P-SCAN

P-SCAN quantifies cDNA microarray spot intensities and applies statistical comparative analysis to identify differential gene expression from phosphorimager-scanned arrays.

Key Features:

• Quantitative Analysis: Measures absolute intensity of individual cDNA spots on microarrays from phosphorimager scans.
• Statistical Evaluation: Applies statistical comparative analysis to detect significant differences in gene expression across samples.
• Low Variability: Demonstrates correlation values of 0.90–0.93 and a coefficient of variation between 16% and 28%.
• Microarray Content: Uses a cDNA microarray containing 5,184 distinct cDNAs derived from cluster analysis of over 35,000 prostate cDNA library-derived ESTs.
• Hybridization and Scanning: Uses total RNA radiolabeled probes hybridized to nylon membrane filters and scanned with a phosphorimager.
• Validation: Differential expression findings were confirmed by northern blot analyses for genes such as keratin 5 and vimentin.

Scientific Applications:

• Differential Gene Expression Analysis: Comparison of prostate-derived cell line 8.4 versus melanoma cell line UACC903 to identify differentially expressed genes such as keratin 5 and vimentin.
• Microarray Result Verification: Supports verification workflows by enabling follow-up northern blot confirmation of candidate genes.

Methodology:

P-SCAN processes phosphorimager-scanned microarray data and applies statistical comparative analysis to evaluate and quantify gene expression differences.