Exploratory and Confirmatory Gene Expression Profiling of mac1Δ

Freitas, Jeane M. De; Kim, Jeung Hyoun; Poynton, Helen C.; Su, Trent; Wintz, Henri; Fox, Tama C.; Holman, Patty S.; Loguinov, Alex; Keleş, Sündüz; Laan, Mark van der; Vulpe, Chris D.

doi:10.1074/jbc.m212308200

Cited by 46 publications

(48 citation statements)

References 60 publications

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“…The relation of the zinc transporter ZRT3 to iron homeostasis is documented in [23]. Finally, [5] provides statistical evidence that the following genes are related to iron homeostasis: LEU1, AKR1, HCR1, CTT1, ERG3 and YER156C. Besides, the paper confirms the relation of the first two genes through miniarray and quantitative PCR.…”

Section: Rosetta Compendiumsupporting

confidence: 57%

Learning Gaussian Graphical Models of Gene Networks with False Discovery Rate Control

Peña

Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics

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Abstract. In many cases what matters is not whether a false discovery is made or not but the expected proportion of false discoveries among all the discoveries made, i.e. the so-called false discovery rate (FDR). We present an algorithm aiming at controlling the FDR of edges when learning Gaussian graphical models (GGMs). The algorithm is particularly suitable when dealing with more nodes than samples, e.g. when learning GGMs of gene networks from gene expression data. We illustrate this on the Rosetta compendium [8].

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Section: Rosetta Compendiumsupporting

confidence: 57%

Learning Gaussian Graphical Models of Gene Networks with False Discovery Rate Control

Peña

Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics

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“…ScMac1p regulates genes involved in the copper and iron uptake systems in response to copper levels (De Freitas et al, 2004;Gross et al, 2000). ScMac1p regulates its target genes by direct binding to consensus binding sites in the promoter, known as CuREs (Martins et al, 1998;Yamaguchi-Iwai et al, 1997).…”

Section: Introductionmentioning

confidence: 99%

Copper-dependent transcriptional regulation by Candida albicans Mac1p

2008

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“…expression have focused on the role of the transcription factor Mac1p using single-point measurements under various conditions (12,22). Here we have generated quadruplicate time course measurements of the changes in gene expression in S. cerevisiae in response to copper excess and deprivation over extended periods of time.…”

mentioning

confidence: 99%

Gene expression profiling and phenotype analyses ofS. cerevisiaein response to changing copper reveals six genes with new roles in copper and iron metabolism

Bakel¹,

Strengman²,

Wijmenga³

et al. 2005

Physiological Genomics

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Aside from identifying targets of established copperand iron-responsive transcription factors, we find that genes encoding mitochondrial proteins are downregulated and that copper-independent iron transport genes are preferentially upregulated, both during prolonged copper deprivation. The experiments also suggest the presence of a small regulatory iron pool that links copper and iron responses. One hundred twenty-eight genes with putative roles in metal metabolism were further investigated by several systematic phenotype screens. Of the novel phenotypes uncovered, hsp12-⌬ and arn1-⌬ display increased sensitivity to copper, cyc1-⌬ and crr1-⌬ show resistance to high copper, vma13-⌬ exhibits increased sensitivity to iron deprivation, and pep12-⌬ results in reduced growth in high copper and low iron. Besides revealing new components of eukaryotic metal trafficking pathways, the results underscore the previously determined intimate links between iron and copper metabolism and mitochondrial and vacuolar function in metal trafficking. The analyses further suggest that copper starvation can specifically lead to downregulation of respiratory function to preserve iron and copper for other cellular processes.

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Exploratory and Confirmatory Gene Expression Profiling of mac1Δ

Cited by 46 publications

References 60 publications

Learning Gaussian Graphical Models of Gene Networks with False Discovery Rate Control

Learning Gaussian Graphical Models of Gene Networks with False Discovery Rate Control

Copper-dependent transcriptional regulation by Candida albicans Mac1p

Gene expression profiling and phenotype analyses ofS. cerevisiaein response to changing copper reveals six genes with new roles in copper and iron metabolism

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