Additional file 1 of Tissue-specific atlas of trans-models for gene regulation elucidates complex regulation patterns

Supplementary Material 1

L'Auto-vélo : automobilisme, cyclisme, athlétisme, yachting, aérostation, escrime, hippisme / dir. Henri Desgranges

28 juillet 19321932/07/28 (A33,N11548)

Different stresses affect telomere length via different genes.

<p>The effect of ethanol, caffeine and high temperature on telomere length was tested on strains carrying individual gene deletions/hypomorphic mutations. Each mutant was grown under the relevant stress for 100 generations and its telomere length was measured using Southern blot analysis. <b>A–C</b>. The X-axis shows the initial length of each mutant and the Y-axis shows the elongation or shortening after 100 generations. Each strain analyzed is represented by a circle (wt in green). A strong correlation (demarked by a red line; ±5% SD) was seen between the initial length and the effect of the stress. <b>A</b>. Ethanol. <b>B</b>. Caffeine. <b>C</b>. 37°C. <b>D</b>. Each bar represents the ratio between the initial telomere length and the elongation after 100 generations in ethanol. Very short <i>tlm</i> mutants (below 200 nt long) could be clearly separated into two groups: mutants of the Tel1 pathway (<i>tel1Δ</i>, <i>mre11Δ</i>, <i>rad50Δ</i>, <i>xrs2Δ</i>) were highly responsive to ethanol stress, while mutants of the NMD (<i>nam7Δ</i>, <i>upf3Δ</i>, <i>nmd2Δ</i>) and Ku (<i>yku70Δ</i>, <i>yku80Δ</i>) pathways show little telomeric elongation under ethanol stress.</p

Kinetics of telomere length change after exposure to environmental stresses.

<p>Wild-type yeast strain BY4741 was grown in the presence of various stresses and then released. <b>A</b>. YEPD containing 5% ethanol (released to YEPD after 300 generations). <b>B</b>. YEPD+8 mM caffeine (released to YEPD after 90 generations). <b>C</b>. YEPD at 37°C (released back to 30°C after 100 generations).</p

T2 UDIPs t-maps

These are 128 UDIPs t-maps derived from T2-FLAIR through PerDI. UDIPs learn representation all over the brain. To identify regions of the brain represented by a specific UDIP, we develop Perturbation-based Decoder Interpretation (PerDI). The regions of the brain of that specific UDIP can then be associated with the SNPs identified by the same UDIP. We add one standard deviation (σ) as noise to the specific UDIP we are trying to interpret while keeping other UDIPs constant. The original decoder is used to reconstruct images from the perturbed UDIPs (perturbed reconstructed images). The process is repeated for 500 MRIs from 500 randomly selected individuals for improving the robustness of the result. Paired t-test is carried out between the 500 original reconstructed images and 500 perturbed reconstructed images. Absolute t-map is obtained. Gaussian filter (σ=3) is used to smoothen the final t-map. Using Gaussian blur reduces the impact of not using non-linear registration.</p