T-WEoN

T-WEoN generates context-specific weighted gene regulatory networks (GRNs) for Drosophila melanogaster to model transcription factor and non-coding RNA regulation using epigenomic and gene expression evidence.

Key Features:

• Context-specific GRNs: Constructs GRNs that represent regulatory interactions within specific biological contexts in Drosophila melanogaster.
• Weighted prioritization: Applies a weighted methodology to refine and prioritize regulatory interactions based on supporting evidence.
• Knowledge-based filters: Removes unlikely regulations using independent filter modules that consider DNA methylation, chromatin accessibility, histone modifications, and gene expression.
• Reference regulatory network: Starts from a reference network containing known gene regulations in Drosophila melanogaster as the input set of candidate interactions.
• Heuristic rules: Uses heuristic rules derived from the literature on Drosophila gene regulation to guide filtering and weighting decisions.

Scientific Applications:

• Contextual gene regulation analysis: Reconstruction of GRNs for studying regulatory dynamics in specific biological contexts.
• Developmental biology: Investigation of gene regulation during developmental processes, including early development in Drosophila melanogaster.
• Epigenetics and transcriptional regulation: Integration of epigenomic signals and expression data to study transcription factor and non-coding RNA regulatory roles.

Methodology:

Begin from a reference network of known Drosophila regulations and apply independent knowledge-based filter modules assessing DNA methylation, chromatin accessibility, histone modifications and gene expression, then weight and prioritize interactions using heuristic rules from the literature.