AnnoMiner

AnnoMiner annotates genomic peaks and integrates transcription factor binding and epigenetic occupancy data to predict transcriptional regulators and characterize regulatory interactions.

Key Features:

• Annotation of User-Provided Peaks: Annotates user-provided peaks with relevant gene features to define the genomic context of these regions.
• Integration of Binding Data: Integrates genome binding data from two distinct transcriptional regulators together with associated gene features to identify potential regulatory interactions.
• Exploration of Transcriptional Deregulation: Explores transcriptional deregulation of up to 10 genes located near a user-provided peak.
• Enrichment Analysis: Performs enrichment analysis for transcription factors or histone marks using ENCODE public datasets across human, mouse, Drosophila, and C. elegans without requiring process-specific chromatin data.

Scientific Applications:

• Gene Regulation Studies: Supports analysis of the interplay between transcription factors and epigenetic modifications in gene regulation.
• Prediction of Transcriptional Regulators: Predicts candidate transcriptional regulators involved in specific biological processes or diseases.
• Regulatory Network Analysis Across Organisms: Integrates and analyzes datasets from multiple sources to study complex regulatory networks in human, mouse, Drosophila, and C. elegans.

Methodology:

Annotates user-provided peaks with gene features; integrates binding data from up to two transcriptional regulators with associated gene features; performs enrichment analysis for transcription factors and histone marks using ENCODE public datasets; and examines transcriptional deregulation of up to 10 genes proximal to a peak.