Dissecting the Gene Network of Dietary Restriction to Identify Evolutionarily Conserved Pathways and New Functional Genes
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Thomas Craig | Olga Vasieva | Richard Connor | Yang Li | Daniel Wuttke | João Pedro de Magalhães | Fusheng Tang | Chintan Vora | J. de Magalhães | D. Wuttke | S. Wood | C. Vora | Yang Li | O. Vasieva | Fusheng Tang | Thomas Craig | Robert Shmookler Reis | Shona Wood | R. Shmookler Reis | Richard A. Connor
[1] S. Deswal,et al. Calorie restriction up-regulates iron and copper transport genes in Saccharomyces cerevisiae. , 2011, Molecular bioSystems.
[2] João Pedro de Magalhães,et al. HAGR: the Human Ageing Genomic Resources , 2004, Nucleic Acids Res..
[3] J. Backer,et al. The Late Endosome is Essential for mTORC1 Signaling , 2010, Molecular biology of the cell.
[4] H. Pelham,et al. Arrestin-Mediated Endocytosis of Yeast Plasma Membrane Transporters , 2009, Traffic.
[5] E. Garí,et al. TOR Regulates the Subcellular Localization of Ime1, a Transcriptional Activator of Meiotic Development in Budding Yeast , 2003, Molecular and Cellular Biology.
[6] Ariel S. Schwartz,et al. An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man , 2010, Cell.
[7] E. Siegel,et al. Modulation of lipid biosynthesis contributes to stress resistance and longevity of C. elegans mutants , 2011, Aging.
[8] Ioannis Xenarios,et al. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions , 2002, Nucleic Acids Res..
[9] Janet M. Thornton,et al. Ribosomal Protein S6 Kinase 1 Signaling Regulates Mammalian Life Span , 2009, Science.
[10] M. Johnston,et al. A chemical genomics approach toward understanding the global functions of the target of rapamycin protein (TOR). , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[11] Jianhua Ruan,et al. Building and analyzing protein interactome networks by cross-species comparisons , 2010, BMC Systems Biology.
[12] Y. Anraku,et al. Properties of H+-translocating adenosine triphosphatase in vacuolar membranes of SAccharomyces cerevisiae. , 1981, The Journal of biological chemistry.
[13] Robin Haw,et al. Using the Reactome Database , 2012, Current protocols in bioinformatics.
[14] Akihiko Nakano,et al. Ergosterol is required for targeting of tryptophan permease to the yeast plasma membrane , 2003, The Journal of cell biology.
[15] L. Partridge,et al. Dietary restriction in Drosophila , 2005, Mechanisms of Ageing and Development.
[16] Eugene V. Koonin,et al. Constraints and plasticity in genome and molecular-phenome evolution , 2010, Nature Reviews Genetics.
[17] Stuart K. Kim. Common aging pathways in worms, flies, mice and humans , 2007, Journal of Experimental Biology.
[18] D. Reinberg,et al. Calorie restriction and the exercise of chromatin. , 2009, Genes & development.
[19] Henning Hermjakob,et al. InteroPORC: automated inference of highly conserved protein interaction networks , 2008, Bioinform..
[20] Matt Kaeberlein,et al. Quantitative evidence for conserved longevity pathways between divergent eukaryotic species. , 2008, Genome research.
[21] D. Sinclair,et al. Nicotinamide and PNC1 govern lifespan extension by calorie restriction in Saccharomyces cerevisiae , 2003, Nature.
[22] M. Cam,et al. Microarray studies on the genes responsive to the addition of spermidine or spermine to a Saccharomyces cerevisiae spermidine synthase mutant , 2009, Yeast.
[23] Jianmin Wu,et al. Integrated network analysis platform for protein-protein interactions , 2009, Nature Methods.
[24] Ian M. Donaldson,et al. iRefIndex: A consolidated protein interaction database with provenance , 2008, BMC Bioinformatics.
[25] A. Bird,et al. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals , 2003, Nature Genetics.
[26] R. Ozawa,et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[27] Adiel Cohen,et al. TOR1 and TOR2 Have Distinct Locations in Live Cells , 2008, Eukaryotic Cell.
[28] B. Kennedy,et al. Dietary restriction suppresses proteotoxicity and enhances longevity by an hsf‐1‐dependent mechanism in Caenorhabditis elegans , 2008, Aging cell.
[29] Igor Jurisica,et al. Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging , 2010, Genome Biology.
[30] E. Levanon,et al. Preferential attachment in the protein network evolution. , 2003, Physical review letters.
[31] A. Hsu,et al. New Genes Tied to Endocrine, Metabolic, and Dietary Regulation of Lifespan from a Caenorhabditis elegans Genomic RNAi Screen , 2005, PLoS genetics.
[32] Frank Sinner,et al. Induction of autophagy by spermidine promotes longevity , 2009, Nature Cell Biology.
[33] L. Aravind,et al. Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. , 2006, Journal of molecular biology.
[34] Rafael C. Jimenez,et al. The IntAct molecular interaction database in 2012 , 2011, Nucleic Acids Res..
[35] Y. Benno,et al. Longevity in Mice Is Promoted by Probiotic-Induced Suppression of Colonic Senescence Dependent on Upregulation of Gut Bacterial Polyamine Production , 2011, PloS one.
[36] A. Barabasi,et al. Network medicine : a network-based approach to human disease , 2010 .
[37] T. Kirkwood,et al. CALORIE RESTRICTION AND AGING: A LIFE‐HISTORY ANALYSIS , 2000, Evolution; international journal of organic evolution.
[38] Puneet Bharill,et al. Positive Feedback between Transcriptional and Kinase Suppression in Nematodes with Extraordinary Longevity and Stress Resistance , 2009, PLoS genetics.
[39] S. Benzer,et al. Regulation of Lifespan in Drosophila by Modulation of Genes in the TOR Signaling Pathway , 2004, Current Biology.
[40] A. E. Hirsh,et al. Evolutionary Rate in the Protein Interaction Network , 2002, Science.
[41] Andrzej Bartke,et al. Targeted disruption of growth hormone receptor interferes with the beneficial actions of calorie restriction , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[42] Y. Anraku,et al. The H+-Translocating ATPase in Vacuolar Membranes of Saccharomyces Cerevisiae , 1985 .
[43] Bin Liu,et al. Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together , 2006, Nucleic Acids Res..
[44] Mike Tyers,et al. PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae , 2010, Database J. Biol. Databases Curation.
[45] E. Nishida,et al. Signalling through RHEB-1 mediates intermittent fasting-induced longevity in C. elegans , 2009, Nature.
[46] Xin Gao,et al. Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups. , 2011, Current protocols in bioinformatics.
[47] M. Whitlock. Combining probability from independent tests: the weighted Z‐method is superior to Fisher's approach , 2005, Journal of evolutionary biology.
[48] Livia Perfetto,et al. MINT, the molecular interaction database: 2012 update , 2011, Nucleic Acids Res..
[49] G. Craciun,et al. A lifespan-extending form of autophagy employs the vacuole-vacuole fusion machinery , 2008, Autophagy.
[50] A. Amon,et al. Gametogenesis Eliminates Age-Induced Cellular Damage and Resets Life Span in Yeast , 2011, Science.
[51] A. Budovsky,et al. Longevity network: Construction and implications , 2007, Mechanisms of Ageing and Development.
[52] G. Church,et al. Analyses of human–chimpanzee orthologous gene pairs to explore evolutionary hypotheses of aging , 2007, Mechanisms of Ageing and Development.
[53] T. Witten,et al. Predicting Aging/Longevity‐Related Genes in the Nematode Caenorhabditis elegans , 2007, Chemistry & biodiversity.
[54] K. Yano,et al. Caloric Restriction, the Traditional Okinawan Diet, and Healthy Aging , 2007, Annals of the New York Academy of Sciences.
[55] A. Owen,et al. A gene recommender algorithm to identify coexpressed genes in C. elegans. , 2003, Genome research.
[56] L. Partridge,et al. Demography of Dietary Restriction and Death in Drosophila , 2003, Science.
[57] W. Kim,et al. Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy , 2008, Genome Biology.
[58] L. Guarente,et al. Genetic links between diet and lifespan: shared mechanisms from yeast to humans , 2007, Nature Reviews Genetics.
[59] Michael L. Creech,et al. Integration of biological networks and gene expression data using Cytoscape , 2007, Nature Protocols.
[60] Jignesh M. Patel,et al. Michigan molecular interactions r2: from interacting proteins to pathways , 2008, Nucleic Acids Res..
[61] Rong Li,et al. Asymmetrically Inherited Multidrug Resistance Transporters are Recessive Determinants in Cellular Replicative Aging , 2010, Nature Cell Biology.
[62] David Bryant,et al. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists , 2007, Nucleic Acids Res..
[63] Arie Budovsky,et al. The Human Ageing Genomic Resources: online databases and tools for biogerontologists , 2009, Aging cell.
[64] Yae-Lim Lee,et al. Transcriptional response according to strength of calorie restriction in Saccharomyces cerevisiae. , 2008, Molecules and cells.
[65] Natalie L. Catlett,et al. Vac8p, a Vacuolar Protein with Armadillo Repeats, Functions in both Vacuole Inheritance and Protein Targeting from the Cytoplasm to Vacuole , 1998, The Journal of cell biology.
[66] Subhash D. Katewa,et al. 4E-BP Extends Lifespan upon Dietary Restriction by Enhancing Mitochondrial Activity in Drosophila , 2009, Cell.
[67] Charlotte M. Deane,et al. Protein protein interactions, evolutionary rate, abundance and age , 2006, BMC Bioinformatics.
[68] B. Lakowski,et al. The genetics of caloric restriction in Caenorhabditis elegans. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[69] Lucy Skrabanek,et al. PDZBase: a protein?Cprotein interaction database for PDZ-domains , 2005, Bioinform..
[70] Shi-Hua Zhang,et al. Disease-Aging Network Reveals Significant Roles of Aging Genes in Connecting Genetic Diseases , 2009, PLoS Comput. Biol..
[71] Erik L. L. Sonnhammer,et al. InParanoid 7: new algorithms and tools for eukaryotic orthology analysis , 2009, Nucleic Acids Res..
[72] H. Arlt,et al. The Rab GTPase Ypt7 is linked to retromer-mediated receptor recycling and fusion at the yeast late endosome , 2010, Journal of Cell Science.
[73] Jason Feser,et al. Chromatin structure as a mediator of aging , 2011, FEBS letters.
[74] J. Bok,et al. Requirement of spermidine for developmental transitions in Aspergillus nidulans , 2002, Molecular microbiology.
[75] M. Babst. MVB vesicle formation: ESCRT-dependent, ESCRT-independent and everything in between. , 2011, Current opinion in cell biology.
[76] J. de Magalhães,et al. GenAge: a genomic and proteomic network map of human ageing , 2004, FEBS letters.
[77] Nicola Neretti,et al. Comparative transcriptional profiling identifies takeout as a gene that regulates life span , 2010, Aging.
[78] Edith D. Wong,et al. Saccharomyces Genome Database: the genomics resource of budding yeast , 2011, Nucleic Acids Res..
[79] A. Fraser,et al. Predicting genetic modifier loci using functional gene networks. , 2010, Genome research.
[80] S. Spindler. Caloric restriction: From soup to nuts , 2010, Ageing Research Reviews.
[81] J. de Magalhães,et al. Genome-Environment Interactions That Modulate Aging: Powerful Targets for Drug Discovery , 2012, Pharmacological Reviews.
[82] M. Bard,et al. Osh6 overexpression extends the lifespan of yeast by increasing vacuole fusion , 2012, Cell cycle.
[83] Christie S. Chang,et al. The BioGRID interaction database: 2013 update , 2012, Nucleic Acids Res..
[84] Seung-Jae V. Lee,et al. Lifespan extension by conditions that inhibit translation in Caenorhabditis elegans , 2007, Aging cell.
[85] Taewon Lee,et al. Gene categories differentially expressed in C. elegans age-1 mutants of extraordinary longevity: new insights from novel data-mining procedures. , 2012, The journals of gerontology. Series A, Biological sciences and medical sciences.
[86] Matt Kaeberlein,et al. Yeast Life Span Extension by Depletion of 60S Ribosomal Subunits Is Mediated by Gcn4 , 2008, Cell.
[87] Alexandre P. Francisco,et al. YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface , 2010, Nucleic Acids Res..
[88] L. Partridge,et al. Interpreting interactions between treatments that slow aging , 2002, Aging cell.
[89] Dirk Repsilber,et al. ExprEssence - Revealing the essence of differential experimental data in the context of an interaction/regulation net-work , 2010, BMC Systems Biology.
[90] I. Jurisica,et al. Unequal evolutionary conservation of human protein interactions in interologous networks , 2007, Genome Biology.
[91] J. Kemnitz. Calorie restriction and aging in nonhuman primates. , 2011, ILAR journal.
[92] Andrea C. Carrano,et al. A conserved ubiquitination pathway determines longevity in response to diet restriction , 2009, Nature.
[93] Hans-Werner Mewes,et al. MPact: the MIPS protein interaction resource on yeast , 2005, Nucleic Acids Res..
[94] E. Marcotte,et al. An Improved, Bias-Reduced Probabilistic Functional Gene Network of Baker's Yeast, Saccharomyces cerevisiae , 2007, PloS one.
[95] Hans-Werner Mewes,et al. CORUM: the comprehensive resource of mammalian protein complexes , 2007, Nucleic Acids Res..
[96] D. Ramotar,et al. Novel role for the Saccharomyces cerevisiae oligopeptide transporter Opt2 in drug detoxification. , 2009, Biochemistry and cell biology = Biochimie et biologie cellulaire.
[97] D. Promislow. Protein networks, pleiotropy and the evolution of senescence , 2004, Proceedings of the Royal Society of London. Series B: Biological Sciences.
[98] Gary D Bader,et al. The Genetic Landscape of a Cell , 2010, Science.
[99] M. Kendall. Statistical Methods for Research Workers , 1937, Nature.
[100] Linda Partridge,et al. Extending Healthy Life Span—From Yeast to Humans , 2010, Science.
[101] Gary D. Bader,et al. The Biomolecular Interaction Network Database in PSI-MI 2.5 , 2011, Database J. Biol. Databases Curation.
[102] J. Kornhauser,et al. PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation , 2004, Proteomics.
[103] Maria Victoria Schneider,et al. MINT: a Molecular INTeraction database. , 2002, FEBS letters.
[104] Y. Kassir,et al. Glucose and Nitrogen Regulate the Switch from Histone Deacetylation to Acetylation for Expression of Early Meiosis-Specific Genes in Budding Yeast , 2004, Molecular and Cellular Biology.
[105] Daniel Wuttke,et al. A meta-analysis of caloric restriction gene expression profiles to infer common signatures and regulatory mechanisms. , 2012, Molecular bioSystems.
[106] M. Hanson,et al. Epigenetic regulation of transcription: a mechanism for inducing variations in phenotype (fetal programming) by differences in nutrition during early life? , 2007, British Journal of Nutrition.
[107] Sandhya Rani,et al. Human Protein Reference Database—2009 update , 2008, Nucleic Acids Res..
[108] Y. Dobashi,et al. Polyamine-rich food decreases age-associated pathology and mortality in aged mice , 2009, Experimental Gerontology.
[109] Corey Nislow,et al. Genome-Wide Screen in Saccharomyces cerevisiae Identifies Vacuolar Protein Sorting, Autophagy, Biosynthetic, and tRNA Methylation Genes Involved in Life Span Regulation , 2010, PLoS genetics.
[110] G. Fink,et al. Calorie restriction extends Saccharomyces cerevisiae lifespan by increasing respiration , 2002, Nature.
[111] A. J. Ferro,et al. Polyamine biosynthesis during germination of yeast ascospores , 1979, Journal of bacteriology.