Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline

Briefings in Bioinformatics
Yasir RahmatallahGalina Glazko

Abstract

Transcriptome sequencing (RNA-seq) is gradually replacing microarrays for high-throughput studies of gene expression. The main challenge of analyzing microarray data is not in finding differentially expressed genes, but in gaining insights into the biological processes underlying phenotypic differences. To interpret experimental results from microarrays, gene set analysis (GSA) has become the method of choice, in particular because it incorporates pre-existing biological knowledge (in a form of functionally related gene sets) into the analysis. Here we provide a brief review of several statistically different GSA approaches (competitive and self-contained) that can be adapted from microarrays practice as well as those specifically designed for RNA-seq. We evaluate their performance (in terms of Type I error rate, power, robustness to the sample size and heterogeneity, as well as the sensitivity to different types of selection biases) on simulated and real RNA-seq data. Not surprisingly, the performance of various GSA approaches depends only on the statistical hypothesis they test and does not depend on whether the test was developed for microarrays or RNA-seq data. Interestingly, we found that competitive methods have lower pow...Continue Reading

References

Apr 16, 1998·Current Biology : CB·M Johnston
Apr 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·V G TusherG Chu
Jul 1, 2004·Nature Genetics·Doris Damian, Malka Gorfine
Sep 22, 2005·Proceedings of the National Academy of Sciences of the United States of America·Lu TianPeter J Park
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Gordon K Smyth
Feb 17, 2007·Bioinformatics·Jelle J Goeman, Peter Bühlmann
Jul 7, 2007·BMC Bioinformatics·Irina DinuYutaka Yasui
Sep 21, 2007·Bioinformatics·Mark D Robinson, Gordon K Smyth
Oct 13, 2007·Journal of Bioinformatics and Computational Biology·Lev KlebanovYuanhui Xiao
Nov 9, 2007·BMC Bioinformatics·Qi LiuYutaka Yasui
Jan 19, 2008·Briefings in Bioinformatics·Dougu Nam, Seon-Young Kim
Jun 3, 2008·Nature Methods·Ali MortazaviBarbara Wold
Oct 7, 2008·Briefings in Bioinformatics·Irina DinuYutaka Yasui
Oct 17, 2008·Nature·Heidi Ledford
Nov 4, 2008·Nature·Eric T WangChristopher B Burge
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Feb 5, 2009·BMC Bioinformatics·Marit Ackermann, Korbinian Strimmer
Apr 18, 2009·BMC Genomics·Xing FuPhilipp Khaitovich
Apr 29, 2009·BMC Genomics·David MontanerJoaquín Dopazo
Feb 6, 2010·Genome Biology·Matthew D YoungAlicia Oshlack
Mar 4, 2010·Genome Biology·Mark D Robinson, Alicia Oshlack
Mar 12, 2010·Nature·Joseph K PickrellJonathan K Pritchard
Jul 9, 2010·Bioinformatics·Di WuGordon K Smyth
Oct 20, 2010·BMC Genomics·Daniel M GattiFred A Wright
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
Mar 9, 2011·Statistical Applications in Genetics and Molecular Biology·Xiaoming WangYutaka Yasui
May 7, 2011·Bioinformatics·Arthur LiberzonJill P Mesirov
Jun 4, 2011·PLoS Computational Biology·Frank Emmert-Streib, Galina V Glazko
Dec 1, 2011·Statistical Methods in Medical Research·Jun Li, Robert Tibshirani
Mar 3, 2012·PLoS Computational Biology·Purvesh KhatriAtul J Butte
May 26, 2012·PloS One·Shailesh Tripathi, Frank Emmert-Streib
Oct 17, 2012·Statistical Methods in Medical Research·Pablo TamayoJill P Mesirov
Jan 18, 2013·BMC Bioinformatics·Sonja HänzelmannJustin Guinney
Feb 16, 2013·Briefings in Bioinformatics·Henryk Maciejewski
Feb 4, 2014·Genome Biology·Charity W LawGordon K Smyth

❮ Previous
Next ❯

Citations

Dec 1, 2017·Cell and Tissue Research·Enrico Glaab
Jul 13, 2019·Briefings in Bioinformatics·Mitra EbrahimpoorJelle Goeman
Jul 5, 2016·Nature Reviews. Genetics·Hubert HacklZlatko Trajanoski
Feb 17, 2017·PLoS Pathogens·Alexander J WestermannJörg Vogel
May 10, 2017·Translational Psychiatry·C WrightD R Weinberger
Jul 7, 2017·Scientific Reports·Tianci SongYanchun Liang
Jul 23, 2020·Frontiers in Genetics·Farhad MalekiAnthony J Kusalik
Jan 26, 2017·BMC Bioinformatics·Yasir RahmatallahGalina Glazko
Mar 16, 2017·Biotechnology Letters·Ángel DomínguezMiguel Viñas
Oct 26, 2018·BMC Bioinformatics·Shu-Ju LinChuhsing Kate Hsiao
Dec 12, 2019·BMC Bioinformatics·Elham Khodayari MoezIrina Dinu
Jul 25, 2019·Cancer Immunology Research·Kristin G AndersonPhilip D Greenberg
Jan 28, 2021·Genes·Michael James GilhooleyPatrick Yu Wai Man
Feb 22, 2017·Statistical Methodology·Sarah E HolteYajun Mei
Mar 19, 2021·The New Phytologist·Jihua DingOve Nilsson

❮ Previous
Next ❯

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.