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Results: 5

1.
Figure 4

Figure 4. Validation of two causative quantitative trait genes. From: Genetic Analysis of Variation in Transcription Factor Binding in Yeast.

a, ChIP-Seq signal tracks showing Ste12 binding of wild-type, amn1Δ, and ics2Δ parent strains, corresponding to variable binding trait B12S708456E710089. b, ChIP-Seq signal tracks showing Ste12 binding of wild-type, flo8Δ, and gle2Δ parent strains, corresponding to variable binding traits B1S202520E202741. ics2Δ and gle2Δ strains have no effect on binding. c, d, Comparison of Ste12 binding across 10 and 5 associated variable binding regions in WT and knockout strains rspectively. Error bar represents s.e.m. Additional results are in Fig. S7.

Wei Zheng, et al. Nature. ;464(7292):1187-1191.
2.
Figure 5

Figure 5. Ste12 binding significantly correlates with downstream gene expression. From: Genetic Analysis of Variation in Transcription Factor Binding in Yeast.

a, Examples of high correlation between binding variation and gene expression variation. Columns in the heat maps are ordered by the genotype of markers with highest association to the Ste12 binding traits. 10 additional clusters are shown in Fig. S8. b, Histogram (blue) and background histogram (yellow) of correlation coefficients between Ste12 binding and expression of nearest gene. Regions with absolute Pearson's correlation |r| > 0.335 are shaded.

Wei Zheng, et al. Nature. ;464(7292):1187-1191.
3.
Figure 3

Figure 3. Motif analysis of cis-variable binding regions. From: Genetic Analysis of Variation in Transcription Factor Binding in Yeast.

a-c, Ste12 binding signals (NormDiff scores) against the genotypes of Ste12 motif, Yhp1 motif and Yap5 motif in two target loci. Each dot plot shows strains with S96 inheritance (red dot), strains with HS959 inheritance (green dot). The mean and standard error of each group, and Ste12 consensus sequence are also shown (Red, S96; green, HS959). d-f, ChIP-Seq signal tracks of the depicted regions in dot plots a-c. The color in each track indicates genotype background in the depicted regions: red (S96), green (HS959). Additional examples are in Fig. S5.

Wei Zheng, et al. Nature. ;464(7292):1187-1191.
4.
Figure 2

Figure 2. Whole-genome linkage analysis of variable Ste12 binding traits. From: Genetic Analysis of Variation in Transcription Factor Binding in Yeast.

a, Chromosomal position of significantly associated binding traits (X axis) relative to markers (Y axis) passing threshold (FDR = 0.01). See Fig. S4 for results with different thresholds. Trans-QTL regions validated by the clustering method are shown on the right. Two experimentally validated causative genes (AMN1 and FLO8) underlying the trans-QTLs are also shown. b, Histogram of markers significantly associated with multiple binding traits. c, Effect size (explained variance in quantitative traits) of cis-QTLs < 10kb to the trait (black), cis-QTLs > 10kb to the trait (red), and trans-QTLs (green).

Wei Zheng, et al. Nature. ;464(7292):1187-1191.
5.
Figure 1

Figure 1. Extensive Ste12 binding variations among S288c × JM789 derivatives. From: Genetic Analysis of Variation in Transcription Factor Binding in Yeast.

a, ChIP-Seq signal tracks showing Ste12 binding sites that segregate in a Mendelian (Left) or transgressive fashion (Middle and Right). The color indicates genotype background in the depicted regions: red (S96), green (HS959). Asterisks indicate peaks of interest. b, Overall genomic positions of Ste12 binding regions in S96 or HS959 under vegetative growth condition (green), pheromone treatment (blue), and most variable binding regions across segregants (red). c, Overlap of target genes (from 6644 annotated genes) between parent strains with pheromone treatment. Enriched GO categories are listed.

Wei Zheng, et al. Nature. ;464(7292):1187-1191.

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