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Transcriptome profiling of a Saccharomyces cerevisiae mutant with a constitutively activated Ras/cAMP pathway.
Physiol Genomics. 2003 Dec 16; 16(1):107-18.PG

Abstract

Often changes in gene expression levels have been considered significant only when above/below some arbitrarily chosen threshold. We investigated the effect of applying a purely statistical approach to microarray analysis and demonstrated that small changes in gene expression have biological significance. Whole genome microarray analysis of a pde2Delta mutant, constructed in the Saccharomyces cerevisiae reference strain FY23, revealed altered expression of approximately 11% of protein encoding genes. The mutant, characterized by constitutive activation of the Ras/cAMP pathway, has increased sensitivity to stress, reduced ability to assimilate nonfermentable carbon sources, and some cell wall integrity defects. Applying the Munich Information Centre for Protein Sequences (MIPS) functional categories revealed increased expression of genes related to ribosome biogenesis and downregulation of genes in the cell rescue, defense, cell death and aging category, suggesting a decreased response to stress conditions. A reduced level of gene expression in the unfolded protein response pathway (UPR) was observed. Cell wall genes whose expression was affected by this mutation were also identified. Several of the cAMP-responsive orphan genes, upon further investigation, revealed cell wall functions; others had previously unidentified phenotypes assigned to them. This investigation provides a statistical global transcriptome analysis of the cellular response to constitutive activation of the Ras/cAMP pathway.

Authors+Show Affiliations

Department of Biomolecular Sciences, University of Manchester Institute of Science and Technology, Manchester M60 1QD, United Kingdom.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

14570984

Citation

Jones, D L., et al. "Transcriptome Profiling of a Saccharomyces Cerevisiae Mutant With a Constitutively Activated Ras/cAMP Pathway." Physiological Genomics, vol. 16, no. 1, 2003, pp. 107-18.
Jones DL, Petty J, Hoyle DC, et al. Transcriptome profiling of a Saccharomyces cerevisiae mutant with a constitutively activated Ras/cAMP pathway. Physiol Genomics. 2003;16(1):107-18.
Jones, D. L., Petty, J., Hoyle, D. C., Hayes, A., Ragni, E., Popolo, L., Oliver, S. G., & Stateva, L. I. (2003). Transcriptome profiling of a Saccharomyces cerevisiae mutant with a constitutively activated Ras/cAMP pathway. Physiological Genomics, 16(1), 107-18.
Jones DL, et al. Transcriptome Profiling of a Saccharomyces Cerevisiae Mutant With a Constitutively Activated Ras/cAMP Pathway. Physiol Genomics. 2003 Dec 16;16(1):107-18. PubMed PMID: 14570984.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Transcriptome profiling of a Saccharomyces cerevisiae mutant with a constitutively activated Ras/cAMP pathway. AU - Jones,D L, AU - Petty,J, AU - Hoyle,D C, AU - Hayes,A, AU - Ragni,E, AU - Popolo,L, AU - Oliver,S G, AU - Stateva,L I, Y1 - 2003/12/16/ PY - 2003/10/23/pubmed PY - 2004/1/27/medline PY - 2003/10/23/entrez SP - 107 EP - 18 JF - Physiological genomics JO - Physiol Genomics VL - 16 IS - 1 N2 - Often changes in gene expression levels have been considered significant only when above/below some arbitrarily chosen threshold. We investigated the effect of applying a purely statistical approach to microarray analysis and demonstrated that small changes in gene expression have biological significance. Whole genome microarray analysis of a pde2Delta mutant, constructed in the Saccharomyces cerevisiae reference strain FY23, revealed altered expression of approximately 11% of protein encoding genes. The mutant, characterized by constitutive activation of the Ras/cAMP pathway, has increased sensitivity to stress, reduced ability to assimilate nonfermentable carbon sources, and some cell wall integrity defects. Applying the Munich Information Centre for Protein Sequences (MIPS) functional categories revealed increased expression of genes related to ribosome biogenesis and downregulation of genes in the cell rescue, defense, cell death and aging category, suggesting a decreased response to stress conditions. A reduced level of gene expression in the unfolded protein response pathway (UPR) was observed. Cell wall genes whose expression was affected by this mutation were also identified. Several of the cAMP-responsive orphan genes, upon further investigation, revealed cell wall functions; others had previously unidentified phenotypes assigned to them. This investigation provides a statistical global transcriptome analysis of the cellular response to constitutive activation of the Ras/cAMP pathway. SN - 1531-2267 UR - https://www.unboundmedicine.com/medline/citation/14570984/Transcriptome_profiling_of_a_Saccharomyces_cerevisiae_mutant_with_a_constitutively_activated_Ras/cAMP_pathway_ L2 - https://journals.physiology.org/doi/10.1152/physiolgenomics.00139.2003?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub=pubmed DB - PRIME DP - Unbound Medicine ER -