Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions

(Downloading may take up to 30 seconds. If the slide opens in your browser, select File -> Save As to save it.)

Click on image to view larger version.

Figure 3.
Figure 3.

Motif discovery results from cisTargetX. (A) Motifs and candidate TFs found by cisTargetX, using different gene set sizes as input (top 75, 100, 245, and 545 genes from the OS-based integrative ranking). (NES) Normalized enrichment score from cisTargetX; (Motif Rank) rank of the motif from a collection of 3731 motifs used by cisTargetX. (B) Gene regulatory network showing the predicted regulatory interactions of Glass, SCRT, SU(H), SOXN, and EY, obtained from the cisTargetX analyses on the top100 and the top245 eye-specific genes. (Dashed arrows) Glass target gene predictions that are found to be up-regulated in the glass mutant by RNA-seq.

This Article

  1. Published in Advance October 15, 2012, doi: 10.1101/gr.140426.112 Genome Res. 23: 74-88

Preprint Server



Current Issue

  1. January 2026, 36 (1)
  1. Current Issue
  1. Alert me to new issues of Genome Research