THREE-WAY CLUSTERING OF MULTI-TISSUE MULTI-INDIVIDUAL GENE EXPRESSION DATA USING SEMI-NONNEGATIVE TENSOR DECOMPOSITION.
15A69
62H30
Primary 62P10
clustering
gene expression
secondary 62H25
tensor decomposition
tensor projection
Journal
The annals of applied statistics
ISSN: 1932-6157
Titre abrégé: Ann Appl Stat
Pays: United States
ID NLM: 101479511
Informations de publication
Date de publication:
Jun 2019
Jun 2019
Historique:
entrez:
31
12
2020
pubmed:
1
1
2021
medline:
1
1
2021
Statut:
ppublish
Résumé
The advent of high-throughput sequencing technologies has led to an increasing availability of large multi-tissue data sets which contain gene expression measurements across different tissues and individuals. In this setting, variation in expression levels arises due to contributions specific to genes, tissues, individuals, and interactions thereof. Classical clustering methods are ill-suited to explore these three-way interactions and struggle to fully extract the insights into transcriptome complexity contained in the data. We propose a new statistical method, called
Identifiants
pubmed: 33381253
doi: 10.1214/18-aoas1228
pmc: PMC7771883
mid: NIHMS1646872
doi:
Types de publication
Journal Article
Langues
eng
Pagination
1103-1127Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM094402
Pays : United States
Références
Ann N Y Acad Sci. 2013 Jun;1288:36-47
pubmed: 23600975
PLoS Genet. 2017 Mar 23;13(3):e1006599
pubmed: 28333934
Linear Algebra Appl. 2017 May 1;520:44-66
pubmed: 28286347
Nat Genet. 2016 Sep;48(9):1094-100
pubmed: 27479908
Database (Oxford). 2016 Apr 05;2016:
pubmed: 27048349
Neuropathology. 2016 Feb;36(1):50-5
pubmed: 26303144
Nat Rev Genet. 2015 Jul;16(7):375
pubmed: 26077371
Ann Appl Stat. 2013 Mar 1;7(1):523-542
pubmed: 23745156
PLoS Comput Biol. 2016 Jul 28;12(7):e1004791
pubmed: 27467526
World J Methodol. 2012 Aug 26;2(4):27-32
pubmed: 25237614
Science. 2015 May 8;348(6235):648-60
pubmed: 25954001
Ann Appl Stat. 2019 Jun;13(2):1103-1127
pubmed: 33381253
Sci Rep. 2015 Oct 19;5:15145
pubmed: 26477495
Nature. 2012 Sep 20;489(7416):391-399
pubmed: 22996553
Am J Med Genet B Neuropsychiatr Genet. 2013 Dec;162B(8):889-97
pubmed: 24591081
Nature. 2017 Oct 11;550(7675):204-213
pubmed: 29022597
Nat Med. 2017 Jun;23(6):678-680
pubmed: 28459436
Ann Appl Stat. 2010 Sep 1;4(3):1579-1601
pubmed: 21116451
PLoS Comput Biol. 2015 May 13;11(5):e1004220
pubmed: 25970446
Nat Genet. 2013 Jun;45(6):580-5
pubmed: 23715323
Psychometrika. 1966 Sep;31(3):279-311
pubmed: 5221127
Nat Genet. 2009 Feb;41(2):192-8
pubmed: 19136949
Science. 2015 May 8;348(6235):660-5
pubmed: 25954002
Proc Natl Acad Sci U S A. 2007 Nov 20;104(47):18371-6
pubmed: 18003902