Express DIY
GEPIA generates dot plots profiling gene/isoform expression across multiple cancer types, paired peritumor, and corresponding GTEx normal samples. Each dot representing a distinct sample.
Parameters:
- Gene: Input a gene/isoform of interest.
- |log2FC| Cutoff: Set custom fold-change threshold.
- q-value: Set custom fold-change threshold.
- Matched Peritumor / Normal tissue: Select "TCGA paired peritumor + GTEx normal" or "TCGA paired peritumor" for matched normal data in plotting.
- Dataset Order: Select cancer types of interest in the "TCGA Tumor" field and click "+" to build a dataset list in the "Selected Datasets" field. Manual input of cancer types split by comma (e.g. ACC,BRCA,BLCA) is also acceptable. The x-axis of the plot will follow the order of datasets.
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Differential Methods: Statistical methods used for differential gene expression analysis.
DESeq2 uses counts as input, while limma uses log2(TPM + 1)-transformed values as input.
GEPIA generates boxplots for comparing expression in several cancer types.
Parameters:
- Gene: Input a gene/isoform of interest.
- |log2FC| Cutoff: Set custom fold-change threshold.
- q-value: Set custom fold-change threshold.
- Color: Color for significant cohorts
- Dataset/Tissue Order: Select cancer types of interest in the "TCGA Tumor" field and click "+" to build a dataset list in the "Selected Datasets" field. Manual input of cancer types split by comma (e.g. ACC,BRCA,BLCA) is also acceptable. The x-axis of the plot will follow the order of datasets.
- Matched Peritumor / Normal tissue: Select "TCGA paired peritumor + GTEx normal" or "TCGA peritumor" as normal data in plotting.
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Differential Methods:
The differential analysis here is based on the selected datasets ("TCGA tumor vs TCGA peritumor + GTEx normal" or "TCGA tumor vs TCGA peritumor"). The method for differential analysis is t-test, using disease state (Tumor or Peritumor/Normal) as variable for linear model:
In this pane, you can profile boxplot to analyze gene expression across various cancer types and stages.
Parameters:
- Gene: Input a gene/isoform of interest.
- Plot Color: Set custom fold-change threshold.
- Dataset/Tissue Order: Select cancer types of interest in the "TCGA Tumor" field and click "+" to build a dataset list in the "Tissue Order" field. Manual input of cancer types split by comma (e.g. ACC,BRCA,BLCA) is also acceptable. The x-axis of the plot will follow the order of datasets.
- Use Stage: ACJJ tumor stage classification
This pane generates heatmaps from a gene list. Color density in each block shows the median gene expression in a cohort. It allows comparison of different genes in same tumors or peritumor/normal tissues in one plot.
Parameters:
- Gene Set: Input genes/isoforms of interest.(num ≥ 2)
- Log2 (TPM+1) Scale Choose to use log2(TPM+1) transformed expression, while using TPM.
- Matched Peritumor / Normal tissue: Select "Only TCGA tumor" or "TCGA peritumor + GTEx normal", "TCGA peritumor" for matched normal data in plotting.
- Dataset/Tissue Order: Select cancer types of interest in the "Dataset" field and click "+" to build a dataset list in the "Tissue Order" field. Manual input of cancer types split by comma (e.g. ACC,BRCA,BLCA) is also acceptable. The x-axis of the plot will follow the order of datasets.
TCGA Abbr.
| Abbr | Detail |
|---|---|
| ACC | Adrenocortical carcinoma |
| BLCA | Bladder Urothelial Carcinoma |
| BRCA | Breast invasive carcinoma |
| CESC | Cervical squamous cell carcinoma and endocervical adenocarcinoma |
| CHOL | Cholangiocarcinoma |
| COAD | Colon adenocarcinoma |
| DLBC | Lymphoid Neoplasm Diffuse Large B-cell Lymphoma |
| ESCA | Esophageal carcinoma |
| GBM | Glioblastoma multiforme |
| HNSC | Head and Neck squamous cell carcinoma |
| KICH | Kidney Chromophobe |
| KIRC | Kidney renal clear cell carcinoma |
| KIRP | Kidney renal papillary cell carcinoma |
| LAML | Acute Myeloid Leukemia |
| LGG | Brain Lower Grade Glioma |
| LIHC | Liver hepatocellular carcinoma |
| LUAD | Lung adenocarcinoma |
| LUSC | Lung squamous cell carcinoma |
| MESO | Mesothelioma |
| OV | Ovarian serous cystadenocarcinoma |
| PAAD | Pancreatic adenocarcinoma |
| PCPG | Pheochromocytoma and Paraganglioma |
| PRAD | Prostate adenocarcinoma |
| READ | Rectum adenocarcinoma |
| SARC | Sarcoma |
| SKCM | Skin Cutaneous Melanoma |
| STAD | Stomach adenocarcinoma |
| TGCT | Testicular Germ Cell Tumors |
| THCA | Thyroid carcinoma |
| THYM | Thymoma |
| UCEC | Uterine Corpus Endometrial Carcinoma |
| UCS | Uterine Carcinosarcoma |
| UVM | Uveal Melanoma |
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