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Description
cisTargetX enables to dissect a set of co-expressed genes into direct target genes of different transcription factor motifs. The analysis is based on gene ranking and recovery curves (See Figure), and works similarly to the Lever method on vertebrate genomes.
Some of the key features of cisTargetX are:
- over-represented motifs are predicted in the set of co-expressed genes, using entire intergenic and intronic sequences
- 12 Drosophila species are used
- For motif scoring, the Cluster-Buster or SWAN algorithms are used; kindly provided by Martin Frith and Saurabh Sinha respectively.
- 1981 position weight matrices (PWM) are used, from various sources such as Transfac, Jaspar, FlyReg, and motif collections from Xie et al., Stark et al., Elemento et al., and Down et al.
- For cross-species comparisons, the cluster-buster scores of orthologous regions are used independently (no requirement of base pair alignment of D. melanogaster motifs), as described previously here.
- For significant motifs determines the optimal subset of genes that are predicted as direct targets
- For the predicted direct targets, cisTargetX presents the predicted enhancer and binding site locations in the UCSC Genome Browser.
Citation
Stein Aerts, Xiao-Jiang Quan, Annelies Claeys, Marina Naval Sanchez, Phillip Tate, Jiekun Yan, and Bassem Hassan (2010). Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in Drosophila uncovers a regulatory basis for sensory specificationPLoS Biology 2010 Jul 27;8(7):e1000435.
Example sets used in Aerts et al., PLoS Biology 2010
- Dorsal downstream genes (Stathopoulos et al 2002) results
- Ato downstream genes (GOF), upregulated genes results
- Ato downstream genes (LOF), downregulated genes results
- Sens downstream genes (GOF), downregulated genes results
- Sens downstream genes (GOF), upregulated genes results
- Genes expressed in proneural clusters (Reeves & Posakony, Dev. Cell 2005) results
- Serpent GOF (Stramer et al 2008) results
- Ey GOF (Ato independent) (Ostrin et al 2006) results
- Biniou LOF + ChIP (Jakobsen et al 2007) results
- MEF2 downstream genes from LOF microarray data (Sandmann et al 2006) (result)
- Pointed GOF (Pointed Leading Edge PLE) (Philippakis et al 2006) results
- GO:0007350 (blastoderm segmentation) results