TEDD: a database of temporal gene expression patterns during multiple developmental periods in human and model organisms

Article


Zhou, Z., Tan, C., Chau, M. H. K., Jiang, X., Ke, Z., Chen, X., Cao, Y., Kwok, Y. K., Bellgard, M., Leung, T. Y., Choy, K. W. and Dong, Z. 2023. TEDD: a database of temporal gene expression patterns during multiple developmental periods in human and model organisms. Nucleic Acids Research. 51 (D1), pp. D1168-D1178. https://doi.org/10.1093/nar/gkac978
AuthorsZhou, Z., Tan, C., Chau, M. H. K., Jiang, X., Ke, Z., Chen, X., Cao, Y., Kwok, Y. K., Bellgard, M., Leung, T. Y., Choy, K. W. and Dong, Z.
Abstract

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/.

JournalNucleic Acids Research
Journal citation51 (D1), pp. D1168-D1178
ISSN 0305-1048
Year2023
PublisherOxford University Press
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Digital Object Identifier (DOI)https://doi.org/10.1093/nar/gkac978
Publication dates
Print09 Nov 2022
Publication process dates
Accepted15 Oct 2022
Deposited21 Apr 2023
FunderShenzhen Science and Technology Innovation Committee
Health and Medical Research Fund
Collaborative Research Fund
Guangdong Genomics Data Center
Direct Grant for Research, The Chinese University of Hong Kong
Copyright holder© 2022, The Authors
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