TEDD: a database of temporal gene expression patterns during multiple developmental periods in human and model organisms.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
06 01 2023
06 01 2023
Historique:
accepted:
15
10
2022
revised:
06
10
2022
received:
09
08
2022
pubmed:
10
11
2022
medline:
12
1
2023
entrez:
9
11
2022
Statut:
ppublish
Résumé
Characterization of the specific expression and chromatin profiles of genes enables understanding how they contribute to tissue/organ development and the mechanisms leading to diseases. Whilst the number of single-cell sequencing studies is increasing dramatically; however, data mining and reanalysis remains challenging. Herein, we systematically curated the up-to-date and most comprehensive datasets of sequencing data originating from 2760 bulk samples and over 5.1 million single-cells from multiple developmental periods from humans and multiple model organisms. With unified and systematic analysis, we profiled the gene expression and chromatin accessibility among 481 cell-types, 79 tissue-types and 92 timepoints, and pinpointed cells with the co-expression of target genes. We also enabled the detection of gene(s) with a temporal and cell-type specific expression profile that is similar to or distinct from that of a target gene. Additionally, we illustrated the potential upstream and downstream gene-gene regulation interactions, particularly under the same biological process(es) or KEGG pathway(s). Thus, TEDD (Temporal Expression during Development Database), a value-added database with a user-friendly interface, not only enables researchers to identify cell-type/tissue-type specific and temporal gene expression and chromatin profiles but also facilitates the association of genes with undefined biological functions in development and diseases. The database URL is https://TEDD.obg.cuhk.edu.hk/.
Identifiants
pubmed: 36350663
pii: 6814466
doi: 10.1093/nar/gkac978
pmc: PMC9825605
doi:
Substances chimiques
Chromatin
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
D1168-D1178Informations de copyright
© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
Nature. 2019 Oct;574(7778):365-371
pubmed: 31597962
Nat Biotechnol. 2021 Sep;39(9):1103-1114
pubmed: 33349700
Nucleic Acids Res. 2021 Jan 8;49(D1):D1413-D1419
pubmed: 33010177
J Genet Genomics. 2022 Jul;49(7):689-692
pubmed: 34973426
Genome Biol. 2019 Dec 23;20(1):296
pubmed: 31870423
Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5
pubmed: 23193258
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Cell. 2018 May 17;173(5):1307
pubmed: 29775597
Science. 2021 Dec 10;374(6573):eabj6641
pubmed: 34882453
Nucleic Acids Res. 2016 Jan 4;44(D1):D726-32
pubmed: 26527727
Cell. 2014 Jun 5;157(6):1324-1338
pubmed: 24906150
Int J Dev Biol. 2004 Feb;48(1):23-9
pubmed: 15005571
Elife. 2017 Dec 05;6:
pubmed: 29206104
Nat Genet. 2022 Jul;54(7):1051-1061
pubmed: 35817981
Sci Adv. 2021 Nov 26;7(48):eabi6178
pubmed: 34818044
Br Med Bull. 1976 Sep;32(3):282-7
pubmed: 788839
Nature. 2020 May;581(7808):303-309
pubmed: 32214235
Gastroenterology. 2017 Feb;152(3):533-545
pubmed: 28003097
Development. 2018 Nov 9;145(21):
pubmed: 30413530
Nat Methods. 2019 Dec;16(12):1289-1296
pubmed: 31740819
Eur J Histochem. 2011;55(3):e25
pubmed: 22073372
Cell. 2021 Jun 24;184(13):3573-3587.e29
pubmed: 34062119
Nat Neurosci. 2021 Apr;24(4):584-594
pubmed: 33723434
Clin Chim Acta. 2016 Dec 1;463:39-44
pubmed: 27732875
Cell. 2016 Oct 6;167(2):566-580.e19
pubmed: 27716510
Nature. 2021 Jul;595(7868):554-559
pubmed: 34163074
Science. 2022 Jun 3;376(6597):eabo0510
pubmed: 35549310
Nature. 2022 Jul;607(7919):540-547
pubmed: 35794482
Science. 2020 Nov 13;370(6518):
pubmed: 33184180
BMC Bioinformatics. 2011 Aug 04;12:323
pubmed: 21816040
Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):2946-51
pubmed: 23382184
Nature. 2020 Dec;588(7839):642-647
pubmed: 33177713
Nucleic Acids Res. 2022 Jan 7;50(D1):D1147-D1155
pubmed: 34643725
Nucleic Acids Res. 2022 Jan 7;50(D1):D867-D874
pubmed: 34634820
PLoS One. 2010 Feb 09;5(2):e9111
pubmed: 20161756
Cell. 2021 Nov 24;184(24):5985-6001.e19
pubmed: 34774128
Science. 2020 Nov 13;370(6518):
pubmed: 33184181
Nucleic Acids Res. 2022 Jan 7;50(D1):D596-D602
pubmed: 34791375
Nucleic Acids Res. 2020 Jan 8;48(D1):D77-D83
pubmed: 31665515
FEBS Lett. 2016 Feb;590(4):559-70
pubmed: 26801864
Nat Commun. 2018 Sep 7;9(1):3634
pubmed: 30194383
Cell. 2022 May 12;185(10):1777-1792.e21
pubmed: 35512705