Profile of Differentially Expressed Genes in Tumor
In this pane, you can list the tumor/normal tissue differentially expressed genes or isoforms in a cancer type.
This feature allows users to apply custom statistical methods and thresholds on a given dataset to dynamically obtain differentially expressed genes.
Parameters:
- Dataset: Select a cancer type of interest.
- Differential Methods: Select a method for differential analysis.
- |log2FC| Cutoff: Set custom fold-change threshold.
- q-value Cutoff: Set custom q-value threshold.
- Percentage Cutoff: Set custom percentage threshold.
- Gene/Isoform: Query differentially expressed genes or isoforms.
Note: limma uses log2(TPM+1) data as input, while DESeq2 requires genes' expected counts
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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