ExpressYourself

ExpressYourself processes DNA microarray data to perform background correction, Cy5 and Cy3 normalization, differential hybridization scoring, replicate combination, problematic-region filtering, and quality assessment for analyses of mRNA expression levels, DNA copy numbers, and transcription factor binding sites.

Key Features:

• Background correction: Performs background correction on microarray probe intensities.
• Cy5/Cy3 normalization: Normalizes Cy5 and Cy3 signal intensities.
• Multiple normalization methods: Implements normalization methods that account for signal intensity and slide location.
• Differential hybridization scoring: Scores differential hybridization levels to identify significantly differentially hybridized array elements.
• Replicate combination: Combines results from replicate experiments.
• Array region filtering: Filters problematic regions on arrays to remove spatial or position-specific artifacts.
• Quality assessment: Assesses quality of individual experiments and combined replicates.
• Modular algorithm integration: Supports modular integration of additional microarray analysis algorithms.
• Image regeneration: Regenerates images of the original microarray after processing to aid identification of position-specific artifacts.
• Pipeline automation: Automates multiple preprocessing and analysis steps into a unified pipeline.

Scientific Applications:

• mRNA expression analysis: Detects changes in mRNA expression levels across conditions.
• DNA copy number analysis: Detects variations in DNA copy number.
• Transcription factor binding analysis: Identifies transcription factor binding sites on a genomic scale.
• Genomic alteration and transcriptional regulation studies: Supports investigations of genomic alterations and transcriptional regulation.

Methodology:

Performs background correction; normalizes Cy5 and Cy3 signals using multiple methods that account for signal intensity and slide location; scores differential hybridization; combines replicate results; filters problematic array regions; assesses individual and replicate experiment quality; and regenerates processed microarray images.