CiiiDER

CiiiDER predicts transcription factor binding sites and performs enrichment analysis to identify transcription factors that regulate sets of genes from regulatory regions such as promoters and enhancers.

Key Features:

• TFBS prediction: Performs motif-based prediction of transcription factor binding sites using experimentally verified binding site motifs.
• Enrichment analysis: Calculates over- and under-representation of transcription factors in a set of regulatory regions compared to a custom background dataset.
• Regulatory region support: Analyzes regulatory regions including promoters and enhancers.
• Data integration: Leverages genomic, transcriptomic, and epigenomic data from high-throughput technologies to inform analyses.
• Implementation: Implemented in Java to provide cross-platform execution.
• Vertebrate TF coverage: Aids identification among the more than 1,000 transcription factors known in vertebrates.

Scientific Applications:

• Candidate TF identification: Identification of candidate transcription factors regulating gene sets based on predicted TFBS and enrichment.
• Pathway regulation analysis: Elucidation of signaling pathways controlling gene expression by detecting enriched transcription factors associated with pathophysiological gene sets.
• Comparative TF analysis: Comparison of transcription factor representation between target and background regulatory region sets to find condition-associated TFs.
• Gene regulatory network studies: Support for analysis of gene regulatory networks through integration of TFBS predictions and enrichment results.

Methodology:

Uses motif-based computational prediction of transcription factor binding sites with experimentally verified motifs on input regulatory regions (e.g., promoters, enhancers), followed by enrichment analysis comparing transcription factor frequencies in the target set versus a custom background dataset.