Review of Statistical Learning Methods in Integrated Omics Studies (An Integrated Information Science)

Bioinformatics and Biology Insights
Irene Sui Lan Zeng, Thomas Lumley

Abstract

Integrated omics is becoming a new channel for investigating the complex molecular system in modern biological science and sets a foundation for systematic learning for precision medicine. The statistical/machine learning methods that have emerged in the past decade for integrated omics are not only innovative but also multidisciplinary with integrated knowledge in biology, medicine, statistics, machine learning, and artificial intelligence. Here, we review the nontrivial classes of learning methods from the statistical aspects and streamline these learning methods within the statistical learning framework. The intriguing findings from the review are that the methods used are generalizable to other disciplines with complex systematic structure, and the integrated omics is part of an integrated information science which has collated and integrated different types of information for inferences and decision making. We review the statistical learning methods of exploratory and supervised learning from 42 publications. We also discuss the strengths and limitations of the extended principal component analysis, cluster analysis, network analysis, and regression methods. Statistical techniques such as penalization for sparsity inductio...Continue Reading

References

Dec 4, 2008·Statistical Applications in Genetics and Molecular Biology·Kim-Anh Lê CaoPhilippe Besse
Feb 26, 2009·Briefings in Bioinformatics·Bill AndreopoulosMichael Schroeder
Aug 27, 2009·Bioinformatics·Kim-Anh Lê CaoSébastien Déjean
Oct 16, 2010·Bioinformatics·Tian XiaJulie A Dickerson
Dec 7, 2010·Cell·Uri David AkaviaDana Pe'er
Dec 15, 2010·Bioinformatics·Michael E SmootTrey Ideker
Jan 14, 2011·Bioinformatics·Riku Louhimo, Sampsa Hautaniemi
Feb 10, 2011·PloS One·Florian Battke, Kay Nieselt
Mar 9, 2011·Statistical Applications in Genetics and Molecular Biology·Claus-Dieter MayerGraham W Horgan
Jun 15, 2011·Bioinformatics·Stephan Symons, Kay Nieselt
Oct 18, 2011·Artificial Intelligence in Medicine·Thanh-Phuong Nguyen, Tu-Bao Ho
Oct 25, 2011·Genome Biology·Svitlana TyekuchevaGiovanni Parmigiani
Nov 29, 2011·BMC Bioinformatics·Laila M PoissonDebashis Ghosh
Jun 16, 2012·Biostatistics·Alexandra JauhiainenRebecka Jörnsten
Jul 21, 2012·Bioinformatics·Dmitry Grapov, John W Newman
Oct 11, 2012·Bioinformatics·Paul KirkDavid L Wild
Nov 13, 2012·BMC Systems Biology·Hendrik RohnFalk Schreiber
Dec 19, 2012·Journal of Biomedical Semantics·Pedro Lopes, José Luís Oliveira
Aug 1, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Mitsunori KayanoSatoru Miyano
Aug 10, 2013·BMC Systems Biology·Ali EbrahimDaniel R Hyduke
Oct 15, 2013·Molecular BioSystems·Ettore Mosca, Luciano Milanesi
Jan 21, 2014·Bioinformatics·Yupeng Cun, Holger Fröhlich
Mar 4, 2014·The Annals of Applied Statistics·Ronglai ShenQianxing Mo
May 7, 2014·Genetic Epidemiology·Heather E WheelerHae Kyung Im
Feb 14, 2015·PLoS Computational Biology·Eric BonnetTom Michoel
May 13, 2015·BMC Bioinformatics·Michele FratelloDario Greco
Jun 26, 2015·BioData Mining·Tomasz WallerWiktor Jurkowski
Aug 19, 2015·BMC Bioinformatics·Angela SerraDario Greco
Jan 21, 2016·Bioinformatics·Daniel StöckelHans-Peter Lenhof
Mar 11, 2016·BMC Bioinformatics·Claudio AngionePietro Lió
May 11, 2016·Biometrics·Eric C ChiRichard G Baraniuk
Aug 25, 2016·BMC Bioinformatics·Alok SharmaTatsuhiko Tsunoda

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Citations

Aug 8, 2018·Osteoporosis International : a Journal Established As Result of Cooperation Between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA·Y S ZhangZ K Zhou
May 28, 2019·Molecular & Cellular Proteomics : MCP·Burcu VitrinelChristine Vogel
Nov 18, 2018·Electrophoresis·Biswapriya B Misra, Subhashree Mohapatra
Dec 11, 2019·Human Reproduction Update·Loren MéarFrançois Vialard
Jan 9, 2020·Bioinformatics·Xiaqiong Wang, Yalu Wen
Jul 12, 2019·PLoS Computational Biology·Guido ZampieriClaudio Angione
Aug 15, 2020·Briefings in Bioinformatics·Mengyun WuShuangge Ma
Apr 3, 2019·BMC Bioinformatics·Wei GuUNKNOWN IMI OncoTrack and the IMI eTRIKS consortia
Sep 10, 2020·Frontiers in Pharmacology·Sandip Kumar PatelVineeta Rai
Feb 6, 2020·Digestive Diseases and Sciences·Ivan Ivanov
Mar 30, 2020·European Journal of Epidemiology·Susana SantosMartine Vrijheid
Jun 9, 2018·Frontiers in Medicine·Anna R Hemnes
Jul 28, 2020·Frontiers in Oncology·Marco ChiericiCesare Furlanello
Aug 9, 2019·Molecular & Cellular Proteomics : MCP·Burcu VitrinelChristine Vogel
Jun 12, 2020·Journal of Biomedical Informatics·Zahra MomeniRiccardo Bellazzi
Nov 2, 2021·Frontiers in Endocrinology·Yu-Sheng ZhangBao-Cheng Xie

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Methods Mentioned

BETA
PCA
feature extraction

Software Mentioned

PARADIGM
TUCKER3
R package randomForest
SysBiomics
Angione
iClusterPlus
netClass
BisoGenet
R package metanetwork
CNAmet

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