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Statistical inferences for isoform expression in RNA-Seq

Hui Jiang, Wing Hung Wong
2009 Computer applications in the biosciences : CABIOS  
Our results show that isoform expression inference in RNA-Seq is possible by employing appropriate statistical methods.  ...  The development of RNA sequencing (RNA-Seq) makes it possible for us to measure transcription at an unprecedented precision and throughput.  ...  ACKNOWLEDGEMENTS We thank Barbara Wold for making the Solexa sequencing data available and Yi Xing for the Pan et al. (2004) reference.  ... 
doi:10.1093/bioinformatics/btp113 pmid:19244387 pmcid:PMC2666817 fatcat:lwruvo4g5jgmtkgssgbgap7liy

A Hierarchical Bayesian Model for Estimating and Inferring Differential Isoform Expression for Multi-sample RNA-Seq Data

Saran Vardhanabhuti, Mingyao Li, Hongzhe Li
2011 Statistics in Biosciences  
We present in this paper a Poisson-Gamma hierarchical model for multi-sample RNA-Seq data analysis in order to simultaneously estimate isoform-specific expression and to identify differentially expressed  ...  RNA-Seq has drastically changed our ways of studying transcrip-tomes in providing more precise estimates of gene expression, including isoform-specific expression.  ...  In this paper, we present an integrated statistical approach for multiple RNA-Seq samples where isoform-specific variability and differential expression are modeled simultaneously.  ... 
doi:10.1007/s12561-011-9052-3 pmid:23737925 pmcid:PMC3669631 fatcat:d6d36spaqrbkbbbvygbo5frcqm

SpliceNet: recovering splicing isoform-specific differential gene networks from RNA-Seq data of normal and diseased samples

Hari Krishna Yalamanchili, Zhaoyuan Li, Panwen Wang, Maria P. Wong, Jianfeng Yao, Junwen Wang
2014 Nucleic Acids Research  
This study demonstrates SpliceNet, a method to infer isoform-specific co-expression networks from exon-level RNA-Seq data, using large dimensional trace.  ...  However, its true merit in quantifying splicing isoforms and isoform-specific exon expressions is not well explored in inferring gene networks.  ...  ACKNOWLEDGEMENT We thank our colleagues at The University of Hong Kong for their critical comments and invaluable suggestions.  ... 
doi:10.1093/nar/gku577 pmid:25034693 pmcid:PMC4150760 fatcat:n4ku6msmzbg7toabj4x6cdz3ri

Utilizing RNA-Seq Data for Cancer Network Inference [article]

Ying Cai, Bernard Fendler, Gurinder S. Atwal
2012 arXiv   pre-print
However, there are onerous statistical and computational issues in interpreting high-dimensional sequencing data and inferring the underlying genetic network.  ...  In particular, we employed a graphical lasso analysis, motivated by considerations of the maximum entropy formalism, to estimate the sparse inverse covariance matrix of RNA-Seq data.  ...  After estimating the confounding covariates in RNA-Seq expression data, which we found to be surprisingly significant, we then corrected the gene/isoform expression levels to obtain modified point estimates  ... 
arXiv:1211.4543v2 fatcat:h6ynxm6whjgcvnjk462zegac5a


Hongyu Zhao
2013 Statistics in Biosciences  
In comparison, RNA sequencing data provide a comprehensive characterization of the transcriptome of the cell population under study, including different isoforms and previously unannotated transcripts.  ...  Based on the inferred variants, Ionita-Laza and colleagues discuss how to perform genetic association analysis for both population-based and family-based samples.  ...  A unique advantage of RNA-sequencing versus gene expression microarrays is the ability to infer and quantify isoforms.  ... 
doi:10.1007/s12561-013-9088-7 fatcat:6vbrds5bwbh5vbrzvzuo5nfcse

Utilizing RNA-Seq data for cancer network inference

Ying Cai, Bernard Fendler, Gurinder S. Atwal
2012 Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)  
However, there are onerous statistical and computational issues in interpreting high-dimensional sequencing data and inferring the underlying genetic network.  ...  In particular, we employed a graphical lasso analysis, motivated by considerations of the maximum entropy formalism, to estimate the sparse inverse covariance matrix of RNA-Seq data.  ...  After estimating the confounding covariates in RNA-Seq expression data, which we found to be surprisingly significant, we then corrected the gene/isoform expression levels to obtain modified point estimates  ... 
doi:10.1109/gensips.2012.6507723 dblp:conf/gensips/CaiFA12 fatcat:c5fse46f3bagnhwtudnnavweam

PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution

Yu Hu, Yichuan Liu, Xianyun Mao, Cheng Jia, Jane F. Ferguson, Chenyi Xue, Muredach P. Reilly, Hongzhe Li, Mingyao Li
2013 Nucleic Acids Research  
However, estimating isoform-specific gene expression is challenging because various biases present in RNA-Seq (RNA sequencing) data complicate the analysis, and if not appropriately corrected, can affect  ...  In this article, we present PennSeq, a statistical method that allows each isoform to have its own non-uniform read distribution.  ...  ACKNOWLEDGEMENTS The authors thank Dr John Hogenesch for helpful discussions.  ... 
doi:10.1093/nar/gkt1304 pmid:24362841 pmcid:PMC3919567 fatcat:pqfumagnarcejlu4whj3b33tbu

RNA-Seq Data: A Complexity Journey

Enrico Capobianco
2014 Computational and Structural Biotechnology Journal  
The aim of this mini-review is to emphasize transcriptome-related problems of direct and inverse nature for which novel inference approaches are needed.  ...  Since the appearance of the ENCODE project and due to follow-up work, a shift from the pervasive transcription observed from RNA-Seq data to its functional validation is gradually occurring.  ...  Acknowledgments The author thanks his colleagues at the University of Miami for fruitful discussions on the topics addressed in this review.  ... 
doi:10.1016/j.csbj.2014.09.004 pmid:25408846 pmcid:PMC4232570 fatcat:znwwul6f5jhhffd73lry2apo6u

Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq

Zhengpeng Wu, Xi Wang, Xuegong Zhang
2010 Computer applications in the biosciences : CABIOS  
Solved by maximum likelihood estimation, isoform expression can be inferred in RNA-Seq using statistical models based on the assumption that sequenced reads are distributed uniformly along transcripts.  ...  The experiments indicate that incorporating N-URD information can improve the accuracy in modeling and inferring isoform expression in RNA-Seq.  ...  Hui Jiang for helpful discussion. We thank the anonymous reviewers for their helpful comments and suggestions.  ... 
doi:10.1093/bioinformatics/btq696 pmid:21169371 fatcat:gzknt56yknapvjnymqnc77uk4u

Bayesian nonparametric discovery of isoforms and individual specific quantification

Derek Aguiar, Li-Fang Cheng, Bianca Dumitrascu, Fantine Mordelet, Athma A. Pai, Barbara E. Engelhardt
2018 Nature Communications  
BIISQ achieves the most significant gains for longer (in terms of exons) isoforms and isoforms that are lowly expressed (over 500% more transcripts correctly inferred at low coverage in simulations).  ...  We develop a stochastic variational inference approach for efficient and robust posterior inference and demonstrate superior precision and recall for short read RNA-seq simulations and simulated short  ...  Discussion We presented a statistical model, BIISQ, for quantifying RNA isoforms in short-read RNA-seq samples, which shares strength across samples to estimate isoforms-especially those at low abundance-without  ... 
doi:10.1038/s41467-018-03402-w pmid:29703885 pmcid:PMC5923247 fatcat:ir3aghs5ujaztpa3i2xz5xmali

Analysis and design of RNA sequencing experiments for identifying isoform regulation

Yarden Katz, Eric T Wang, Edoardo M Airoldi, Christopher B Burge
2010 Nature Methods  
To infer isoform regulation from high-throughput sequencing of cDNA fragments (RNA-seq), we developed the mixture-of-isoforms (MISO) model, a statistical model that estimates expression of alternatively  ...  Our results provide a probabilistic framework for RNA-seq analysis, give functional insights into pre-mRNA processing and yield guidelines for the optimal design of RNA-seq experiments for studies of gene  ...  RNA-seq library for inference of mRNA isoform abundance together with a lane of shorter-insert single-end sequencing for analysis of gene expression.  ... 
doi:10.1038/nmeth.1528 pmid:21057496 pmcid:PMC3037023 fatcat:yfkluezxpnghlkp3d6gnoqjruq

Simulation based benchmarking of isoform quantification in single-cell RNA-seq [article]

Jennifer Westoby, Marcela Sjoberg, Anne Ferguson-Smith, Martin Hemberg
2018 biorxiv/medrxiv   pre-print
An important biological insight comes from our analysis of real data which showed that genes that express two isoforms in bulk RNA-seq predominantly express one or neither isoform in individual cells.  ...  Importantly, the reduction in performance for single-cell RNA-seq compared with bulk RNA-seq was small.  ...  We would like to thank to John Marioni from Cancer Research UK Cambridge Institute, for funding the sequencing runs of B and T lymphocytes scRNA-seq datasets.  ... 
doi:10.1101/248716 fatcat:ph7jb4kvmjbkbkfsqnfmwibylu

TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference

Naoki Nariai, Osamu Hirose, Kaname Kojima, Masao Nagasaki
2013 Computer applications in the biosciences : CABIOS  
Results: We propose a statistical method to estimate transcript isoform abundances from RNA-Seq data.  ...  Although RNA sequencing (RNA-Seq) technologies have been widely used in measuring amounts of transcribed mRNA, accurate estimation of transcript isoform abundances from RNA-Seq data is challenging, because  ...  This work was supported (in part) by MEXT Tohoku Medical Megabank Project. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btt381 pmid:23821651 fatcat:ghudes5vlfft5bt4czpy6wf2aq

LIQA: long-read isoform quantification and analysis

Yu Hu, Li Fang, Xuelian Chen, Jiang F. Zhong, Mingyao Li, Kai Wang
2021 Genome Biology  
AbstractLong-read RNA sequencing (RNA-seq) technologies can sequence full-length transcripts, facilitating the exploration of isoform-specific gene expression over short-read RNA-seq.  ...  LIQA incorporates base pair quality score and isoform-specific read length information in a survival model to assign different weights across reads, and uses an expectation-maximization algorithm for parameter  ...  Peer review information Anahita Bishop was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.  ... 
doi:10.1186/s13059-021-02399-8 pmid:34140043 pmcid:PMC8212471 fatcat:d4qtmrybpfezjouqmfyvvbyji4

Bioinformatics Tools for RNA-seq Gene and Isoform Quantification

Chi Zhang, Baohong Zhang, Michael S Vincent, Shanrong Zhao
2016 Journal of Next Generation Sequencing & Applications  
Recently, a number of tools have been developed for RNA-seq isoform quantification.  ...  In recent years, RNA-seq has emerged as a powerful technology in estimation of gene or transcript expression. 'Union-exon' and transcript based approaches are widely used in gene quantification.  ...  RNA-seq is emerging as a powerful approach for identification and quantification of transcript isoforms.  ... 
doi:10.4172/2469-9853.1000140 fatcat:5ov3cuwjrngfnjicxofzlw6rd4
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