iSMOD

iSMOD integrates image-based single-cell genomic, transcriptomic, and proteomic data—particularly DNA and RNA fluorescence in situ hybridization (FISH) and nuclear proteomics—to analyze spatial relationships among chromatin, messenger RNAs, and nuclear proteins for studies of gene regulation.

Key Features:

• Data Integration: Aggregates DNA- and RNA-FISH and nuclear proteomics data from over 20,000 published studies to enable centralized multi-omics analyses.
• Exemplar Demonstrations: Includes demonstrations for profiling multi-omics research to identify molecular targets for diseases, exploring biological phenomena through multi-omics interactions, and integrating 3D multi-omics data within a virtual cell nucleus model.
• Research Facilitation: Consolidates spatial multi-omics data to reveal previously missing components of molecular pathways and provide new mechanistic insights.
• Wide Applications: Supports analyses across genomics, transcriptomics, proteomics, disease profiling, mechanism exploration, and 3D nuclear spatial studies.

Scientific Applications:

• Disease Profiling: Identify molecular targets for diseases by integrating FISH (DNA/RNA) and nuclear proteomics spatial data.
• Mechanism Exploration: Elucidate gene regulation and molecular pathway mechanisms by examining spatial relationships among chromatin, mRNAs, and nuclear proteins.
• 3D Nuclear Modeling: Integrate and analyze 3D multi-omics data within a virtual cell nucleus model to study spatial organization.

Methodology:

Aggregation and integration of FISH (DNA/RNA) and nuclear proteomics data from published studies, profiling of multi-omics datasets, and integration of 3D multi-omics data within a virtual cell nucleus model.