Table Ia

Table Ib

Table IIa

Table IIb

Table IIIa

Table IIIb

Table IVa

Table IVb

Upstream sequence datasets

Create your own yeast upstream sequence database

David Landsman's Research Group

NCBI

Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomyces cerevisiae.

Our goal is to identify sequence elements in yeast that are responsible for cell cycle-dependent transcriptional regulation. A study by Cho et al. identified the 420 genes whose mRNA expression levels exhibit cell cycle peridodicity. They classified the genes by whether their expression peaked in the early G1, late G1, S, G2, or M phase of the cell cycle. We have used standard statistical techniques to predict short sequence elements that may be involved in the expression of groups of co-regulated genes. Our strategy is to look for pentamers and hexamers that are over-represented among the upstream regions of genes whose expression peaks at a particular phase of the cell cycle. We have identified potential regulatory elements that may function as position-independent, orientation-independent (Table Ia), position-independent, orientation-dependent (Table Ib), position-dependent, orientation-independent (Table IIa, IIIa, IVa), or position-dependent, orientation-dependent (Table IIb, IIIb, IVb) sequences.

This site is a companion to the following article:
Wolfsberg TG, Gabrielian AE, Campbell, MJ, Cho, RJ, Spouge, JL, and Landsman D. (1999) Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomyces cerevisiae. Genome Research 9:775-92.

Abstract | Full text | Reprint requests

Tables I-IV from the manuscript are available here. In all four tables, clicking on a sequence element links to a list of genes that contain that element. In addition, links from Tables I and II access longer versions of those tables.

We are also making available the files of upstream regions sequences that we used for our calculations. For each of the cell cycle-regulated yeast genes, we extracted the sequence 600 nucleotides upstream of the ATG start codon. All upstream region sequences are oriented in the direction of transcription, with the start of the sequence at position -600 and the end of the sequence at position -1 with respect to the start codon. Researchers who want to create their own set of yeast upstream sequences from different genes or of other lengths should access "Create your own yeast upstream sequence database"

Yeast gene names and titles were obtained from
Cherry, J. M., Ball, C., Dolinski, K., Dwight, S., Harris, M., Kasarskis, A., Scafe, C., Sherlock, G., Binkley, G., Jin, H., Weng, S., and Botstein, D. "Saccharomyces Genome Database"
ftp://genome-ftp.stanford.edu/pub/yeast/data_download/gene_registry/registry.genenames.txt
(updated on 12/13/2007).

Yeast upstream sequences and gene coordinates were obtained from
Mewes H.W., Hani J., Pfeiffer F., Frishman D. "MIPS: a database for protein sequences and complete genomes"
ftp://ftpmips.gsf.de/yeast/sequences/
This link has been updated and the new sequences might not be identical to the one used for this study. Our calculations remain valid with the yeast sequences provided on this site. (December 13, 2007)



Questions or comments: tyra@nhgri.nih.gov or landsman@ncbi.nlm.nih.gov
Last updated: December 13, 2007.