TCGA

TCGA ICGA DepMap

Step1: Select Cancer

 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

Step2: Input gene list

Paste genes
Upload a file about genes
supporting csv or txt file!
Select gene set by pathway
An user can select gene set from a predefined pathways
OR Example
 
OR

Step3: Select analysis type

Survival
Whether to conduct survival analysis
Phenotype
Whether to output co-mutation analysis based on race, age, or gender.
Single Mutation Frequency
Whether to output single mutation frequencies
 Yes       Race       Age       Gender       Yes     

Step4: Optional

Mutation Type
Silent: mutations that do not alter amino acid; Nonsilent: mutations that alter amino acid; All: include both silent and nonsilent mutations.
Co-mutation logic
And: all genes specified in the input must be mutated; Or: only one gene from the specified input needs to be mutated
Co-mutation gene limit
 The upper limit of co-mutated genes.  This number indicates how many genes needs to be mutated simultaneously to be considered co-mutated. The upper limit is set as 4. However, the number of input genes can be greater than 4. For example, if 20 genes are inputted and 4 is selected here, all combination of 4 genes from the 20 genes will be tested.
 silent       nonsilent       all  And       Or  2     3     4   
Survival Type
DSS = disease specific survival; DFI = disease free interval; PFI = progression free interval; OS = overall survival
Email (optional)
Due to long runtime, results can be emailed to you.
 DSS    DFI    PFI     OS