The identification of transcription factor (TF) target genes is central in biology. A popular
approach is based on the location by pattern matching of potential cis-regulatory elements …

The regulation of gene expression by transcription factors (TFs) has been studied for a long
time, but no model that can accurately predict transcriptome profiles based on TF activities …

Although gene regulation in specific organs, developmental stages or conditions has been
under intense investigation in the last several decades, the full extent of the molecular …

Abstract The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN. itps. ncku. edu.
tw/) is an effective resource for predicting regulatory elements and reconstructing …

Position weight matrix (PWM) is the traditional motif model representing the transcription
factor (TF) binding sites. It proposes that the positions contribute independently to TFs …

Transcription factors (TFs) are proteins that regulate the expression of target genes by
binding to specific cis-elements in promoter regions. Transcriptional regulators (TRs) also …

The thale cress Arabidopsis thaliana is a powerful model organism for studying a wide
variety of biological processes. Recent advances in sequencing technology have resulted in …

The transcription regulatory network inside a eukaryotic cell is defined by the combinatorial
actions of transcription factors (TFs). However, TF binding studies in plants are too few in …

Motivation Both the lack or limitation of experimental data of transcription factor binding sites
(TFBS) in plants and the independent evolutions of plant TFs make computational …

EAT-UpTF (E nrichment A nalysis T ool for Up stream T ranscription F actors of a group of
plant genes) is an open-source Python script that analyzes the enrichment of upstream …