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Fig. 2 | BMC Genomics

Fig. 2

From: Nearby transposable elements impact plant stress gene regulatory networks: a meta-analysis in A. thaliana and S. lycopersicum

Fig. 2

Fold enrichment of differentially expressed genes near specific TE superfamilies (TEFs) upon stress for A) A. thaliana and B) S. lycopersicum. The Chi-squared test was conducted separately for up- and downregulated genes with TEFs upstream, downstream or within introns. The intensity from yellow to red reflects the enrichment score with values between 1 and 4.5, as compared to all differentially expressed genes near all TEFs in that specific genomic positioning and stress condition. The significance of enrichment is indicated within the tiles: * = FDR adjusted p-value < 0.05, ** = FDR adjusted p-value < 0.01, *** = FDR adjusted p-value < 0.001. We additionally filtered out significant results for which the observed number of differentially expressed genes near a TEF was less than 5 and the expected number was less than 2. Only TEFs, stress conditions and genomic positionings for which a valid enrichment was found are shown. A. thaliana: heat_B = 1 h incubation at 44 °C - leaves, paraquat_A = spray with 25 μM paraquat, photorespiratory_mutant_B = SHORT_ROOT (shr) mutant – 24 h photorespiratory stress, proteasome_inh_A = 100 μM proteasome inhibitor MG132, proteasome_mutant_B = rpn-10 mutant – RPN10 is a subunit of the 26S proteasome, salt_heat_A = 150 mM NaCl for 15 days + 1 h incubation at 44 °C – leaves. S. lycopersicum: hormone_B = 48 h after treatment with ACC (ethylene precursor), infection_necrotrophic_A = infection by Colletotrichum gloeosporioides - leaves, infection_necrotrophic_C = infection by Pseudomonas syringae pv. tomato DC3000 - leaves, infection_viral_A = infection by Tomato yellow leaf curl virus - leaves, light_A = constant shade – shoot apical meristem / leaf primordia, light_B = constant sun – shoot apical meristem / leaf primordia, light_C = sun to shade – shoot apical meristem / leaf primordia, light_D = constant sun - shoot apical meristem / leaf primordia, stress_tolerance_A = male-sterile, stress tolerant mutant

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