Dimensionality Reduction
In this pane, you can perform PCA dimensionality reduction on samples from different cancer types and tissues based on their expression of a group of genes. Some gene signature lists are provided.
Performs Principal Component Analysis (PCA) for a given gene list using custom TCGA and/or GTEx expression data. First, GEPIA presents a 2D plot of top principal components (PCs).
Parameters:
- Gene List: Input a gene list of interest. Manual input of genes(e.g. ERBB2,EGFR)
- TCGA Tumor/TCGA Peritumor/GTEx, Used Expression Datasets: Select cancer types of interest in the "TCGA Tumor", "TCGA Peritumor" or "GTEx" field and click "add" to build dataset list in the "Used Expression Datasets" field. Also, manual input of cancer types split by comma (e.g. COAD Tumor,READ Tumor) is also acceptable.
- Log Scale: Data are first log2(TPM+1) scaled before computation, then mean-centered and standardized during the process.
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