ABSTRACT

Identification of enriched regulatory factors among the regulatory regions of co-expressed or differentially expressed genes facilitates the identification of regulators involved in the expression of those genes. We have developed a computational pipeline which can identify the enriched transcription factors (in the promoter region) and miRNAs (in the 3’UTR region) in the given gene list. Experimentally identified transcription factor (TF) and miRNA targets are integrated to identify the regulatory factors and their targets that likely to play a role in the biology under study. We utilize, TF binding sites (from JASPAR, TRANSFAC & HOCOMOCO) and miRNA seed sequence (from miRBase) to calculate enrichment using the original (TFBS enrichment) and modified version (miRNA enrichment) of the Clover algorithm (Frith et al., 2004). To enhance the predictions further, we integrate the experimental associated datasets obtained from ENCODE (J Wang et al., 2012) and ChEA (Lachmann A et al., 2010) for TF targets and for miRNA targets we utilized miRTarBase (Sheng-Da Hsu et al., 2011) and miRecords (Xiao F et al., 2009).

When you use the results from this pipeline please cite:

V. Chandran, S. Azariah, D. H. Geschwind.: A computational pipe-line protocol for identifying regulatory factor enrichment (In preparation). Until published this pipeline should be used collaboratively. Website interface developed and hosted by Yining and Giovanni Coppola.