What question did this study set out to answer?

To develop and validate an integrated transcriptome database and open-access web application (TNMplot.com) for real-time comparative gene expression analysis across normal, tumor, and metastatic tissues.

March 5, 2021SHILAP Revista de lepidopterologíaOpen Access

TNMplot.com: A Web Tool for the Comparison of Gene Expression in Normal, Tumor and Metastatic Tissues

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To develop and validate an integrated transcriptome database and open-access web application (TNMplot.com) for real-time comparative gene expression analysis across normal, tumor, and metastatic tissues.
Integrated 56,938 transcriptome samples across multiple repositories, including 33,520 gene chip samples from NCBI-GEO, 11,010 RNA-seq samples from TCGA, 1,193 samples from TARGET, and 11,215 normal samples from GTEx.
Evaluated platform-specific differential gene expression using Mann-Whitney or Kruskal-Wallis tests, with False Discovery Rate (FDR) correction via the Benjamini-Hochberg procedure.
Validated database reliability by splitting breast, colon, and lung cancer data into equally sized training and test sets.
Identified TOP2A (fold change [FC] = 7.8), SPP1 (FC = 7.0), and CENPA (FC = 6.03) as the most consistently upregulated genes across multiple cancer types, whereas ADH1B was the most consistently downregulated gene (FC = 0.15).
Confirmed reproducible differential gene expression between normal, tumorous, and metastatic tissues in breast, colon, and lung cancers at an FDR threshold below 10%.

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Implication

Bioinformatic database analysis demonstrates differential gene expression patterns across 56,938 tissue samples, highlighting potential targets for cancer therapy.

Cite This Study

Bartha et al. (2021) studied this question.

synapsesocial.com/papers/69da543b0d540cafc5838e7b https://doi.org/10.3390/ijms22052622

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Implication

Bioinformatic database analysis demonstrates differential gene expression patterns across 56,938 tissue samples, highlighting potential targets for cancer therapy.

TNMplot.com: A Web Tool for the Comparison of Gene Expression in Normal, Tumor and Metastatic Tissues

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TNMplot.com: A Web Tool for the Comparison of Gene Expression in Normal, Tumor and Metastatic Tissues

Key Points

Discussion

Implication

Cite This Study

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