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3USS: a web server for detecting alternative 3′UTRs from RNA-seq experiments

Loredana Le Pera, Mariagiovanna Mazzapioda, Anna Tramontano
2015 Computer applications in the biosciences : CABIOS  
stability, localization and translation efficiency. 3USS is a web-server developed with the aim of giving experimentalists the possibility to automatically identify alternative 3 0 UTRs (shorter or longer  ...  Furthermore, if data from two related samples are uploaded, common and specific alternative 3 0 UTRs are identified and reported by the server.  ...  Acknowledgements The authors thank the Biocomputing Unit for interesting discussions. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btv035 pmid:25617413 pmcid:PMC4443675 fatcat:6vcp7wjjbjdmtgkj2ovchgwqry

ExUTR: a novel pipeline for large-scale prediction of 3′-UTR sequences from NGS data

Zixia Huang, Emma C. Teeling
2017 BMC Genomics  
Results: Here, we propose ExUTR, a novel NGS-based pipeline to predict and retrieve 3′-UTR sequences from RNA-Seq experiments, particularly designed for non-model species lacking well-annotated genomes  ...  Current 3′-UTR mining tools, such as GETUTR, 3USS and UTRscan, all depend on a well-annotated reference genome or curated 3′-UTR sequences, which hinders their application on a myriad of non-model organisms  ...  Hughes for the helpful suggestions on the pipeline.  ... 
doi:10.1186/s12864-017-4241-1 pmid:29110697 pmcid:PMC5674806 fatcat:u7yf23qntrb3xpde2ssobqdhcq

The Detection and Bioinformatic Analysis of Alternative 3′ UTR Isoforms as Potential Cancer Biomarkers

Nitika Kandhari, Calvin A. Kraupner-Taylor, Paul F. Harrison, David R. Powell, Traude H. Beilharz
2021 International Journal of Molecular Sciences  
This has led researchers to develop methods to detect and bioinformatically analyse alternative polyadenylation as potential cancer biomarkers.  ...  Alternative transcript cleavage and polyadenylation is linked to cancer cell transformation, proliferation and outcome.  ...  Acknowledgments: We thank members of the Beilharz laboratory and the Monash Bioinformatics platform for constructive feedback on the manuscript.  ... 
doi:10.3390/ijms22105322 pmid:34070203 pmcid:PMC8158509 fatcat:u2xzsq7wrvbahbkm32qbqm7bla

Alternative Polyadenylation: a new frontier in post transcriptional regulation

Fanggang Ren, Na Zhang, Lan Zhang, Eric Miller, Jeffrey J. Pu
2020 Biomarker Research  
Alternative polyadenylation (APA) is an important post-transcriptional regulatory mechanism that processes RNA products depending on its 3′-untranslated region (3′-UTR) specific sequence signal.  ...  APA processing can generate several mRNA isoforms from a single gene, which may have different biological functions on their target gene.  ...  Ethics approval and consent for participate All researches conducted in this study were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964  ... 
doi:10.1186/s40364-020-00249-6 pmid:33292571 fatcat:qdp7xsrkrbf6xmejcbw6hp4lcy

Analyses of alternative polyadenylation: from old school biochemistry to high-throughput technologies

Hsin-Sung Yeh, Wei Zhang, Jeongsik Yong
2017 BMB Reports  
In addition, various bioinformatics algorithms for APA isoform analysis using publicly available RNA-seq datasets are introduced. [BMB Reports 2017; 50(4): 201-207].  ...  Alternations in usage of polyadenylation sites during transcription termination yield transcript isoforms from a gene.  ...  Roar (36) It is based on Fisher test to detect disequilibriums in the number of RNA-seq reads mapped to the 3'UTRs.  ... 
doi:10.5483/bmbrep.2017.50.4.019 pmid:28148393 pmcid:PMC5437964 fatcat:nyjrp2w5mvap7pes3ohppt73dq

Untranslated Parts of Genes Interpreted: Making Heads or Tails of High-Throughput Transcriptomic Data via Computational Methods

Krzysztof J. Szkop, Irene Nobeli
2017 Bioessays  
RNA-seq Abbreviations APA, alternative poly-adenylation; PCS, poly-adenylation and cleavage site; RNA-seq, RNA sequencing; TSS, transcription start site; UTR, untranslated region.  ...  We present a number of computational approaches for the discovery and quantification of alternative transcription start and poly-adenylation events, focusing on technical challenges and arguing for the  ...  The 3'UTR Sequence Seeker (3USS) server[66] is an example of a method that relies on the output from genome-guided transcript reconstruction carried out by Cufflinks.  ... 
doi:10.1002/bies.201700090 pmid:29052251 fatcat:gdsprlpb5ncirksexutxmpwmje

Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma [article]

Swati Venkat, Arwen A Tisdale, Johann R Schwarz, Abdulrahman A Alahmari, H Carlo Maurer, Kenneth P Olive, Kevin H Eng, Michael E Feigin
2019 bioRxiv   pre-print
Alternative polyadenylation (APA) is a gene regulatory process that dictates mRNA 3'-UTR length, resulting in changes in mRNA stability and localization.  ...  Survival analyses reveal a subset of 3'-UTR alterations that independently characterize a poor prognostic cohort among PDA patients.  ...  . & Tramontano, A. 3USS: a web server for detecting 581 alternative 3'UTRs from RNA-seq experiments. Bioinformatics 31, 1845-7 (2015). , X., Li, L., Wagner, E. J. & Li, W.  ... 
doi:10.1101/752295 fatcat:cs57mks37zfzzb3fqyquoti6ou