ctcRbase

ctcRbase integrates high-throughput RNA-seq gene expression data for circulating tumor cells (CTCs) and circulating tumor microemboli (CTMs) to enable comparative analysis of mRNA and lncRNA expression across primary tumors, metastases, and white blood cells for biomarker discovery.

Key Features:

• Extensive Transcriptome Data: Integrates high-throughput transcriptomic data from published studies, providing gene expression profiles for CTCs and CTMs.
• Sample Coverage: Aggregates 526 samples spanning seven different cancer types.
• mRNA and lncRNA Content: Contains expression data for 14,631 mRNAs and 3,642 long non-coding RNAs (lncRNAs) derived from RNA-seq analyses.
• Comparative Expression Analysis: Provides matched expression data for primary tumors, metastatic sites, and white blood cells (WBC) to facilitate identification of CTC-specific gene signatures.
• Experimental Validation Annotations: Incorporates experimental validations from published literature linked to expression data.

Scientific Applications:

• Non-Invasive Cancer Monitoring: Analyzing CTC/CTM expression profiles to monitor cancer progression and treatment response.
• Early Detection of Metastasis: Identifying biomarkers associated with early metastatic events.
• Tumor Heterogeneity Analysis: Studying genetic diversity and molecular mechanisms underlying metastasis using CTC/CTM expression data.
• Gene Signature Discovery: Comparing expression across primary tumors, CTCs/CTMs, and metastases to discover unique diagnostic or therapeutic gene signatures.

Methodology:

Integrates RNA-seq-derived transcriptomic datasets from published studies and compiles mRNA and lncRNA expression matrices for CTCs/CTMs, primary tumors, metastases, and white blood cells, with curated experimental validation annotations from the literature.