ViTraM

ViTraM visualizes overlapping transcriptional modules within gene expression datasets, representing genes, co-expression patterns, regulatory elements, motifs, and putative regulators.

Key Features:

• Visualization of overlapping transcriptional modules: Represents genes and their co-expression patterns across experiments and shows overlapping modules together with regulatory elements and motifs.
• Integration of regulators and motifs: Integrates information about regulators and regulatory motifs to link observed gene co-expression to putative regulatory influences.
• Interpretation of module-detection outputs: Maps outputs from module detection tools to modules, regulators, and motifs to aid biological interpretation.

Scientific Applications:

• Systems biology and genomics: Aids interpretation of transcriptomic datasets by clarifying module structure and associated regulatory components.
• Identification and analysis of transcriptional modules: Facilitates identification and analysis of groups of genes co-expressed under specific conditions or regulatory influences.
• Gene regulatory network analysis: Supports hypothesis generation about gene regulation by linking co-expression patterns to regulatory elements and motifs.

Methodology:

Integrates gene expression data from multiple experiments and leverages co-expression patterns together with information on regulatory elements and motifs to construct representations of overlapping transcriptional modules.