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m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence

Jüri Reimand1,2,3*, Anu Aun4, Jaak Vilo2, Juan M Vaquerizas1, Juhan Sedman4 and Nicholas M Luscombe1,5*

1 EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK

2 University of Tartu, Institute of Computer Science, Liivi 2, Tartu 50409, Estonia

3 Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada

4 University of Tartu, Institute of Molecular and Cell Biology, Riia 23, Tartu 51010, Estonia

5 EMBL-Heidelberg Gene Expression Unit, Meyerhofstrasse 1, Heidelberg D-69117, Germany

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Genome Biology 2012, 13:R55 doi:10.1186/gb-2012-13-6-r55

Published: 21 June 2012

Additional files

Additional file 1:

Supplementary Online Material. Additional file 1 contains Supplementary Methods, Figures s1-s5 and Tables s1-s3.

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Additional file 2:

Additional file 2contains normalized colony forming unit measurements for tested ΔTF strains, wildtypes and controls of the six-week quiescence time-course.

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Additional file 3:

Additional file 3contains normalized colony forming unit measurements for tested ΔTF strains, wildtypes and controls of the 72-hour quiescence time-course. Abbreviations. ΔTF - transcription factor knockout strain; AUC - area under curve; CFU - colony forming units; ChIP - chromatin immunoprecipitation; DNA - deoxyribonucleic acid; FDR - false discovery rate; G0 - stationary phase, quiescence; G1 - gap-1; G2 - gap-2; GO - gene ontology; KEGG - Kyoto encyclopedia of genes and genomes; LR - likelihood ratio; M - mitosis; MBF - mlu1-box binding factor; NADPH - nicotinamide adenine dinucleotide phosphate; NDTFBS - nucleosome-depleted transcription factor binding site; OD - optical density; PKA - protein kinase A; PKC - protein kinase C; S - synthesis; SAGA - Spt-Ada-Gcn5-acetyltransferase; SBF - SCB binding factor; TF - transcription factor; TFBS - transcription factor binding site; TOR - target of rapamycin; WT+ - super-wildtype; YPD - yeast extract peptone dextrose; YPG - yeast extract peptone glycerol.

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