MEPP

MEPP quantifies motif enrichment in a position-dependent manner to characterize positional dependencies of regulatory DNA motifs relative to biological landmarks such as transcription start sites (TSS) and transcription factor (TF) binding motifs.

Key Features:

• Positional Enrichment Profiling: Generates a detailed positional profile of motif enrichment relative to landmarks such as transcription start sites (TSS) and other transcription factor (TF) binding motifs.
• Distance-Dependent Analysis: Analyzes spatial relationships between motifs and anchor points to reveal how motif positioning influences TF binding and chromatin state.
• Bias Correction: Corrects for lower-order nucleotide biases to distinguish genuine enrichment from sequence-composition artifacts.

Scientific Applications:

• Transcription initiation and TF binding analysis: Identifies sequence positions where motif presence correlates with transcriptional initiation or transcription factor binding.
• Interpretation of transcriptional activity and chromatin structure data: Aids interpretation of experimental data on transcriptional activity and chromatin structure by highlighting positional dependencies of binding site function.
• Regulatory mechanism exploration and hypothesis generation: Supports hypothesis generation and exploration of positional regulatory mechanisms involving TF interactions.

Methodology:

Integrates positional information into motif enrichment analysis to assess motif presence within DNA sequences and infer functional dependencies from the spatial arrangement of motifs relative to biologically meaningful features.