Effect of 21 different nitrogen sources on global gene expression in the yeast Saccharomyces cerevisiae.

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Published in Mol Cell Biol on February 16, 2007

Authors

Patrice Godard1, Antonio Urrestarazu, Stéphan Vissers, Kevin Kontos, Gianluca Bontempi, Jacques van Helden, Bruno André

Author Affiliations

1: Physiologie Moléculaire de la Cellule, IBMM, Université Libre de Bruxelles, Rue des Pr. Jeener et Brachet 12, 6041 Gosselies, Belgium.

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Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52

Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19

Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast (1998) 48.29

Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res (2002) 40.03

TM4: a free, open-source system for microarray data management and analysis. Biotechniques (2003) 38.02

Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell (2000) 36.09

Improved method for high efficiency transformation of intact yeast cells. Nucleic Acids Res (1992) 34.33

Global analysis of protein localization in budding yeast. Nature (2003) 33.22

Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature (2003) 29.16

Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21

Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation. Cell (2000) 13.44

Translational regulation of GCN4 and the general amino acid control of yeast. Annu Rev Microbiol (2005) 11.48

Unipolar cell divisions in the yeast S. cerevisiae lead to filamentous growth: regulation by starvation and RAS. Cell (1992) 10.94

Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res (2002) 10.65

Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell (2001) 9.63

The TOR signalling pathway controls nuclear localization of nutrient-regulated transcription factors. Nature (1999) 9.29

The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res (2004) 8.79

PCR-synthesis of marker cassettes with long flanking homology regions for gene disruptions in S. cerevisiae. Yeast (1996) 8.45

Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J Mol Biol (1998) 8.34

KAR2, a karyogamy gene, is the yeast homolog of the mammalian BiP/GRP78 gene. Cell (1989) 8.14

Statistical tests for differential expression in cDNA microarray experiments. Genome Biol (2003) 7.65

Computational discovery of gene modules and regulatory networks. Nat Biotechnol (2003) 6.55

Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast. Mol Cell Biol (2001) 6.05

Regulatory sequence analysis tools. Nucleic Acids Res (2003) 5.72

Preparation of high molecular weight RNA. Methods Enzymol (1991) 5.60

Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein. Mol Cell Biol (1989) 5.23

Intracellular signaling from the endoplasmic reticulum to the nucleus: the unfolded protein response in yeast and mammals. Curr Opin Cell Biol (2001) 5.08

Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast. Proc Natl Acad Sci U S A (2000) 4.30

S. cerevisiae encodes an essential protein homologous in sequence and function to mammalian BiP. Cell (1989) 4.28

New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. Mol Biol Cell (2000) 4.17

Metabolism of sulfur amino acids in Saccharomyces cerevisiae. Microbiol Mol Biol Rev (1997) 4.11

The URE2 gene product of Saccharomyces cerevisiae plays an important role in the cellular response to the nitrogen source and has homology to glutathione s-transferases. Mol Cell Biol (1991) 3.52

Nitrogen regulation in Saccharomyces cerevisiae. Gene (2002) 3.43

Partitioning the transcriptional program induced by rapamycin among the effectors of the Tor proteins. Curr Biol (2001) 3.26

Mutations affecting the repressibility of arginine biosynthetic enzymes in Saccharomyces cerevisiae. Eur J Biochem (1970) 3.17

RTG1 and RTG2: two yeast genes required for a novel path of communication from mitochondria to the nucleus. Cell (1993) 3.13

Coordinated remodeling of cellular metabolism during iron deficiency through targeted mRNA degradation. Cell (2005) 3.05

Physiological regulation of membrane protein sorting late in the secretory pathway of Saccharomyces cerevisiae. J Cell Biol (1997) 3.00

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The unfolding tale of the unfolded protein response. Cell (2001) 2.90

Biological role of the general control of amino acid biosynthesis in Saccharomyces cerevisiae. Mol Cell Biol (1981) 2.88

Nitrogen catabolite repression in yeasts and filamentous fungi. Adv Microb Physiol (1985) 2.82

GAP1, the general amino acid permease gene of Saccharomyces cerevisiae. Nucleotide sequence, protein similarity with the other bakers yeast amino acid permeases, and nitrogen catabolite repression. Eur J Biochem (1990) 2.80

The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur. J Biol Chem (2002) 2.71

Amino acid signaling in Saccharomyces cerevisiae: a permease-like sensor of external amino acids and F-Box protein Grr1p are required for transcriptional induction of the AGP1 gene, which encodes a broad-specificity amino acid permease. Mol Cell Biol (1999) 2.62

Expression of the DAL80 gene, whose product is homologous to the GATA factors and is a negative regulator of multiple nitrogen catabolic genes in Saccharomyces cerevisiae, is sensitive to nitrogen catabolite repression. Mol Cell Biol (1991) 2.62

Genome microarray analysis of transcriptional activation in multidrug resistance yeast mutants. FEBS Lett (2000) 2.22

The nitrilase superfamily: classification, structure and function. Genome Biol (2001) 2.19

The permease homologue Ssy1p controls the expression of amino acid and peptide transporter genes in Saccharomyces cerevisiae. Mol Microbiol (1998) 2.18

Sensors of extracellular nutrients in Saccharomyces cerevisiae. Curr Genet (2001) 2.09

Nitrogen repression of the allantoin degradative enzymes in Saccharomyces cerevisiae. J Bacteriol (1974) 2.03

Cross regulation of four GATA factors that control nitrogen catabolic gene expression in Saccharomyces cerevisiae. J Bacteriol (1997) 1.90

Peptides accelerate their uptake by activating a ubiquitin-dependent proteolytic pathway. Nature (2000) 1.90

Ssy1p and Ptr3p are plasma membrane components of a yeast system that senses extracellular amino acids. Mol Cell Biol (1999) 1.83

Glucose limitation induces GCN4 translation by activation of Gcn2 protein kinase. Mol Cell Biol (2000) 1.80

Classification of all putative permeases and other membrane plurispanners of the major facilitator superfamily encoded by the complete genome of Saccharomyces cerevisiae. FEMS Microbiol Rev (1997) 1.77

Specific induction of catabolism and its relation to repression of biosynthesis in arginine metabolism of Saccharomyces cerevisiae. J Mol Biol (1978) 1.77

The pleitropic drug ABC transporters from Saccharomyces cerevisiae. J Mol Microbiol Biotechnol (2001) 1.72

Global expression profiling of yeast treated with an inhibitor of amino acid biosynthesis, sulfometuron methyl. Physiol Genomics (2000) 1.67

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Global analysis of nutrient control of gene expression in Saccharomyces cerevisiae during growth and starvation. Proc Natl Acad Sci U S A (2004) 1.61

A cis-dominant regulatory mutation linked to the argB-argC gene cluster in Saccharomyces cerevisiae. J Mol Biol (1980) 1.61

Receptor-mediated endoproteolytic activation of two transcription factors in yeast. Genes Dev (2002) 1.59

Identification and characterization of MAE1, the Saccharomyces cerevisiae structural gene encoding mitochondrial malic enzyme. J Bacteriol (1998) 1.59

Control of enzyme synthesis in the lysine biosynthetic pathway of Saccharomyces cerevisiae. Evidence for a regulatory role of gene LYS14. Eur J Biochem (1988) 1.52

A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes cross-hybridization. BMC Genomics (2003) 1.51

Characterisation of Saccharomyces cerevisiae ARO8 and ARO9 genes encoding aromatic aminotransferases I and II reveals a new aminotransferase subfamily. Mol Gen Genet (1998) 1.46

The mechanism of the formation of higher alcohols from amino acids by Saccharomyces cerevisiae. Biochem J (1960) 1.41

Genome-wide transcriptional analysis in S. cerevisiae by mini-array membrane hybridization. Yeast (1999) 1.41

The UGA3 gene regulating the GABA catabolic pathway in Saccharomyces cerevisiae codes for a putative zinc-finger protein acting on RNA amount. Mol Gen Genet (1990) 1.40

Proline: an essential intermediate in arginine degradation in Saccharomyces cerevisiae. J Bacteriol (1980) 1.40

Cloning and expression of the UGA4 gene coding for the inducible GABA-specific transport protein of Saccharomyces cerevisiae. Mol Gen Genet (1993) 1.39

Transcriptional induction by aromatic amino acids in Saccharomyces cerevisiae. Mol Cell Biol (1999) 1.38

The UGA43 negative regulatory gene of Saccharomyces cerevisiae contains both a GATA-1 type zinc finger and a putative leucine zipper. Curr Genet (1992) 1.37

TOR modulates GCN4-dependent expression of genes turned on by nitrogen limitation. J Bacteriol (2001) 1.37

G1n3p is capable of binding to UAS(NTR) elements and activating transcription in Saccharomyces cerevisiae. J Bacteriol (1996) 1.36

The unfolded protein response represses nitrogen-starvation induced developmental differentiation in yeast. Genes Dev (2000) 1.31

Mutations affecting the enzymes involved in the utilization of 4-aminobutyric acid as nitrogen source by the yeast Saccharomyces cerevisiae. Eur J Biochem (1985) 1.28

Identification and characterization of phenylpyruvate decarboxylase genes in Saccharomyces cerevisiae. Appl Environ Microbiol (2003) 1.28

Evidence for positive regulation of the proline utilization pathway in Saccharomyces cerevisiae. Genetics (1987) 1.27

Combining pattern discovery and discriminant analysis to predict gene co-regulation. Bioinformatics (2004) 1.27

A member of the YER057c/yjgf/Uk114 family links isoleucine biosynthesis and intact mitochondria maintenance in Saccharomyces cerevisiae. Genes Cells (2001) 1.24

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New insights into the pleiotropic drug resistance network from genome-wide characterization of the YRR1 transcription factor regulation system. Mol Cell Biol (2002) 1.20

The unfolded protein response: no longer just a special teams player. Traffic (2001) 1.20

The putative monocarboxylate permeases of the yeast Saccharomyces cerevisiae do not transport monocarboxylic acids across the plasma membrane. Yeast (2001) 1.18

Two mutually exclusive regulatory systems inhibit UASGATA, a cluster of 5'-GAT(A/T)A-3' upstream from the UGA4 gene of Saccharomyces cerevisiae. Nucleic Acids Res (1995) 1.17

Cis- and trans-acting elements determining induction of the genes of the gamma-aminobutyrate (GABA) utilization pathway in Saccharomyces cerevisiae. Nucleic Acids Res (1995) 1.17

Tryptophan degradation in Saccharomyces cerevisiae: characterization of two aromatic aminotransferases. Arch Microbiol (1982) 1.17

Genomic exploration of the hemiascomycetous yeasts: 19. Ascomycetes-specific genes. FEBS Lett (2000) 1.16

Cha4p of Saccharomyces cerevisiae activates transcription via serine/threonine response elements. Genetics (1996) 1.14

Genetic analysis of the signalling pathway activated by external amino acids in Saccharomyces cerevisiae. Mol Microbiol (2001) 1.14

Role of GATA factor Nil2p in nitrogen regulation of gene expression in Saccharomyces cerevisiae. J Bacteriol (1997) 1.12

Amino acids induce expression of BAP2, a branched-chain amino acid permease gene in Saccharomyces cerevisiae. J Bacteriol (1996) 1.12

A general strategy to uncover transcription factor properties identifies a new regulator of drug resistance in yeast. J Biol Chem (2003) 1.11

Molecular genetics of serine and threonine catabolism in Saccharomyces cerevisiae. Genetics (1988) 1.11

The role of the yeast plasma membrane SPS nutrient sensor in the metabolic response to extracellular amino acids. Mol Microbiol (2001) 1.10

Signalling between mitochondria and the nucleus regulates the expression of a new D-lactate dehydrogenase activity in yeast. Yeast (1999) 1.08

yMGV: helping biologists with yeast microarray data mining. Nucleic Acids Res (2002) 1.07

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