I am looking to do transcription factor (TF) and miRNA enrichment analysis.
I have a list of DE genes from RNAseq experiment and I am wanting to do transcription factor / miRNA enrichment analysis to ask, which of these DE genes are targets to transcription factors / miRNAs?
Specifically looking for recently published articles that have done such analysis either on RNAseq or microarray data.
I have tried GATHER tool to use TRANSFAC for transcription factor that performs statistical analysis computing Bayes factor. http://gather.genome.duke.edu
For miRNA enrichment analysis, I have tried doing enrichment analysis (fischer exact test) using predicted miRNA targets listed in TragetScanHuman database (http://www.targetscan.org/vert_70/)
But would be great to see any articles that are recently published that have done TF and miRNA enrichment analysis, to follow and validate my study.
Please share any info.