Research article
Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast
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* Corresponding author: Simon J Hubbard simon.hubbard@manchester.ac.uk
1 Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
2 School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
3 Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
BMC Genomics 2009, 10:7 doi:10.1186/1471-2164-10-7
Published: 7 January 2009Additional files
Additional file 1:
Comparison of UTR lengths in two datasets. Comparison of 5' and 3' UTR lengths from the dataset generated for this study with that of David et al's tiling arrat study [23].
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Additional file 2:
Observed and expected frequencies of uORFs in mapped 5' UTRs. This file contains a figure showing the distribution of observed and expected frequencies of uORFs in 5'UTRs
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Additional file 3:
Observed reading frame distribution of uORFs in mapped 5' UTR. Figure showing the relative frequency of uORF open reading frames with respect to the main ORF reading frame. For those uORFs wholly contained within the 5' UTR there is clearly no bias towards any frame suggesting that there are no likely missannotations of the true ORF start or independent ORFs.
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Additional file 4:
Summary statistics for long uORFs greater than 35 amino acids in length. This Excel format file file contains statistics for individual uORFs (one per line) whose length exceeds 35 amino acids. For each uORF, the ORF, ORF length, 5' UTR length, frame and start position are indicated, as well as the total number of uORFs contained in the given 5' UTR.
Format: XLS Size: 44KB Download file
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Additional file 5:
GoStat over-representation statistics for translationally controlled gene subsets under H2O2 stress. This Figure shows similar over-representation statistics as shown in Figure 5 but for both the butanol stress conditions.
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Additional file 6:
UTR length distributions for different gene sets under stress conditions using tiling array definitions of TSS. Length distributions equivalent to those shown in Figure 6 but using the subset of genes defined by tiling array studies which overlap the differential regulation data sets generated for yeast stress responses used in this study.
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Additional file 7:
Full Statistics for conserved 61 uORF sub set. This spreadsheet provides the full data for conserved uORFs, listing the parent gene, position of uORF in the UTR, PhastCons score, conservation Z-score, and number of aligned species in which a uORF is directly conserved.
Format: XLS Size: 58KB Download file
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Additional file 8:
Analyses of 5' UTR secondary structures using RanFold. Tabulated statistics of Randfold calculations are shown for the 5 most likely secondary structure containing UTRs along with potential secondary structure diagrams.
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Additional file 9:
Complete statistics for all uORFs and UTRs used in the study. This details all the uORFs from all UTRs used in this study, providing locations, parent genes, and sequence information, as well as the details on all the 5' UTRs used, and their start sites with respect to each named yeast gene.
Format: XLS Size: 1.5MB Download file
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