1. How to obtain list of top differentally expressed genes?

Step 1: Go to analysis page of UALCAN

Step 2: Choose cancer of interest from left panel by clicking it.

Step 3: UALCAN lists top 25 up-/down-regulated genes in cancer of interest compared to normal samples.

Step 4: User can analyze gene expression and survival profiles of individual gene by clicking the on the heat map.

2. How to query UALCAN for gene(s) of interest in specific cancer?

Step 1: Go to analysis page of UALCAN

Step 2: Enter offical symbol of gene(s) in the text area.

Step 3: Choose the TCGA data set of interest from the drop down menu.

Step 4: Then click explore to query UALCAN for input genes.

Step 5: UALCAN lists the input genes and facilitates users to analyze expression and survival profiles of the input genes.

a. How to explore expression profile of gene of interest based on clinico-pathologic factors?

Obtaining EZH2 expression profile in breast invasive carcinoma dataset based on patient’s race.

Downloading the box plot from UALCAN

b. How to obtain effect of gene expression level and clinico-pathologic factors on patient survival?

Analyzing survival plots of EZH2 in prostate adenocarcinoma TCGA dataset

3. How to obtain expression and survival profile for pre-compiled gene classes?

Step 1: Go to analysis page of UALCAN

Step 2: Query UALCAN for pre-compiled gene classes

Step 3: Select gene class of interest (e.g. Kinase coding genes) and click “Explore” to see results

Step 4: UALCAN lists all kinase coding genes and indicates their expression status and survival effect in different cancers.

Cancer with red border show up regulation of gene

Cancer with green border show down regulation of gene

Step 5: User can click on any of these link to visualize expression and survival profiles

Introduction to Cancer terms

CancerTCGA code
Adrenocortical carcinomaACC
Bladder urothelial carcinomaBLCA
Brain lower grade gliomaLGG
Breast invasive carcinomaBRCA
Cervical squamous cell carcinomaCESC
Colon adenocarcinomaCOAD
Esophageal carcinomaESCA
Glioblastoma multiformeGBM
Head and Neck squamous cell carcinomaHNSC
Kidney ChoromophobeKICH
Kidney renal clear cell carcinomaKIRC
Kidney renal papillary cell carcinomaKIRP
Liver hepatocellular carcinomaLIHC
Lung adenocarcinomaLUAD
Lung squamous cell carcinomaLUSC
Lymphoid Neoplasm Diffuse Large B-cell LymphomaDBLC
Ovarian serous cystadenocarcinomaOV
Pancreatic adenocarcinomaPAAD
Pheochromocytoma and ParagangliomaPCPG
Prostate adenocarcinomaPRAD
Rectum adenocarcinomaREAD
Skin Cutaneous MelanomaSKCM
Testicular Germ Cell TumorsTGCT
Thyroid carcinomaTHCA
Uterine CarcinosarcomaUCS
Uterine Corpus Endometrial CarcinomaUCEC
Uveal MelanomaUVM