Six Core Gene Markers for Colorectal Cancer Diagnosis

Tao He's research provides a ridge regression diagnostic model built on six core genes (EIF2S3, GTF3A, HMGA1, HSP90AB1, PABPC1, S100A11) identified as malignant transformation markers in colorectal polyps. The model was validated using the TCGA-COADREAD cohort and an external independent dataset, GSE41258. It includes data on gene expression in CRC cell lines and protein expression levels from the UALCAN database.

Use Cases

• Validate the diagnostic model's performance using the six core genes (EIF2S3, GTF3A, HMGA1, HSP90AB1, PABPC1, S100A11) against new patient RNA-seq data.
• Investigate the correlation between high expression of EIF2S3 and S100A11 and poor prognosis in colorectal cancer patients via survival analysis.
• Compare mRNA expression levels of the six core genes between CRC cell lines (SW480, HCT116) and normal epithelial cell line NCM460 using qRT-PCR data.
• Analyze protein expression levels of the six genes in tumor tissues using data from the UALCAN database to confirm upregulation.

Strengths

• Model is validated on an external independent cohort (GSE41258), supporting generalizability.
• Findings are supported by multiple analysis methods: differential expression, single-cell RNA-seq, and machine learning feature selection.
• Data includes validation at both mRNA (qRT-PCR) and protein (UALCAN database) expression levels for the six core genes.

Limitations

• The dataset is very small at 62.5 KB, indicating it contains summary results or a model, not raw genomic data.
• Specific row counts, column features, and sample-level data are unavailable, limiting direct analytical reuse.
• Geographic and demographic coverage of the underlying patient cohorts (TCGA, GSE41258) is not specified, potentially introducing bias.

Provenance

Source

Tao He, via figshare.

Collection Method

Bioinformatics analysis combining edgeR, WGCNA, Boruta algorithm, LASSO regression, and XGBoost on datasets GSE209741, GSE161277, and TCGA-COADREAD.

Freshness

Last updated March 2026.