Application of t-SNE to human genetic data

Journal of Bioinformatics and Computational Biology
Wentian LiHenry Han

Abstract

The t-distributed stochastic neighbor embedding t-SNE is a new dimension reduction and visualization technique for high-dimensional data. t-SNE is rarely applied to human genetic data, even though it is commonly used in other data-intensive biological fields, such as single-cell genomics. We explore the applicability of t-SNE to human genetic data and make these observations: (i) similar to previously used dimension reduction techniques such as principal component analysis (PCA), t-SNE is able to separate samples from different continents; (ii) unlike PCA, t-SNE is more robust with respect to the presence of outliers; (iii) t-SNE is able to display both continental and sub-continental patterns in a single plot. We conclude that the ability for t-SNE to reveal population stratification at different scales could be useful for human genetic association studies.

References

Sep 13, 1996·Science·N Risch, K Merikangas
Oct 31, 2000·Genetic Epidemiology·N M LairdX Xu
Apr 21, 2001·Biometrics·B Devlin, K Roeder
Feb 25, 2003·Lancet·Lon R Cardon, Lyle J Palmer
Sep 25, 2004·IEEE Transactions on Neural Networks·Mark D Plumbley, Erkki Oja
Feb 18, 2005·Nature Reviews. Genetics·Joel N Hirschhorn, Mark J Daly
Sep 20, 2006·Nature Reviews. Genetics·David J Balding
Dec 30, 2006·PLoS Genetics·Nick PattersonDavid Reich
Sep 6, 2007·Psychological Methods·Mariëlle LintingAnita J van der Koojj
Dec 18, 2007·Briefings in Bioinformatics·Wentian Li
Apr 9, 2008·BMC Bioinformatics·Jengnan TzengWen-Hsiung Li
Apr 22, 2008·Nature Genetics·John Novembre, Matthew Stephens
Apr 30, 2008·Nature Genetics·David ReichNick Patterson
Aug 12, 2008·Current Biology : CB·Oscar LaoManfred Kayser
Jul 22, 2010·The New England Journal of Medicine·Teri A Manolio
Jul 31, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Xiaoxu Han
Oct 12, 2010·Bioinformatics·Ani ManichaikulWei-Min Chen
Oct 29, 2010·Nature·Gonçalo R AbecasisGil A McVean
Mar 9, 2012·Genome Research·Maximilian P A SalmCarol C Shoulders
Nov 7, 2012·Nature·UNKNOWN 1000 Genomes Project ConsortiumGil A McVean
Mar 5, 2013·PloS One·Alexander Platzer
Nov 12, 2013·American Journal of Human Genetics·Stacey L EdwardsAlison M Dunning
Dec 10, 2013·Nucleic Acids Research·Danielle WelterHelen Parkinson
Jan 30, 2014·Nature Genetics·Jian YangAlkes L Price
Apr 11, 2014·PloS One·Gad Abraham, Michael Inouye
Oct 4, 2015·Nature·UNKNOWN 1000 Genomes Project ConsortiumGonçalo R Abecasis
Mar 1, 2016·American Journal of Human Genetics·Kevin J GalinskyAlkes L Price
Oct 7, 2016·Frontiers in Genetics·Olivier B PoirionLana Garmire
Nov 9, 2016·Nature Biotechnology·Allon WagnerNir Yosef
Dec 3, 2016·Nucleic Acids Research·Jacqueline MacArthurHelen Parkinson

❮ Previous
Next ❯

Citations

Aug 21, 2018·Omics : a Journal of Integrative Biology·Dmitry GrapovSakda Khoomrung
Aug 24, 2019·Science·Alfred Amambua-NgwaAbdoulaye A Djimde
Aug 24, 2019·Science·Carol Hopkins Sibley
May 18, 2020·Medical Physics·John KangSarah L Kerns
May 30, 2020·PLoS Genetics·Aman AgrawalSriram Sankararaman
Oct 12, 2017·Frontiers in Genetics·Gustavo GlusmanMax Robinson
Jan 10, 2019·Frontiers in Immunology·Malini ManoharanAmitabha Chaudhuri
Apr 3, 2020·International Journal of Molecular Sciences·Chao FengXiaoyue Feng
Nov 30, 2019·Nature Communications·Dmitry Kobak, Philipp Berens
Jan 1, 2021·Frontiers in Genetics·Xueli XuXiming Xu
Nov 3, 2020·Computational and Structural Biotechnology Journal·Yuchen LiShenglin Huang
Jun 3, 2021·Entropy·António M Lopes, Jóse A Tenreiro Machado

❮ 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.

Related Papers

The Journal of Immunology : Official Journal of the American Association of Immunologists
Yang ChengEvan W Newell
Dental press journal of orthodontics
Glaucia Cristina Rodrigues NascimentoDavid Normando
© 2021 Meta ULC. All rights reserved