Enter the Matrix: Factorization Uncovers Knowledge from Omics

Trends in Genetics : TIG
Genevieve L Stein-O'BrienElana J Fertig

Abstract

Omics data contain signals from the molecular, physical, and kinetic inter- and intracellular interactions that control biological systems. Matrix factorization (MF) techniques can reveal low-dimensional structure from high-dimensional data that reflect these interactions. These techniques can uncover new biological knowledge from diverse high-throughput omics data in applications ranging from pathway discovery to timecourse analysis. We review exemplary applications of MF for systems-level analyses. We discuss appropriate applications of these methods, their limitations, and focus on the analysis of results to facilitate optimal biological interpretation. The inference of biologically relevant features with MF enables discovery from high-throughput data beyond the limits of current biological knowledge - answering questions from high-dimensional data that we have not yet thought to ask.

References

Mar 4, 1999·Journal of Magnetic Resonance·M F OchsT R Brown
Aug 18, 2000·Neural Networks : the Official Journal of the International Neural Network Society·A Hyvärinen, E Oja
Aug 30, 2000·Proceedings of the National Academy of Sciences of the United States of America·O AlterD Botstein
Sep 6, 2001·Proceedings of the National Academy of Sciences of the United States of America·K FellenbergM Vingron
Oct 24, 2001·Bioinformatics·K Y YeungW L Ruzzo
Feb 12, 2002·Bioinformatics·Wolfram Liebermeister
May 23, 2002·Bioinformatics·T D MoloshokM F Ochs
Nov 13, 2003·Genome Biology·Su-In Lee, Serafim Batzoglou
Dec 16, 2003·Proceedings of the National Academy of Sciences of the United States of America·James C LiaoVwani P Roychowdhury
Mar 16, 2004·Proceedings of the National Academy of Sciences of the United States of America·Jean-Philippe BrunetJill P Mesirov
Sep 28, 2004·Nature Genetics·Eran SegalAviv Regev
Nov 2, 2004·Neural Computation·David R HardoonJohn Shawe-Taylor
Apr 23, 2005·Nature Methods·Rafael A IrizarryWayne Yu
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Mar 2, 2006·BMC Bioinformatics·Ghislain BidautMichael F Ochs
Oct 25, 2006·Proceedings of the National Academy of Sciences of the United States of America·Orly Alter
Aug 22, 2007·PLoS Computational Biology·Andrew E TeschendorffCarlos Caldas
Apr 10, 2008·Nature Reviews. Genetics·Mark I McCarthyJoel N Hirschhorn
Sep 2, 2008·Nature·John NovembreCarlos D Bustamante
Mar 7, 2009·Science·Gordon BellAlex Szalay
Jul 30, 2009·Molecular Systems Biology·Anna Bauer-MehrenFerran Sanz
Jan 6, 2010·Statistical Methods in Medical Research·Rafael A IrizarryTerence P Speed
Jul 16, 2010·Bioinformatics·Timo ErkkiläHarri Lähdesmäki
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
Mar 3, 2012·PLoS Computational Biology·Purvesh KhatriAtul J Butte
May 23, 2012·Cell·Serena Nik-ZainalUNKNOWN Breast Cancer Working Group of the International Cancer Genome Consortium
Jul 19, 2012·Nature Reviews. Genetics·Ziv Bar-JosephItamar Simon
May 23, 2013·IEEE Transactions on Nanobioscience·Elana J FertigMichael F Ochs
Aug 13, 2013·Genomics, Proteomics & Bioinformatics·Ruiqi LiaoShuigeng Zhou
Aug 16, 2013·Nature·Ludmil B AlexandrovMichael R Stratton
Sep 17, 2013·Nature Methods·Matan HofreeTrey Ideker
Nov 16, 2013·Methods in Molecular Biology·Elana J FertigCarlo Colantuoni
Mar 19, 2014·Nature Methods·Andrew RothSohrab P Shah
Nov 18, 2014·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Patricia HeynKarla M Neugebauer
Jan 22, 2015·Nucleic Acids Research·Matthew E RitchieGordon K Smyth

❮ Previous
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Citations

Nov 2, 2019·Genes·Enrique Hernández-LemusSoledad Ochoa
Jul 28, 2020·Frontiers in Oncology·Marco ChiericiCesare Furlanello
Jul 31, 2020·Nature·Wouter MeulemanJohn Stamatoyannopoulos
Sep 21, 2020·Bulletin of Mathematical Biology·Raina S RobevaLouis J Gross
Apr 16, 2019·Frontiers in Neuroscience·David PopovicPeter Falkai
Dec 29, 2019·BMC Bioinformatics·Lingxi ChenShuai Cheng Li
Jun 28, 2019·Molecular & Cellular Proteomics : MCP·Chen MengAedín C Culhane
Sep 11, 2019·International Journal of Molecular Sciences·Nicolas SompairacAndrei Zinovyev
Jun 30, 2019·International Journal of Molecular Sciences·Alessandro GrecoLaura Cantini
Apr 3, 2020·PLoS Computational Biology·Nam D Nguyen, Daifeng Wang
Jul 14, 2020·Frontiers in Oncology·Lauren L Hsu, Aedin C Culhane
Dec 29, 2020·Environmental Pollution·Jeremy P KoelmelKrystal J Godri Pollitt
Feb 3, 2021·PLoS Computational Biology·Anand V SastryBernhard O Palsson
Jan 7, 2021·Nature Communications·Laura CantiniAnaïs Baudot
Aug 9, 2019·Molecular & Cellular Proteomics : MCP·Chen MengAedín C Culhane
Oct 28, 2020·Nature Communications·Shahin MohammadiManolis Kellis
Mar 23, 2021·Frontiers in Genetics·Nuria PlanellDavid Gomez-Cabrero
Apr 9, 2021·Proceedings of the National Academy of Sciences of the United States of America·Kevin E WuJames Zou
May 22, 2021·Nucleic Acids Research·Guangyan ZhouJianguo Xia
Jun 18, 2021·Cell Systems·Yuge JiFabian J Theis
Jul 31, 2021·Cancer Cell·Emily F Davis-MarcisakLuciane T Kagohara
Aug 7, 2021·Genome Biology·Kim-Anh Lê CaoElana Fertig
Aug 12, 2021·Science Immunology·UNKNOWN IMPACC Manuscript Writing Team, UNKNOWN IMPACC Network Steering Committee
Apr 18, 2020·American Journal of Human Genetics·Daniel I ChasmanMiriam S Udler

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Methods Mentioned

BETA
RNA-seq
PCA
scRNA-seq

Software Mentioned

GTEx
Bioconductor package
R
fastICA
CoGAPS
CRAN package

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