Methodology article
Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis
-
* Corresponding author: Joshua M Akey akeyj@u.washington.edu
1 Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Seattle, WA, 98195, USA
2 Department of Biostatistics, University of Washington, 1705 NE Pacific Street, Seattle, WA, 98195, USA
BMC Bioinformatics 2008, 9:244 doi:10.1186/1471-2105-9-244
Published: 20 May 2008Additional files
Additional file 1:
Linkage hotspot information. List of all significant genes from the single trait linkage analyses where the linkage results were binned into 20 kilobase bins across each chromosome to identify "hotspots". Using a poisson distribution, the probability of having 20 linkages present in a bin by chance is < 2.1E-4. 17 such "hotspots" were identified.
Format: TXT Size: 23KB Download file
Additional file 2:
Eigentrait composition. List of all transcripts that are significantly correlated with each of the top 20 eigentraits.
Format: TXT Size: 27KB Download file
Additional file 3:
ICAtrait composition. List of all genes that are significantly correlated with each of the top 20 ICAtraits.
Format: TXT Size: 22KB Download file
Additional file 4:
Multipoint linkage profile of Eigentrait – 4 and Eigentrait – 19. The multipoint linkage profile of Eigentrait 4 and 19 are plotted in the upper and lower half of the figure, respectively. In each case, only a section of the chromosome spanning the maximum LOD score is plotted with the 1 LOD support interval denoted by solid black bar. For Eigentrait 4, the position of the tandem array of three genes that are involved in asparaginase catabolism are represented by blue vertical bars. Similarly, for Eigentrait 19 the position of the tandem array of sodium ion efflux genes are denoted by blue vertical bars.
Format: TIFF Size: 10.9MB Download file
Additional file 5:
Multipoint linkage profile of ICAtrait – 7 and ICAtrait – 9. Similar to S4, the multipoint linkage profile spanning the maximum LOD score for ICAtrait 7 and 9 are plotted in the upper and lower half of the figure, respectively. In both plots, the position of a subset of genes that lie in the 1 LOD support interval represented by solid black bar is shown. For ICAtrait 7, only YERCTy1-1, a retrotransposon, shows significantly correlation while for ICAtrait 9, only ZAP1 shows a significant correlation with the ICAtrait.
Format: TIFF Size: 10.7MB Download file
Additional file 6:
Multiple sequence alignment of YJL056C. CLUSTALW was used to create a sequence alignment of the protein encoded by YJL056C/ZAP1 from two strains of Saccharomyces cerevisiae and two related species Saccharomyces mikatae and Saccharomyces paradoxus. The alignment output was then run through BOXSHADE to generate a colored output based on the conservation and degree of identity of the aligned residues. Nineteen SNPs were detected in the protein alignment, of which 10 were non-synonymous.
Format: TIFF Size: 3.7MB Download file
Additional file 7:
Differential expression of two Eigentraits showing cis-linkage. The top panel represents Eigentrait 4 and the bottom panel represents Eigentrait 19. Scatter plot of eigentrait values on the y-axis against the parental genotypes at the marker with the highest linkage statistics on the x-axis shows marked differential expression in the segregants (p < 0.0001).
Format: PDF Size: 16KB Download file
This file can be viewed with: Adobe Acrobat Reader