORFs only - alpha factor] and [ORFs only - cdc28]. Please also see the README file.

References

Marina Granovskaia, Lars J. Jensen, Matthew E. Ritchie et al. High-resolution transcription atlas of the mitotic cell cycle in budding yeast, Genome Biology 2010, 11:R24.

See here for the most recent and best-annotated transcriptome data browser, based on the paper by Xu Z., Wei W. et al.

The segmentation algorithm was described by Huber, Toedling and Steinmetz, Transcript mapping with high-density oligonucleotide tiling arrays, Bioinformatics 2006, 22(16): 1963-1970, and software is available in the tilingArray package in the Bioconductor project.

The actinomycin D protocol for avoiding antisense artifacts was described by Fabiana Perocchi et al., Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D, Nucleic Acids Research 2007 35(19):e128.

Contact: Lars Steinmetz