Web-MCOT

Web-MCOT identifies co-occurring transcription factor binding motifs and composite elements in ChIP-seq datasets to improve annotation of cis-regulatory modules.

Key Features:

• Detection of Composite Elements: Identifies overrepresented pairs or groups of motifs that may include spacers and overlaps and can occur in any mutual orientation.
• Anchor and Partner Motifs: Aligns an Anchor motif to the target transcription factor from the ChIP-seq experiment and accepts Partner motifs provided by the user or selected from a public library.
• Significance Computation: Calculates significance of detected composite elements without relying on motif conservation and evaluates motifs across varying conservation levels for both Anchor and Partner types.
• Structural Abundance Metrics: Reports composite element abundance stratified by motif orientations, overlap types, and spacer lengths.
• Visualization Outputs: Generates histograms, sequence logos for common overlapping CE structures, and heatmaps illustrating abundance patterns related to differential motif conservation.

Scientific Applications:

• Regulatory network inference: Reveal co-occurrence patterns of motifs that inform interactions among transcription factors within regulatory networks.
• Cis-regulatory module annotation: Improve annotation of cis-regulatory modules by detecting composite elements and their structural variants.
• ChIP-seq experiment planning: Inform design and interpretation of subsequent ChIP-seq experiments by maximizing information extracted from existing datasets.

Methodology:

Aligns an Anchor motif to the ChIP-seq target TF, accepts a user-defined or public-library Partner motif, identifies overrepresented motif pairs/groups including spacers and overlaps in any orientation, computes significance of detected composite elements without requiring conservation while assessing conservation levels for Anchor and Partner, and produces histograms, logos, and heatmaps of the resulting composite element properties.