SpUR is an interactive web portal to access the data of 3’UTR splicing from 7,917 RNA-seq samples across 10 cancer types from The Cancer Genome Atlas (TCGA) and the corresponding tissues from The Genotype-Tissue Expression (GTEx). SpUR is a collaborative project between Prof. Yvonne Tay’s lab at the Cancer Science Institute of Singapore, National University of Singapore (CSI, NUS), and Prof. Xin Gao’s lab at King Abdullah University of Science and Technology (KAUST).
Sample Information
|
TCGA cohorts |
Cancer type |
GTEx tissue |
TCGA NT |
TCGA TP |
GTEx |
|
BRCA |
Breast invasive carcinoma |
Breast |
113 |
1135 |
220 (216) |
|
COAD |
Colon adenocarcinoma |
Colon |
41 |
502 |
385 (375) |
|
HNSC |
Head and Neck squamous cell carcinoma |
N/A |
44 |
520 |
N/A |
|
KIRC |
Kidney renal clear cell carcinoma |
Kidney |
72 |
545 |
72 (36) |
|
LIHC |
Liver hepatocellular carcinoma |
Liver |
50 |
371 |
142 (136) |
|
LUAD |
Lung adenocarcinoma |
Lung |
59 |
540 |
368 (361) |
|
LUSC |
Lung squamous cell carcinoma |
Lung |
51 |
504 |
368 (361) |
|
PRAD |
Prostate adenocarcinoma |
Prostate |
52 |
505 |
121 (118) |
|
STAD |
Stomach adenocarcinoma |
Stomach |
37 |
416 |
210 (203) |
|
THCA |
Thyroid carcinoma |
Thyroid |
59 |
505 |
358 (351) |
General statistics of the RNA-seq samples for each cancer type used in this study. These are derived from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) project. The first numbers in the GTEx column are the total number of samples and numbers in the brackets are the numbers used after filtering (splicing junctions > 1000). TP: primary tumor, NT: adjacent normal tissue.
Contact Information
Cancer Science Institute of Singapore, National University of Singapore (CSI, NUS)
- Jia Jia Chan email: jia.chan@nus.edu.sg
- Yvonne Tay email: yvonnetay@nus.edu.sg
King Abdullah University for Science and Technology, KAUST
- Bin Zhang email: zb.picb@gmail.com
- Adil Salhi email: adil.salhi@kaust.edu.sa
- Xin Gao email: xin.gao@kaust.edu.sa