PreDREM

PreDREM provides a catalog of predicted transcription factor binding motifs and motif modules derived from DNase I hypersensitive sites across diverse human samples to support analysis of regulatory elements and transcriptional regulation.

Key Features:

• Extensive motif predictions: Contains between 845 and 1325 predicted motifs per sample, totaling 2684 non-redundant motifs across all samples.
• High similarity with known motifs: Over 84% of PreDREM predicted motifs show similarity to known motifs, and 54-76% of known motifs are similar to PreDREM predictions.
• Motif modules and cofactor motifs: Stores between 43,663 and 201,288 motif modules per sample, including cofactor motifs for each predicted motif, with on average 84% of motif pairs corresponding to known interacting transcription factor pairs represented in predicted modules.
• Motif instances across genome and tissues: Records occurrences of motifs and motif modules in genomic regions and across different tissues and cell types.

Scientific Applications:

• Transcriptional dynamics and regulatory networks: Enables investigation of transcriptional regulation and TF interactions in human cells and tissues.
• Cell- and tissue-specific regulatory element identification: Supports discovery of cell- and tissue-specific regulatory elements for genomics and molecular biology studies.
• Personalized medicine research: Provides motif and module data relevant to studies of regulatory variation with potential implications for personalized medicine.

Methodology:

Motifs and motif modules were predicted by analyzing DNase I hypersensitive sites across a diverse array of human samples.