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Fig. 4 | BMC Genomics

Fig. 4

From: Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information

Fig. 4

Comparative analysis on the two types of TEPs. a Distinct U-rich intrinsic terminator motif. The motif was detected from the 41 nt upstream to 20 nt downstream sequences of TEP using the MEME suite. b Nucleotide enrichment analysis of the two types of TEPs. Nucleotide enrichment was calculated by dividing the frequency of each nucleotide of the TEP set with the frequency of the same nucleotide of random intergenic positions. c ΔG distribution of TEPs. The ΔG was calculated from 41 nt upstream sequences, including TEPs or randomly selected intergenic positions, using RNAfold with the temperature parameter of 30 °C. d RNA-Seq read density near the two types of TEPs. e The distribution of the 3′-UTR length. The 3′-UTR length was calculated as the distance from primary TEP to its associated CDS. f Differences in expression of genes exploiting two different types of TEPs. RPKM was calculated for each biological replicate and the average value was used. Only 5th and 95th percentile outliers were represented with dots. *P-value < 0.001 (Wilcoxon rank sum test, two-sided) g Base interaction frequency comparison of U-rich and U-lacking TEPs. The RNA structure was predicted with 101 nt upstream sequence of each TEP or randomly selected position using RNAfold with the temperature parameter of 30 °C and the interaction frequency of each set of two positions was calculated by dividing the number of observed interactions in the predicted RNA structure with the number of total entries. h Base interaction frequency comparison of U-rich and U-lacking TEPs

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