aiMeRA

aiMeRA implements modular response analysis (MRA) in an R package to quantify coupling strengths in molecular networks from perturbation experiments under steady-state conditions and to integrate genomic data such as qPCR and RNA sequencing (GEO) for genome-wide exploration.

Key Features:

• Modular Response Analysis (MRA): Employs MRA to quantify coupling strengths within molecular networks from perturbation experiments.
• Mathematical derivation of MRA equations: Provides a systematic mathematical derivation of MRA equations to support quantitative interpretation.
• Genomic data integration: Enables a posteriori exploration of genome-wide datasets and identification of genes associated with networks modeled by MRA.
• qPCR and RNA-seq support: Integrates quantitative PCR (qPCR) and RNA sequencing data, with RNA-seq datasets accessible from GEO.
• Steady-state modeling: Applies MRA explicitly under steady-state conditions for network inference.
• Receptor crosstalk modeling: Has been applied to study crosstalk between estrogen and retinoic acid nuclear receptors, including analyses of promoter competition and co-repressors NRIP1/RIP140 and LCoR.

Scientific Applications:

• Crosstalk Analysis: Investigates receptor crosstalk to reveal interactions between estrogen and retinoic acid receptors and shared regulatory mechanisms.
• Transcription Factor Activity Modulation: Explores how nuclear receptors and co-repressors modulate transcription factor activities relevant to gene regulation in cancer contexts.

Methodology:

Derivation and application of MRA equations to perturbation experiments under steady-state conditions, together with a posteriori genome-wide data exploration using qPCR and RNA sequencing (GEO).