MPSBase

MPSBase aggregates differentially expressed gene data from RNA-Seq and microarray studies of Mucopolysaccharidoses (MPS) to support research into lysosomal storage disease mechanisms and glycosaminoglycan metabolism.

Key Features:

• Extensive Data Collection: Aggregates data from 13 studies deposited in the Gene Expression Omnibus (GEO).
• Data Types: Includes both RNA-Seq and microarray-derived differential expression results.
• Species Coverage: Contains data from Canis lupus familiaris, Homo sapiens, Mus musculus, and Rattus norvegicus.
• Differential Expression Comparisons: Provides approximately 54 possible comparisons with between ~5,000 and ~10,000 genes per comparison.
• Search and Filtering: Allows selection and retrieval of differentially expressed genes and ontologies by species, MPS type, or tissue type.
• Visualizations: Generates heatmaps showing the top 50 differentially expressed genes per comparison and dot plots for the top 30 enriched ontologies.
• Ontology Categories and Tables: Reports enriched ontologies categorized by biological process, cellular component, KEGG pathways, and molecular function, alongside detailed tabular data.

Scientific Applications:

• Molecular mechanism elucidation: Enables analysis of gene expression changes to investigate pathways and mechanisms underlying MPS-related lysosomal dysfunction.
• Comparative model analysis: Supports cross-species comparisons among Canis lupus familiaris, Homo sapiens, Mus musculus, and Rattus norvegicus MPS models.
• Tissue-specific expression profiling: Facilitates examination of tissue-dependent differential expression patterns relevant to MPS pathology.
• Experimental treatment assessment: Allows evaluation of gene expression responses to experimental interventions in MPS models.
• Pathway and ontology-driven interpretation: Provides enriched GO and KEGG pathway information to contextualize differential expression results.

Methodology:

Aggregates differentially expressed gene data from 13 GEO studies (RNA-Seq and microarray) and produces heatmaps (top 50 DE genes), dot plots (top 30 ontologies by biological process, cellular component, KEGG pathways, and molecular function), and accompanying tables.