MIGNON

MIGNON integrates RNA-Seq genomic and transcriptomic data into mechanistic models of signaling pathway activities.

Key Features:

• Raw read processing: Efficient management of raw RNA-Seq reads for downstream analysis.
• Gene expression quantification: Estimation of gene expression levels from RNA-Seq data.
• Variant detection in transcripts: Identification of genomic variants within transcripts.
• Multi-omic integration: Integration of transcriptomic and genomic data through mechanistic models of signaling pathway activities.
• Signaling circuit activity estimation: Estimation of signaling circuit activity to profile functional cell activity.
• End-to-end workflow: End-to-end processing from raw reads to signaling circuit activity estimates using state-of-the-art tools.

Scientific Applications:

• Mechanistic interpretation: Detailed biological interpretation of RNA-Seq results within signaling networks.
• Functional profiling: Comprehensive functional profiling of cellular activity via signaling circuit activities.
• Variant contextualization: Contextual analysis of genomic variants within transcripts and their potential impact on signaling.
• Systems biology and genomics: Applications in genomics and systems biology to study mechanistic underpinnings of cellular processes and signaling pathways.

Methodology:

Computational steps include management of raw sequencing reads, estimation of gene expression levels, identification of genomic variants within transcripts, and integration of transcriptomic and genomic data into mechanistic models to estimate signaling circuit activities using state-of-the-art tools.