RNAinteract

RNAinteract maps genetic interactions from RNAi perturbations in tissue culture cells to infer gene function and cellular network connectivity.

Key Features:

• High-Throughput Interaction Mapping: Performs over 70,000 pairwise RNAi perturbations in tissue culture cells and identifies more than 600 interactions affecting quantitative phenotypes in Drosophila melanogaster cells.
• Quantitative Phenotype Analysis: Processes cell number, cell area, and fluorescence intensity from multi-well plate assays to construct matrices of quantitative interaction profiles for gene-function inference.
• Pathway Reconstruction and Network Connectivity: Analyzes interaction matrices to reconstruct signaling pathways and identify key regulators, including conserved regulators of Ras-MAPK signaling.
• Scalability for Higher Organisms: Applies a scalable approach suitable for use in higher organisms where traditional genetic interaction mapping is challenging.
• Reporting of Interacting Gene Pairs: Provides functions to report interacting gene pairs identified from pairwise perturbation data.
• Data Visualization: Produces heatmaps and double RNAi plots to visualize interaction matrices and quantitative phenotype relationships.

Scientific Applications:

• Gene Function Inference: Infers gene functions by comparing quantitative interaction profiles across pairwise perturbations.
• Signaling Pathway Analysis: Reconstructs signaling pathways from interaction matrices to elucidate molecular mechanisms.
• Network Connectivity Studies: Maps network connectivity and identifies key regulators within cellular networks.

Methodology:

Employs RNAi to systematically perturb genes in tissue culture cells, measures quantitative phenotypes (cell number, area, fluorescence intensity) from multi-well plate assays, constructs matrices of quantitative interaction profiles from pairwise perturbation data, and performs computational analysis of those interaction matrices to infer functional relationships and reconstruct signaling pathways.