RNA-seq assistant: machine learning based methods to identify more transcriptional regulated genes

BMC Genomics
Likai WangHong Qiao

Abstract

Although different quality controls have been applied at different stages of the sample preparation and data analysis to ensure both reproducibility and reliability of RNA-seq results, there are still limitations and bias on the detectability for certain differentially expressed genes (DEGs). Whether the transcriptional dynamics of a gene can be captured accurately depends on experimental design/operation and the following data analysis processes. The workflow of subsequent data processing, such as reads alignment, transcript quantification, normalization, and statistical methods for ultimate identification of DEGs can influence the accuracy and sensitivity of DEGs analysis, producing a certain number of false-positivity or false-negativity. Machine learning (ML) is a multidisciplinary field that employs computer science, artificial intelligence, computational statistics and information theory to construct algorithms that can learn from existing data sets and to make predictions on new data set. ML-based differential network analysis has been applied to predict stress-responsive genes through learning the patterns of 32 expression characteristics of known stress-related genes. In addition, the epigenetic regulation plays critic...Continue Reading

References

Sep 15, 2001·Science·E Mjolsness, D DeCoste
Feb 16, 2002·Methods : a Companion to Methods in Enzymology·K J Livak, T D Schmittgen
Nov 1, 2003·Science·Kayoko YamadaJoseph R Ecker
Mar 26, 2005·Science·Jill ChengThomas R Gingeras
Jun 17, 2005·Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire·Loredana VerdoneErnesto Di Mauro
Jun 28, 2007·The Journal of Biological Chemistry·Yi-Feng ChenG Eric Schaller
May 10, 2008·BMC Proceedings·Radoslav Z Nickolov, Valentin B Milanov
May 14, 2008·BioTechniques·Heather D VanGuilderWillard M Freeman
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Oct 31, 2009·PLoS Computational Biology·Donna K Slonim, Itai Yanai
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
May 4, 2010·Nucleic Acids Research·Zhou DuZhen Su
Sep 14, 2010·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Zahava Siegfried, Itamar Simon
Dec 15, 2010·Current Protocols in Bioinformatics·Ben Langmead
Dec 31, 2010·Nature Reviews. Genetics·Fatih Ozsolak, Patrice M Milos
Jan 25, 2011·The Plant Journal : for Cell and Molecular Biology·Zhao-Yang ZhouGuang-Qin Guo
Dec 6, 2011·Nucleic Acids Research·Philippe LameschEva Huala
Mar 20, 2012·Genome Biology·Zhen ShaoDavid J Waxman
Apr 4, 2013·G3 : Genes - Genomes - Genetics·Jonathan J M LandryLars M Steinmetz
Apr 10, 2013·Epigenomics·Xianjun Dong, Zhiping Weng
Mar 26, 2014·Nature Reviews. Genetics·Ye FuChuan He
Jun 25, 2014·Plant Physiology·Likai WangJian Xu
Jul 9, 2014·Proceedings. Mathematical, Physical, and Engineering Sciences·M Vidyasagar
Sep 17, 2014·Trends in Plant Science·Chuang MaXiangfeng Wang
Mar 10, 2015·Computational and Structural Biotechnology Journal·Konstantina KourouDimitrios I Fotiadis
Mar 31, 2015·The Journal of Biological Chemistry·Samina N ShakeelG Eric Schaller
Apr 11, 2015·BMC Bioinformatics·Jeffery LiLana X Garmire
Apr 15, 2015·Cold Spring Harbor Protocols·Kimberly R Kukurba, Stephen B Montgomery
Sep 4, 2015·The Plant Journal : for Cell and Molecular Biology·Cory D HirschCandice N Hirsch
Nov 1, 2015·Methods in Molecular Biology·Sreya Ghosh, Chon-Kit Kenneth Chan
Jan 8, 2016·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·I MedinaJ Dopazo
Jan 28, 2016·Genome Biology·Ana ConesaAli Mortazavi

❮ Previous
Next ❯

Citations

Nov 8, 2019·Current Pharmaceutical Design·Dan ZhangHao Lin
Jul 22, 2019·Trends in Pharmacological Sciences·Manish D ParanjpeMarina Sirota
Jan 28, 2021·Journal of Personalized Medicine·I-Shiang Tzeng
Jul 1, 2021·Computational and Structural Biotechnology Journal·A StupnikovD G McArt

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE68299

Methods Mentioned

BETA
reverse transcription PCR
RNA-seq
ChIP-seq
acetylation
histone acetylation

Software Mentioned

cuffdiff
agriGO
bowtie
Weka
RandomForest
R scripts
Cufflinks
R
InfoGain
TopHat

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.