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. Author manuscript; available in PMC: 2019 Apr 22.
Published in final edited form as: Dev Biol. 2018 Jan 31;435(2):150–161. doi: 10.1016/j.ydbio.2017.12.023

Fig. 3. Pairwise comparisons of transcriptomes of the four strains: wild-type, elt-2(−), elt-7(−), and elt-7(−); elt-2(−).

Fig. 3.

A. Pairwise comparisons between transcriptome profiles (MA plots) of four strains of L1 worms: N2 (wild type), elt-2(−), elt-7(−), and elt-7(−); elt-2(−). The log2-fold change of gene expression (y-axis) between the two labeled samples is plotted against the mean intensity (logarithmic scale) for a given gene (x-axis). Differentially expressed genes for each comparison are shown in red (criteria for differential expression: total read counts > 10, BH-adjusted Wald Test p-value < 0.1, and log2-fold change > 0.8). The total number of genes in each plot is 16,708. Genes that were down-regulated in elt-7(−) compared to wild type would be identified within the green ellipse. The orange ellipse contains genes down-regulated in elt-2(−) compared to wild type. The blue ellipse contains genes down-regulated in the elt-7(−); elt-2(−) double mutant compared to the elt-2(−) single mutant. Up-regulated and down-regulated genes in key differentially expressed subsets were searched for over-represented categories using the WORMEXP tool (Yang et al., 2016).

B. Promoter sequences from genes categorized in Fig. 3A as “down-regulated in elt-2(−) versus wt” (n = 619, orange ellipse) or “down-regulated in elt-7(−);elt-2(−) versus elt-2(−)” (n = 647, blue ellipse) were searched for enriched binding motifs using HOMER, (Heinz et al., 2010). The top hit for each search is shown; the two top-scoring motifs are highly similar to each other and to the extended TGATAA motif previously found to be associated with intestine-specific genes (McGhee et al., 2007; McGhee et al., 2009).

C. The number of incidences of the extended TGATAA motif discovered in B within promoters of each gene set is given. Motifs occurred either once, twice, or three times per promoter as tabulated by the stacked barplot.

D. The locations of TGATAA motifs discovered in B were identified within promoters of genes “down-regulated in elt-2(−) versus wt” or “down-regulated in elt-7(−);elt-2(−) versus elt-2(−)”. A histogram (10 bp bins) of the motif locations in relation to the transcriptional start site (TSS) is shown.