curatedAdipoArray

curatedAdipoArray compiles a curated microarray compendium of MDI-induced 3T3-L1 pre-adipocyte differentiation experiments to enable analysis of gene expression dynamics under genetic (knockdown and overexpression) and pharmacological perturbations.

Key Features:

• Data Source: Microarray samples of MDI-induced 3T3-L1 pre-adipocytes collected at multiple time points and sourced from Gene Expression Omnibus (GEO).
• Experimental Perturbations: Includes samples subjected to genetic perturbations (knockdown and overexpression) and diverse pharmacological treatments.
• Time-course Sampling: Time-resolved measurements capture differentiation from pre-adipocytes to mature adipocytes.
• Metadata Curation: Metadata were manually unified across studies using a consistent language to ensure comparability.
• Probe-to-Gene Mapping: Probe intensities were systematically mapped to genes via a reproducible processing pipeline.
• Classification and Homogenization: Samples are classified by modification status (none, genetically modified, pharmacologically treated) and two aggregated datasets were homogenized for comparative analyses.
• Batch Effect Correction: A subset of the data was used to remove batch effects to preserve biological signal across studies.

Scientific Applications:

• Adipogenesis expression profiling: Analysis of gene expression dynamics during 3T3-L1 adipocyte differentiation.
• Perturbation studies: Assessment of the molecular effects of genetic manipulations and pharmacological treatments on adipogenesis.
• Metabolic disease research: Investigation of pathways and mechanisms relevant to obesity, insulin resistance, and type 2 diabetes.
• Comparative analyses: Cross-study comparisons enabled by unified metadata, probe mapping, homogenization, and batch correction.

Methodology:

Data were collected from GEO, metadata were manually unified, probe intensities were mapped to genes via a reproducible pipeline, batch effects were removed using a data subset, and aggregated datasets were homogenized.