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Fig. 3 | BMC Genomics

Fig. 3

From: Comprehensive investigation of the gene expression system regulated by an Aspergillus oryzae transcription factor XlnR using integrated mining of gSELEX-Seq and microarray data

Fig. 3

Scatter plots showing correlation between various factors related to AoXlnR binding and differential expression levels. (a) Correlations between parameters obtained from gSELEX-Seq analysis and the differential expression levels in the 51 genes in the intersecting set in Fig. 1. Detected Peak Fold Enrichment, fold enrichment detected in the promoter regions of the 51 genes by gSELEX-Seq analysis; Detected Peak Position, the summit of the peaks detected in the promoter regions of the 51 genes by gSELEX-Seq analysis. Here, the position of the base just before the start codon is set to 1000. (b) Correlations between the numbers of AoXlnR-binding sites and the differential expression levels in the 72 DEGs [22]. GGCTGA, the number of 5′-GGCTGA-3′ sites; GGCTAA, the number of 5′-GGCTAA-3′ sites; GGCTAG, the number of 5′-GGCTAG-3′ sites; Total Number of Binding Sites, the total number of 5′-GGCTAG-3′, 5′-GGCTAA-3′ and 5′-GGCTGA-3′ sites; CGGNTAAW, the number of 5′- CGGNTAAW-3′ sites; TTAGSCTAA, the number of 5′-TTAGSCTAA-3′ sites. (c) Correlations between the coexistence of two kinds of canonical AoXlnR-binding motifs and the differential expression levels of the 72 DEGs. GGCTGA∩GGCTAA, the set intersection of promoter regions containing 5′-GGCTGA-3′ and 5′-GGCTAA-3′; GGCTAA∩GGCTAG, the set intersection of promoter regions containing 5′-GGCTAA-3′ and 5′-GGCTAG-3′; GGCTGA∩GGCTAG, the set intersection of promoter regions containing 5′-GGCTGA-3′ and 5′-GGCTAG-3′. The promoter regions containing both of the two kinds of motifs are categorized in T wheres the others are in F. The vertical axis in each scattergram shows the differential expression levels. Values in parentheses show the Spearman’s rank correlation coefficient with the differential expression levels

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