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Verification of gene expression profiles for colorectal cancer using 12 internet public microarray datasets
Yu-Tien Chang1, Chung-Tay Yao1, Sui-Lung Su1
1Yu-Tien Chang, Chi-Ming Chu, Yun-Wen Shih, Division of Biomedical Statistics and Informatics, School of Public Health, National Defense Medical Center, Taipei 114, Taiwan.
World Journal of Gastroenterology
|December 18, 2014
Summary
A novel gene expression profile was identified for colorectal cancer (CRC) using public microarray data. This 7-gene signature shows promise for blood-based CRC detection assays.
Area of Science:
- Genomics
- Oncology
- Bioinformatics
Background:
- Colorectal cancer (CRC) diagnosis relies on invasive procedures.
- Gene expression profiling offers a potential non-invasive diagnostic approach.
- Previous studies identified candidate genes associated with CRC.
Purpose of the Study:
- To validate gene expression profiles for colorectal cancer (CRC).
- To assess the external generalizability of previously identified CRC-associated genes.
- To identify a robust gene signature for CRC detection.
Main Methods:
- Pooled analysis of 12 public microarray datasets (519 CRC cases, 88 controls).
- Logistic regression analysis to determine odds ratios for 17 selected genes.
- External validation and goodness-of-fit testing (Hosmer-Lemeshow) for gene models.
Main Results:
- A 7-gene model (CPEB4, EIF2S3, MGC20553, MS4A1, ANXA3, TNFAIP6, IL2RB) demonstrated excellent performance.
- The 7-gene model achieved high accuracy (0.968), specificity (0.966), and sensitivity (0.994).
- The model showed strong calibration with a Hosmer-Lemeshow P-value of 1.000.
Conclusions:
- A novel 7-gene expression profile is strongly associated with colorectal cancer.
- This gene signature holds potential for developing blood-based diagnostic assays for CRC.
- The findings support the utility of public microarray data for biomarker discovery.
