Research article
Novel insights into iron metabolism by integrating deletome and transcriptome analysis in an iron deficiency model of the yeast Saccharomyces cerevisiae
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* Corresponding author: Chris D Vulpe vulpe@berkeley.edu
- † Equal contributors
1 Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720, USA
2 Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA
3 Department of Bioengineering, University of California, Berkeley, California 94720, USA
4 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
5 University of Toronto, Department of Molecular Genetics, Toronto, Ontario M5S3E1, Canada
6 University of Toronto, Banting and Best Department of Medical Research, Toronto, Ontario M5S3E1, Canada
7 University of Toronto, Department of Pharmaceutical Sciences, Toronto, Ontario M5S3E1, Canada
8 University of Toronto, Donnelley Centre for Cellular and Biomolecular Research, Toronto, Ontario M5S3E1, Canada
BMC Genomics 2009, 10:130 doi:10.1186/1471-2164-10-130
Published: 25 March 2009Additional files
Additional file 1:
List of all genes that were identified by functional profiling in three out of three independent experiments. Deletion of these genes resulted in significant growth alterations in the presence of BPS compared to YPD media.
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Additional file 2:
List of all genes that were identified by functional profiling in at least two out of three independent experiments. Deletion of these genes resulted in significant growth alterations in the presence of BPS compared to YPD media.
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Additional file 3:
Comparison of yeast functional data in iron deficiency between this and other published studies. Genes identified in this study y functional profiling were compared to those reported by Davis-Kaplan et al. (2004), Dudley et al. (2005) and Lesuisse et al. (2005).
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Additional file 4:
Gene Ontology enrichment analysis of functional profiling data. Gene Ontology molecular functions, biological processes and cellular components that were significantly enriched with genes identified by functional profiling.
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Additional file 5:
Functional identification of transcriptional response networks in iron deficiency. All 13 hubs from figure 2A are individually shown with their transcriptional targets, colored in green if deletion of the gene resulted in mutant strain sensitivity to BPS, or red if resistance.
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Additional file 6:
Hierarchical clustering analysis of the genes identified by functional profiling in iron deficiency under diverse growth conditions. Cluster shows the reanalyzed data from previous functional studies of yeast mutants compared to data from this study.
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Additional file 7:
Differentially-expressed genes in nutritional iron-deficient yeast model. Yeast wild type was treated with 100 μM BPS for 1 hour. Genes that were up or down-regulated in at least two out of three independent experiments are listed with average log2 expression values.
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Additional file 8:
Differentially-expressed genes in nutritional iron-deficient yeast model, data for each of three independent experiments. Yeast wild type was treated with 100 μM BPS for 1 hour. Genes that were up or down-regulated in any of three independent experiments are listed with log2 expression values.
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Additional file 9:
Gene Ontology enrichment analysis of expression profiling data for up- and down-regulated genes. Gene Ontology molecular functions, biological processes and cellular components that were significantly enriched with genes identified by expression profiling.
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Additional file 10:
Summary of differentially-expressed genes from individual experiments in the dap1Δ, mrs4Δ and yhr045wΔ. Gene expression profiling was performed in the deletion mutants and wild type strain grown in YPD media.
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Additional file 11:
List of differentially-expressed genes in cti6Δ. Gene expression profiling was performed in cti6Δ and wild type strain grown in YPD media. Cti6p relieves transcriptional repression by binding to the Cyc8p-Tup1p corepressor and recruiting the SAGA complex to repressed promoters.
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Additional file 12:
List of differentially-expressed genes in the dap1Δ. Gene expression profiling was performed in dap1Δ and wild type strain grown in YPD media. Dap1p is a heme-binding protein involved in regulation of cytochrome P450 protein Erg11p, related to mammalian membrane progesterone receptors.
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Additional file 13:
List of differentially-expressed genes in mrs4Δ. Gene expression profiling was performed in mrs4Δ and wild type strain grown in YPD media. Mrs4p is a mitochondrial iron transporter that functions under low-iron conditions.
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Additional file 14:
List of differentially-expressed genes in the yhr045wΔ. Gene expression profiling was performed in yhr045wΔ and wild type strain grown in YPD media. Yhr045wp is a putative protein of unknown function.
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Additional file 15:
Yeast iron map organized by the force-directed layout in Cytoscape. Map was constructed using all molecular interactions associated to iron metabolism compiled from the literature, including ones from the present study. The iron metabolism cluster, enriched with known genes associated to it, is circled in red. Genes in this cluster are highly interconnected with each other by edges that represent different molecular interactions retrieved from the literature. Specific genes can be searched in the map by using the Find feature in Adobe Reader or Acrobat.
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Additional file 16:
Yeast iron map organized by iron-related pathway and Gene Ontology cellular localization. Map was constructed using molecular interactions associated to iron metabolism compiled from the literature, excluding those ones obtained from genomic screens. The map can be browsed from the main menu by cellular component or iron-related pathway. Specific genes can be searched in the map by using the Find feature in Adobe Reader or Acrobat.
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