iFORM

iFORM identifies transcription factor (TF) binding sites in DNA sequences by scanning sequences with position weight matrices (PWMs) to map regulatory motifs for studies of transcriptional regulation and disease.

Key Features:

• Position Weight Matrix scanning: Scans DNA sequences using position weight matrices (PWMs) to detect TF motif matches.
• Integration of five motif discovery programs: Consolidates outputs from five classical motif discovery programs to increase detection sensitivity.
• Fisher's combined probability test: Uses Fisher's combined probability test to merge p-values from multiple motif discovery methods.
• Performance assessment: Evaluates accuracy and sensitivity using receiver operating characteristic (ROC) curves and correlation-based approaches.
• Application to large consortia datasets: Has been applied to datasets from the ENCODE Project and the NIH Roadmap Epigenomics Project to analyze functional elements across human cell and tissue types.
• Deposited TF binding sites: TF binding sites identified are deposited in the Gene Expression Omnibus (GEO) under accession GSE53962.

Scientific Applications:

• TF binding site mapping: Precise mapping of TF binding sites to support analysis of transcriptional regulatory networks.
• Functional element characterization: Characterization of roles of functional elements across human cell and tissue types using ENCODE and NIH Roadmap data.
• Genomics and epigenetics research: Support for studies linking TF binding patterns to gene regulation and disease mechanisms.

Methodology:

Scans DNA sequences with PWMs, integrates outputs from five classical motif discovery programs, combines p-values using Fisher's combined probability test, and assesses performance via ROC curves and correlation-based approaches.