GCSscore

GCSscore analyzes probe-level intensities from Affymetrix/Thermo Fisher whole transcriptome microarrays, including ClariomD/XTA and ClariomS, to detect differential gene and exon expression while accounting for non-specific binding.

Key Features:

• Probe-Level Analysis: Uses direct probe-level intensities instead of summarizing probes into a single expression value for each transcript.
• GCSscore Algorithm: Estimates non-specific binding using GC-content of oligonucleotide probes and antigenomic background probes to refine signal estimates.
• Gene-Level and Exon-Level Grouping: Provides methods to group individual probes on ClariomD/XTA chips for differential expression analysis at gene and exon resolution.
• Compatibility with Modern Arrays: Optimized for modern oligonucleotide whole transcriptome arrays, specifically Affymetrix/Thermo Fisher ClariomD/XTA and ClariomS platforms.
• Stringent Statistical Criteria: Applies stringent statistical criteria to detect differentially expressed genes (DEGs) from probe-level measurements.
• Multiple-Oligonucleotide Leverage: Leverages the statistical power inherent in multiple oligonucleotides representing each gene or exon.
• Comparative Sensitivity: Identifies larger sets of DEGs and associated biological functions compared with summary-based approaches.

Scientific Applications:

• Transcriptome Differential Expression: Detection of differentially expressed genes and exons from Affymetrix/Thermo Fisher whole transcriptome microarrays.
• Gene- and Exon-Level Profiling: Detailed expression profiling at both gene and exon resolution for studies of alternative splicing or isoform-specific regulation.
• Analysis of Complex Arrays: Sensitive analysis of complex designs such as ClariomD/XTA arrays for comprehensive transcriptome studies.
• Biological Function Discovery: Improved identification of DEGs to support downstream functional and pathway analyses.

Methodology:

Builds on the Sscore methodology, uses probe-level intensities, estimates non-specific binding via GC-content and antigenomic background probes, groups probes for gene- and exon-level analyses, and applies stringent statistical criteria for DEG detection.