Systematic profiling of alternative splicing signature reveals prognostic predictor for prostate cancer

Cancer Science
Jiyu ZhaoXi Wei

Abstract

Alternative splicing (AS) provides the primary mechanism for producing protein diversity. There is growing evidence that AS is involved in the development and progression of cancers. The rapid accumulation of high-throughput sequencing technologies and clinical data sets offers an opportunity to systematically profile the relationship between mRNA variants and clinical outcomes. However, there is a lack of systematic analysis of AS in prostate cancer: Download RNA-seq data and clinical information from The Cancer Genome Atlas (TCGA) data portal. Evaluate RNA splicing patterns by SpliceSeq and calculate splicing percentage (PSI) values. Different expressions were identified as differently expressed AS events (DEAs) based on PSI values. Bioinformatics methods were used for further analysis of DEAs and their splicing networks. Kaplan-Meier, Cox proportional regression, and unsupervised cluster analysis were used to assess the correlation between DEAs and clinical characteristics. In total, 43 834 AS events were identified, of which 1628 AS events were differentially expressed. The parental genes of these DEAs played a significant role in the regulation of prostate cancer-related processes. In total, 226 DEAs events were found to b...Continue Reading

References

Nov 3, 2004·Cancer Research·Julian P Venables
Feb 6, 2007·International Journal of Cancer. Journal International Du Cancer·Raul CatenaAlfonso Calvo
Nov 21, 2007·Cancer Causes & Control : CCC·Ruth EtzioniEric Feuer
Dec 7, 2007·Trends in Genetics : TIG·Eddo KimGil Ast
Nov 3, 2010·Genes & Development·Charles J David, James L Manley
Nov 3, 2012·Nucleic Acids Research·Matteo GiuliettiGraziano Pesole
Dec 18, 2013·Oncogene·S Oltean, D O Bates
May 14, 2014·Nature Reviews. Urology·Claudia A SalinasKathleen A Cooney
Jun 3, 2014·European Urology·Eleni EfstathiouChristopher J Logothetis
Sep 4, 2014·The New England Journal of Medicine·Emmanuel S AntonarakisJun Luo
Nov 26, 2014·Nuclear Receptor Signaling·Dai-Ying WuMichael R Stallcup
Sep 1, 2015·The Surgical Clinics of North America·William Tabayoyong, Robert Abouassaly
Apr 26, 2016·Oncology Reports·Syamalima DubeBernard J Poiesz
Sep 8, 2016·Nature Medicine·Stanley Chun-Wei Lee, Omar Abdel-Wahab
Dec 21, 2016·International Journal of Cancer. Journal International Du Cancer·Lindsay D SmithDiana Baralle
Jan 10, 2018·CA: a Cancer Journal for Clinicians·Rebecca L SiegelAhmedin Jemal
Apr 4, 2018·Nature Genetics·Joshua ArmeniaEliezer M Van Allen

❮ Previous
Next ❯

Methods Mentioned

BETA
SpliceSeq

Software Mentioned

clusterProfiler
Consensus Cluster Plus ( R package )
SpliceSeq
Cytoscape

Related Concepts

Related Feeds

Alternative splicing

Alternative splicing a regulated gene expression process that allows a single genetic sequence to code for multiple proteins. Here is that latest research.