Enhanced Permutation Tests via Multiple Pruning

Frontiers in Genetics
Sangseob LeemTaesung Park

Abstract

Big multi-omics data in bioinformatics often consists of a huge number of features and relatively small numbers of samples. In addition, features from multi-omics data have their own specific characteristics depending on whether they are from genomics, proteomics, metabolomics, etc. Due to these distinct characteristics, standard statistical analyses using parametric-based assumptions may sometimes fail to provide exact asymptotic results. To resolve this issue, permutation tests can be a way to exactly analyze multi-omics data because they are distribution-free and flexible to use. In permutation tests, p-values are evaluated by estimating the locations of test statistics in an empirical null distribution generated by random shuffling. However, the permutation approach can be infeasible when the number of features increases, because more stringent control of type I error is needed for multiple hypothesis testing, and consequently, much larger numbers of permutations are required to reach significance. To address this problem, we propose a well-organized strategy, "ENhanced Permutation tests via multiple Pruning (ENPP)." ENPP prunes the features in every permutation round if they are determined to be non-significant. In other w...Continue Reading

References

Jun 19, 2004·BMC Bioinformatics·Helene H Thygesen, Aeilko H Zwinderman
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Jan 8, 2008·Nucleic Acids Research·Simon M LinWarren A Kibbe
Feb 14, 2009·PLoS Genetics·Bo Eskerod Madsen, Sharon R Browning
Nov 13, 2009·Pacific Symposium on Biocomputing·Casey S GreeneJason H Moore
Jul 22, 2010·The New England Journal of Medicine·Teri A Manolio
Aug 16, 2011·Genomics·Marina BibikovaRichard Shen
Mar 29, 2014·Genetic Epidemiology·ChangJiang XuUNKNOWN UK10K Consortium
May 29, 2014·Briefings in Bioinformatics·Swarnaseetha AdusumalliTouati Benoukraf
Sep 3, 2016·Bioinformatics·Sungyoung LeeTaesung Park
Nov 4, 2016·Journal of Bioinformatics and Computational Biology·Sohee OhTaesung Park
May 11, 2018·BMC Bioinformatics·Yongkang KimTaesung Park

❮ Previous
Next ❯

Citations

Jul 16, 2021·Translational Vision Science & Technology·Louise A Mesentier-LouroYaping Joyce Liao

❮ Previous
Next ❯

Methods Mentioned

BETA
ICE

Software Mentioned

ENPP
EPNN
R script

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.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
G A Miller
Proceedings of the National Academy of Sciences of the United States of America
F Harary, E Palmer
PLoS Computational Biology
Spencer Bliven, Andreas Prlić
Advances in Neural Information Processing Systems
Chunxiao ZhouYongmei Michelle Wang
© 2021 Meta ULC. All rights reserved