TFM-Explorer

TFM-Explorer identifies putative transcription factor binding sites (TFBS) and overrepresented binding motifs in upstream regulatory sequences to support analysis of transcriptional regulation across human, mouse, rat, chicken, and Drosophila.

Key Features:

• Target Organisms: Supported organisms include human, mouse, rat, chicken, and Drosophila.
• Identification of Binding Sites: Detects local regions within upstream regulatory sequences that exhibit an overrepresentation of transcription factor binding sites and motifs.
• Visualization of TFBS: Provides visualization of selected binding sites mapped onto genomic sequences.
• Cis-Regulatory Module Selection: Detects and selects cis-regulatory modules, i.e., regions of non-coding DNA that regulate nearby genes.

Scientific Applications:

• Transcriptional regulation analysis: Identification of potential TFBS to elucidate mechanisms of transcription regulation.
• Regulatory interaction inference: Inference of regulatory interactions and prediction of how changes in TFBS may affect gene expression.
• Comparative and evolutionary studies: Analysis of regulatory elements across multiple species for developmental biology, molecular genetics, and evolutionary research.

Methodology:

Computational detection of overrepresented binding motifs within upstream regulatory sequences by focusing on regions with a high density of potential TFBS.