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Bioinformatics analysis of alternative splicing

C. Lee
2005 Briefings in Bioinformatics  
Over the past few years, the analysis of alternative splicing using bioinformatics has emerged as an important new field, and has significantly changed our view of genome function.  ...  Common to many bioinformatics studies is a new emphasis on graph representations of alternative splicing structures, which have many advantages for analysis.  ...  INTRODUCTION Over the past few years, the analysis of alternative splicing using bioinformatics has emerged as an important new field, and has significantly changed our view of genome function.  ... 
doi:10.1093/bib/6.1.23 pmid:15826354 fatcat:6abvovvbwvdgfnn374o2glirju

Alternative splicing and bioinformatic analysis of human U12-type introns

Wen-Cheng Chang, Yung-Chia Chen, Kuo-Ming Lee, Woan-Yuh Tarn
2007 Nucleic Acids Research  
Due to incompatibility of these two spliceosomes, alternative splicing involving a U12-type intron may give rise to a relatively complicated impact on gene expression.  ...  We studied alternative U12-type intron splicing in an attempt to gain more mechanistic insights.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkm026 pmid:17332017 pmcid:PMC1874599 fatcat:w6sy7cavdzf2xkjvb7nxh75mei

Deep Learning Deepens the Analysis of Alternative Splicing

Xudong Zou, Xin Gao, Wei Chen
2019 Genomics, Proteomics & Bioinformatics  
Now, Yi Xing's lab reported DARTS [1], a novel computational framework that leverages the power of both deep learning and Bayes hierarchical framework for differential alternative splicing (AS) analysis  ...  Trained on the huge volume of publicly-available RNA-seq datasets, DARTS could largely increase the accuracy of AS analysis, in particular for those with low sequencing depth, by taking both genomic features  ...  DARTS -deep-learning augmented RNA-seq analysis of transcript splicing The new tool, DARTS, mainly consists of two components, i.e., a deep learning model (DARTS DNN) to estimate the prior probability  ... 
doi:10.1016/j.gpb.2019.05.001 pmid:31100357 pmcid:PMC6620263 fatcat:zo4ujnrmqbdp3kt4k7467srtbq

Integrative bioinformatics analysis of prognostic alternative splicing signatures in gastric cancer

Zhen Zong, Hui Li, Zhikun Ning, Cegui Hu, Fuxin Tang, Xiaojian Zhu, Huakai Tian, Taicheng Zhou, He Wang
2020 Journal of Gastrointestinal Oncology  
Prognostic prediction models and splicing correlation networks were assessed using an integrative bioinformatics analysis approach.  ...  The potential prognostic value of alternative splicing (AS) variants and regulatory splicing factors in gastric carcinogenesis is unclear.  ...  Acknowledgments Funding: This study was supported by the National Natural Science Foundation of China (grant Nos. 81860433), the Natural Science Youth Foundation of Jiangxi Province (Grant Number: 20192BAB215036  ... 
doi:10.21037/jgo-20-117 pmid:32953152 pmcid:PMC7475320 fatcat:hqachy766jftpnrhbuunuiklcu

Theoretical analysis of alternative splice forms using computational methods

S. Boue, M. Vingron, E. Kriventseva, I. Koch
2002 Bioinformatics  
They concern the coverage quality of the protein sequence of a known structure, an EST analysis, the validation of splice variants, the determination of the alternative splice type, and finally the link  ...  We found some interesting features of alternative splicing which are presented here. We discuss the results of one chosen example.  ...  ACKNOWLEDGEMENTS We would like to thank Dr Jörg Schultz for helpful discussions, Johanna Holbrook for critical reading of the manuscript, and the University of Potsdam for the possibility using SYBYL.  ... 
doi:10.1093/bioinformatics/18.suppl_2.s65 pmid:12385985 fatcat:ely6knpyf5gfhe47xbrpdq3gp4

IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences

2019 Bioinformatics  
Therefore, we extended IsoformSwitchAnalyzeR R library to enable analysis of genome-wide changes in specific types of alternative splicing and predicted functional consequences of the resulting isoform  ...  Alternative splicing is an important mechanism involved in health and disease.  ...  Vitting-Seerup,K. et al. (2014) spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. BMC Bioinformatics, 15, 81.  ... 
doi:10.1093/bioinformatics/btz247 pmid:30989184 fatcat:vl223gzwxfb6for5bzayv7jodi

A new advance in alternative splicing databases: from catalogue to detailed analysis of regulation of expression and function of human alternative splicing variants

Pierre de la Grange, Martin Dutertre, Margot Correa, Didier Auboeuf
2007 BMC Bioinformatics  
of the regulation of transcript expression at multiple levels, including transcription and splicing, particularly in terms of tissue specificity; and (3) to assist in experimental analysis of the expression  ...  Most human genes produce several transcripts with different exon contents by using alternative promoters, alternative polyadenylation sites and alternative splice sites.  ...  Sebastien Jauliac and the members of his team for their comments and suggestions. We thank the fast DB users for their support and comments.  ... 
doi:10.1186/1471-2105-8-180 pmid:17547750 pmcid:PMC1904244 fatcat:pepnlvnk5bf7pgvcxfrnm3jvha

Extraction, integration and analysis of alternative splicing and protein structure distributed information

Matteo D'Antonio, Marco Masseroli
2009 BMC Bioinformatics  
Further analysis of such valuable information might reveal interesting relationships between alternative splicing and protein structure differences, which may be significantly associated with different  ...  Alternative splicing has been demonstrated to affect most of human genes; different isoforms from the same gene encode for proteins which differ for a limited number of residues, thus yielding similar  ...  This article has been published as part of BMC Bioinformatics Volume 10 Supplement 12, 2009: Bioinformatics Methods for Biomedical Complex System Applications.  ... 
doi:10.1186/1471-2105-10-s12-s15 pmid:19828075 pmcid:PMC2762064 fatcat:qeukr3shobgl3amqbn3n66nkei

Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis

Matteo Carrara, Josephine Lum, Francesca Cordero, Marco Beccuti, Michael Poidinger, Susanna Donatelli, Raffaele Calogero, Francesca Zolezzi
2015 BMC Bioinformatics  
detection of alternative splicing events (AltDE).  ...  Two crucial steps that affect RNA-Seq experiment results are Library Sample Preparation (LSP) and Bioinformatics Analysis (BA).  ...  Discussion In this work we present the first comparative evaluation of the combined effect of Library Sample Preparation and Bioinformatics Analysis on alternative splicing detection.  ... 
doi:10.1186/1471-2105-16-s9-s2 pmid:26050971 pmcid:PMC4464605 fatcat:riqcbeu2mzbrdaqne5oqb4afoa

Transcriptome Bioinformatical Analysis of Vertebrate Stages of Schistosoma japonicum Reveals Alternative Splicing Events

Xinye Wang, Xindong Xu, Xingyu Lu, Yuanbin Zhang, Weiqing Pan, Zhi-Ming Zheng
2015 PLoS ONE  
Understanding the mechanisms of stage-specific alternative splicing can provide a better understanding of the development of eukaryotes and the functions of different genes.  ...  We found 11,623 alternative splicing events among 7,099 protein encoding genes and average proportion of alternative splicing events per gene was 42.14%.  ...  Contributed reagents/materials/analysis tools: XYW XDX WQP. Wrote the paper: XYW WQP.  ... 
doi:10.1371/journal.pone.0138470 pmid:26407301 pmcid:PMC4583307 fatcat:diire7fqhvajzlctoejr5rl7sy

A bioinformatic analysis identifies circadian expression of splicing factors and time-dependent alternative splicing events in the HD-MY-Z cell line

Nikolai Genov, Alireza Basti, Mónica Abreu, Rosario Astaburuaga, Angela Relógio
2019 Scientific Reports  
Our results highlight a role for the clock as a temporal regulator of alternative splicing, which may impact malignancy in this cellular model.  ...  We investigated the temporal phenotype of clock-controlled genes and splicing factors, and evaluated their impact in alternative splice patterns in the Hodgkin Lymphoma cell line HD-MY-Z.  ...  Using our bioinformatics pipeline applied to multiple comparisons of time points, we investigated the impact of the differential oscillations of SFs in alternative splicing, and identified several alternatively  ... 
doi:10.1038/s41598-019-47343-w pmid:31363108 pmcid:PMC6667479 fatcat:yawwadrnefeplipcvpng72lbdu

Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis [article]

Matteo Carrara, Josephine Lum, Francesca Cordero, Marco Beccuti, Michael Poidinger, Susanna Donatelli, Raffaele A Calogero, Francesca Zolezzi
2014 biorxiv/medrxiv   pre-print
Statistical detection of alternative splicing (AltDE) was done using prototypes of BA for isoform-reconstruction (Cuffdiff) and exon-level analysis (DEXSeq).  ...  The effect on statistical detection of alternative splicing considering low input LSP (NuGEN v2) with respect to high input LSP (TruSeq) on statistical detection of alternative splicing was studied using  ...  Discussion In this work we present the first comparative evaluation of the combined effect of Library Sample Preparation and Bioinformatics Analysis on alternative splicing detection.  ... 
doi:10.1101/005546 fatcat:5mq5gpyd7bdnxhz5pytahhf3um

Integrative Visual Analysis of the Effects of Alternative Splicing on Protein Domain Interaction Networks

Dorothea Emig, Melissa S. Cline, Karsten Klein, Anne Kunert, Petra Mutzel, Thomas Lengauer, Mario Albrecht
2008 Journal of Integrative Bioinformatics  
Protein domains affected by alternative splicing are highlighted and splicing patterns can be compared.  ...  Alternative splicing is an important molecular mechanism for increasing the protein diversity in eukaryotic cells.  ...  Additionally, alternative splicing events complicate the analysis of protein interaction data further.  ... 
doi:10.1515/jib-2008-101 fatcat:62mmylmhkfayxljrerc5ldphym

Integrative visual analysis of the effects of alternative splicing on protein domain interaction networks

Dorothea Emig, Melissa S Cline, Karsten Klein, Anne Kunert, Petra Mutzel, Thomas Lengauer, Mario Albrecht
2008 Journal of Integrative Bioinformatics  
Protein domains affected by alternative splicing are highlighted and splicing patterns can be compared.  ...  Alternative splicing is an important molecular mechanism for increasing the protein diversity in eukaryotic cells.  ...  The research has been conducted in the context of the BioSapiens Network of Excellence funded by the European Commission (grant number LSHG-CT-2003-503265).  ... 
doi:10.2390/biecoll-jib-2008-101 pmid:20134061 fatcat:brn6j6gnyzex7lvjofrpghv5qa

Alternative Splicing and Expression Profile Analysis of Expressed Sequence Tags in Domestic Pig

Liang Zhang, Lin Tao, Lin Ye, Ling He, Yuan-Zhong Zhu, Yue-Dong Zhu, Yan Zhou
2007 Genomics, Proteomics & Bioinformatics  
Expression sequence tags (ESTs) have been widely used for gene discovery, expression prof ile analysis, and alternative splicing detection.  ...  The overview of expression prof iles would change when we take alternative splicing into account.  ...  Acknowledgements This work was supported by the National Natural Science Foundation of China (Grant No. 30300068).  ... 
doi:10.1016/s1672-0229(07)60011-4 pmid:17572361 pmcid:PMC5054103 fatcat:rlrwnpz4izeldlml6yarbidti4
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