MARACAS

MARACAS processes raw RNA-seq and ChIP-seq data from microalgae to generate differentially expressed gene sets and genomic loci for downstream functional interpretation.

Key Features:

• MARACAS (MicroAlgae RnA-seq and Chip-seq AnalysiS): A fully automated computational pipeline that processes raw RNA-seq and ChIP-seq data from microalgae.
• RNA-seq analysis: Generates sets of differentially expressed genes from RNA-seq experiments.
• ChIP-seq analysis: Produces lists of genomic loci from ChIP-seq experiments.
• ALGAEFUN (microALGAE FUNctional enrichment tool) input handling: Accepts gene sets from RNA-seq and genomic loci lists from ChIP-seq as inputs for downstream analysis.
• Functional enrichment: Performs Gene Ontology and biological pathways enrichment analysis on gene sets.
• ChIP-seq locus interpretation: Identifies potential target genes from ChIP-seq results and analyzes the distribution of loci over gene features.
• Results export: Produces graphical representations and downloadable tables with gene annotations.

Scientific Applications:

• Transcriptomics: RNA-seq analysis to identify differentially expressed genes and elucidate microalgae responses to environmental changes.
• Epigenomics: ChIP-seq analysis to explore chromatin modifications and transcription factor binding sites in microalgae.
• Functional Genomics: Gene Ontology and biological pathways enrichment to link gene sets or genomic loci to biological pathways and processes.

Methodology:

Processes raw RNA-seq and ChIP-seq data to generate differentially expressed gene sets and genomic loci; performs Gene Ontology and biological pathways enrichment; links ChIP-seq loci to potential target genes and analyzes loci distribution over gene features; outputs graphical representations and annotation tables.