SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 07 2019
01 07 2019
Historique:
received:
31
05
2018
revised:
24
10
2018
accepted:
26
11
2018
pubmed:
28
11
2018
medline:
12
6
2020
entrez:
28
11
2018
Statut:
ppublish
Résumé
Skeletal diseases are prevalent in society, but improved molecular understanding is required to formulate new therapeutic strategies. Large and increasing quantities of available skeletal transcriptomics experiments give the potential for mechanistic insight of both fundamental skeletal biology and skeletal disease. However, no current repository provides access to processed, readily interpretable analysis of this data. To address this, we have developed SkeletalVis, an exploration portal for skeletal gene expression experiments. The SkeletalVis data portal provides an exploration and comparison platform for analysed skeletal transcriptomics data. It currently hosts 287 analysed experiments with 739 perturbation responses with comprehensive downstream analysis. We demonstrate its utility in identifying both known and novel relationships between skeletal expression signatures. SkeletalVis provides users with a platform to explore the wealth of available expression data, develop consensus signatures and the ability to compare gene signatures from new experiments to the analysed data to facilitate meta-analysis. The SkeletalVis data portal is freely accessible at http://phenome.manchester.ac.uk. Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 30481257
pii: 5210874
doi: 10.1093/bioinformatics/bty947
pmc: PMC6596879
doi:
Types de publication
Journal Article
Meta-Analysis
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2283-2290Subventions
Organisme : Wellcome Trust
ID : 203128/Z/16/Z
Pays : United Kingdom
Informations de copyright
© The Author(s) 2018. Published by Oxford University Press.
Références
J Mol Endocrinol. 2012 May 29;49(1):1-10
pubmed: 22525354
Bioinformatics. 2016 Oct 1;32(19):3047-8
pubmed: 27312411
Ann Rheum Dis. 2014 Jul;73(7):1397-404
pubmed: 23723318
Arthritis Rheum. 2012 Jul;64(7):2278-88
pubmed: 22307759
PLoS One. 2013;8(1):e54633
pubmed: 23382930
Osteoarthritis Cartilage. 2016 Dec;24(12):2013-2021
pubmed: 27492463
Bioinformatics. 2017 Sep 1;33(17):2774-2775
pubmed: 28481966
Nucleic Acids Res. 2018 Jan 4;46(D1):D246-D251
pubmed: 29165655
Bioinformatics. 2012 Mar 15;28(6):882-3
pubmed: 22257669
Nucleic Acids Res. 2012 Jan;40(Database issue):D400-12
pubmed: 22140110
Funct Integr Genomics. 2018 Jan;18(1):79-87
pubmed: 29134405
Nat Commun. 2016 Nov 29;7:13685
pubmed: 27897169
Nat Commun. 2017 Jun 19;8:15889
pubmed: 28627522
Nucleic Acids Res. 2003 Jan 1;31(1):258-61
pubmed: 12519996
Nucleic Acids Res. 2002 Jan 1;30(1):207-10
pubmed: 11752295
BMC Bioinformatics. 2018 Oct 19;19(1):386
pubmed: 30340461
Ann Rheum Dis. 2018 Mar;77(3):423
pubmed: 29273645
Proc Natl Acad Sci U S A. 2010 May 25;107(21):9546-51
pubmed: 20460310
Osteoarthritis Cartilage. 2013 Apr;21(4):599-603
pubmed: 23376013
Nat Biotechnol. 2016 May;34(5):525-7
pubmed: 27043002
Rheumatol Int. 2012 Dec;32(12):3751-60
pubmed: 22159913
Genome Biol. 2014;15(12):550
pubmed: 25516281
Nucleic Acids Res. 2016 Jul 8;44(W1):W3-W10
pubmed: 27137889
Nat Commun. 2016 Sep 26;7:12846
pubmed: 27667448
Nucleic Acids Res. 2015 Apr 20;43(7):e47
pubmed: 25605792
Nat Genet. 2000 May;25(1):25-9
pubmed: 10802651
Genome Biol. 2010;11(2):R14
pubmed: 20132535
Nucleic Acids Res. 2015 Jan;43(Database issue):D1113-6
pubmed: 25361974
Nat Methods. 2016 Aug 30;13(9):705-6
pubmed: 27575621
Nat Methods. 2017 Nov;14(11):1083-1086
pubmed: 28991892
PLoS One. 2011;6(9):e24600
pubmed: 21935428
J Child Orthop. 2013 Jun;7(3):213-23
pubmed: 24432080
PLoS One. 2011;6(7):e21800
pubmed: 21789182
Arthritis Res Ther. 2013;15(5):R110
pubmed: 24020899
Ann Rheum Dis. 2017 Oct;76(10):1764-1773
pubmed: 28705915
F1000Res. 2015 Dec 30;4:1521
pubmed: 26925227
Neuro Oncol. 2017 Jan;19(1):139-141
pubmed: 28031383
Nucleic Acids Res. 2011 Jan;39(Database issue):D685-90
pubmed: 21071392
J Cell Physiol. 2018 Aug;233(8):6135-6147
pubmed: 29323710
Osteoporos Int. 2014 Apr;25(4):1357-67
pubmed: 24504099
Nucleic Acids Res. 2011 Jan;39(Database issue):D19-21
pubmed: 21062823
NPJ Syst Biol Appl. 2016;2:
pubmed: 28413689
PLoS One. 2017 Oct 31;12(10):e0187030
pubmed: 29088242
J Mol Med (Berl). 2003 Apr;81(4):235-45
pubmed: 12700891
J Orthop Res. 2016 Jul;34(7):1105-10
pubmed: 27176659
Nucleic Acids Res. 2011 Jan;39(Database issue):D28-31
pubmed: 20972220
Bone. 2014 Mar;60:68-77
pubmed: 24333171
Arthritis Rheum. 2003 Jun;48(6):1582-93
pubmed: 12794826
Osteoarthritis Cartilage. 2016 Aug;24(8):1431-40
pubmed: 26973327
Nat Commun. 2016 Jun 22;7:12047
pubmed: 27329220
BMC Bioinformatics. 2004 Jul 23;5:100
pubmed: 15272936
Ann Rheum Dis. 2014 Jul;73(7):1323-30
pubmed: 24553908
Nat Rev Drug Discov. 2017 Dec;16(12):843-862
pubmed: 29104284
BMC Bioinformatics. 2014 Mar 21;15:79
pubmed: 24650281