Dynamic Model for RNA-seq Data Analysis

BioMed Research International
Lerong Li, Momiao Xiong

Abstract

By measuring messenger RNA levels for all genes in a sample, RNA-seq provides an attractive option to characterize the global changes in transcription. RNA-seq is becoming the widely used platform for gene expression profiling. However, real transcription signals in the RNA-seq data are confounded with measurement and sequencing errors and other random biological/technical variation. To extract biologically useful transcription process from the RNA-seq data, we propose to use the second ODE for modeling the RNA-seq data. We use differential principal analysis to develop statistical methods for estimation of location-varying coefficients of the ODE. We validate the accuracy of the ODE model to fit the RNA-seq data by prediction analysis and 5-fold cross validation. To further evaluate the performance of the ODE model for RNA-seq data analysis, we used the location-varying coefficients of the second ODE as features to classify the normal and tumor cells. We demonstrate that even using the ODE model for single gene we can achieve high classification accuracy. We also conduct response analysis to investigate how the transcription process responds to the perturbation of the external signals and identify dozens of genes that are rela...Continue Reading

References

Oct 23, 2008·The Journal of Immunology : Official Journal of the American Association of Immunologists·Yu-Huei LiuJung-Yaw Lin
Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder
Apr 17, 2010·Nucleic Acids Research·Kasper D HansenSandrine Dudoit
Apr 28, 2011·Genome Research·Li LuoMomiao Xiong
May 31, 2011·Nature Methods·Manuel GarberCole Trapnell
Jul 13, 2011·Nature Biotechnology·Kasper D HansenJeffrey T Leek

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Citations

Jul 12, 2017·Journal of Aerosol Medicine and Pulmonary Drug Delivery·Rokhsana RasooliAli Mandegary
Sep 7, 2017·Biotechnology and Applied Biochemistry·Laxmi Sagwan-Barkdoll, Aldwin M Anterola

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Methods Mentioned

BETA
RNA-seq
GTPase

Software Mentioned

Ensembl
bedtools
Samtools
UCSC genome browser
bvpSolve
R package bvpSolve
R
R package glmnet
BWA
Picard

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