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Literature DB >> 30053266

TC3A: The Cancer 3' UTR Atlas.

Xin Feng¹, Lei Li¹, Eric J Wagner², Wei Li¹.

Abstract

Widespread alternative polyadenylation (APA) occurs during enhanced cellular proliferation and transformation. Recently, we demonstrated that CFIm25-mediated 3' UTR shortening through APA promotes glioblastoma tumor growth in vitro and in vivo, further underscoring its significance to tumorigenesis. Here, we report The Cancer 3' UTR Atlas (TC3A), a comprehensive resource of APA usage for 10,537 tumors across 32 cancer types. These APA events represent potentially novel prognostic biomarkers and may uncover novel mechanisms for the regulation of cancer driver genes. TC3A is built on top of the now de facto standard cBioPortal. Therefore, the large community of existing cBioPortal users and clinical researchers will find TC3A familiar and immediately usable. TC3A is currently fully functional and freely available at http://tc3a.org.

Entities: Chemical Disease Gene Species

Mesh：

Substances：
3' Untranslated Regions

Year: 2018 PMID： 30053266 PMCID： PMC5753254 DOI： 10.1093/nar/gkx892

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

14 in total

1. TAIL-seq: genome-wide determination of poly(A) tail length and 3' end modifications.

Authors: Hyeshik Chang; Jaechul Lim; Minju Ha; V Narry Kim
Journal: Mol Cell Date: 2014-02-27 Impact factor: 17.970

2. miR-132 regulates antiviral innate immunity through suppression of the p300 transcriptional co-activator.

Authors: Dimitrios Lagos; Gabriel Pollara; Stephen Henderson; Fiona Gratrix; Martin Fabani; Richard S B Milne; Frances Gotch; Chris Boshoff
Journal: Nat Cell Biol Date: 2010-04-25 Impact factor: 28.824

3. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.

Authors: Ethan Cerami; Jianjiong Gao; Ugur Dogrusoz; Benjamin E Gross; Selcuk Onur Sumer; Bülent Arman Aksoy; Anders Jacobsen; Caitlin J Byrne; Michael L Heuer; Erik Larsson; Yevgeniy Antipin; Boris Reva; Arthur P Goldberg; Chris Sander; Nikolaus Schultz
Journal: Cancer Discov Date: 2012-05 Impact factor: 39.397

4. International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data.

Authors: Junjun Zhang; Joachim Baran; A Cros; Jonathan M Guberman; Syed Haider; Jack Hsu; Yong Liang; Elena Rivkin; Jianxin Wang; Brett Whitty; Marie Wong-Erasmus; Long Yao; Arek Kasprzyk
Journal: Database (Oxford) Date: 2011-09-19 Impact factor: 3.451

5. PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes.

Authors: Ju Youn Lee; Ijen Yeh; Ji Yeon Park; Bin Tian
Journal: Nucleic Acids Res Date: 2007-01 Impact factor: 16.971

6. Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression.

Authors: Steve Lianoglou; Vidur Garg; Julie L Yang; Christina S Leslie; Christine Mayr
Journal: Genes Dev Date: 2013-10-21 Impact factor: 11.361

7. APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals.

Authors: Leiming You; Jiexin Wu; Yuchao Feng; Yonggui Fu; Yanan Guo; Liyuan Long; Hui Zhang; Yijie Luan; Peng Tian; Liangfu Chen; Guangrui Huang; Shengfeng Huang; Yuxin Li; Jie Li; Chengyong Chen; Yaqing Zhang; Shangwu Chen; Anlong Xu
Journal: Nucleic Acids Res Date: 2014-11-06 Impact factor: 16.971

8. The 3'UTR signature defines a highly metastatic subgroup of triple-negative breast cancer.

Authors: Lei Wang; Xin Hu; Peng Wang; Zhi-Ming Shao
Journal: Oncotarget Date: 2016-09-13

9. APADB: a database for alternative polyadenylation and microRNA regulation events.

Authors: Sören Müller; Lukas Rycak; Fabian Afonso-Grunz; Peter Winter; Adam M Zawada; Ewa Damrath; Jessica Scheider; Juliane Schmäh; Ina Koch; Günter Kahl; Björn Rotter
Journal: Database (Oxford) Date: 2014-07-22 Impact factor: 3.451

10. CFIm25 links alternative polyadenylation to glioblastoma tumour suppression.

Authors: Chioniso P Masamha; Zheng Xia; Jingxuan Yang; Todd R Albrecht; Min Li; Ann-Bin Shyu; Wei Li; Eric J Wagner
Journal: Nature Date: 2014-05-11 Impact factor: 49.962

23 in total

1. Role of alternative polyadenylation dynamics in acute myeloid leukaemia at single-cell resolution.

Authors: Congting Ye; Qian Zhou; Yiling Hong; Qingshun Quinn Li
Journal: RNA Biol Date: 2019-03-13 Impact factor: 4.652

2. scAPAatlas: an atlas of alternative polyadenylation across cell types in human and mouse.

Authors: Xiaoxiao Yang; Yang Tong; Gerui Liu; Jiapei Yuan; Yang Yang
Journal: Nucleic Acids Res Date: 2022-01-07 Impact factor: 16.971

3. Using population-scale transcriptomic and genomic data to map 3' UTR alternative polyadenylation quantitative trait loci.

Authors: Xudong Zou; Ruofan Ding; Wenyan Chen; Gao Wang; Shumin Cheng; Qin Wang; Wei Li; Lei Li
Journal: STAR Protoc Date: 2022-07-19

TC3A: The Cancer 3' UTR Atlas.

1. TAIL-seq: genome-wide determination of poly(A) tail length and 3' end modifications.

2. miR-132 regulates antiviral innate immunity through suppression of the p300 transcriptional co-activator.

3. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.

4. International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data.

5. PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes.

6. Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression.

7. APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals.

8. The 3'UTR signature defines a highly metastatic subgroup of triple-negative breast cancer.

9. APADB: a database for alternative polyadenylation and microRNA regulation events.

10. CFIm25 links alternative polyadenylation to glioblastoma tumour suppression.

1. Role of alternative polyadenylation dynamics in acute myeloid leukaemia at single-cell resolution.

2. scAPAatlas: an atlas of alternative polyadenylation across cell types in human and mouse.

3. Using population-scale transcriptomic and genomic data to map 3' UTR alternative polyadenylation quantitative trait loci.

4. CFIm25 in Solid Tumors: Current Research Progress.

5. HPV shapes tumor transcriptome by globally modifying the pool of RNA binding protein-binding motif.

6. Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma.

7. SNP2APA: a database for evaluating effects of genetic variants on alternative polyadenylation in human cancers.

Review 8. The Detection and Bioinformatic Analysis of Alternative 3^' UTR Isoforms as Potential Cancer Biomarkers.

9. Construction of Two Alternative Polyadenylation Signatures to Predict the Prognosis of Sarcoma Patients.

10. APAatlas: decoding alternative polyadenylation across human tissues.

Review 8. The Detection and Bioinformatic Analysis of Alternative 3' UTR Isoforms as Potential Cancer Biomarkers.

Review 8. The Detection and Bioinformatic Analysis of Alternative 3^' UTR Isoforms as Potential Cancer Biomarkers.