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

Area of Science:

• Genomics
• Developmental Biology
• Bioinformatics

Background:

• Understanding gene expression and chromatin profiles is crucial for studying development and disease mechanisms.
• The increasing volume of single-cell sequencing data presents challenges in data mining and reanalysis.

Purpose of the Study:

• To systematically curate and analyze large-scale sequencing datasets to create a comprehensive database of gene expression and chromatin profiles during development.
• To develop a user-friendly platform, TEDD, for researchers to explore temporal and cell-type specific gene expression patterns and regulatory interactions.

Main Methods:

• Systematic curation of 2760 bulk samples and over 5.1 million single-cell sequencing datasets from humans and model organisms.
• Unified and systematic analysis to profile gene expression and chromatin accessibility across 481 cell types, 79 tissue types, and 92 timepoints.
• Identification of co-expressed genes, temporal/cell-type specific expression patterns, and potential upstream/downstream gene-gene regulatory interactions within biological processes and KEGG pathways.

Main Results:

• Creation of the Temporal Expression during Development Database (TEDD) with a user-friendly interface.
• Comprehensive profiling of gene expression and chromatin accessibility across diverse cell types, tissues, and developmental timepoints.
• Facilitation of the identification of genes associated with specific developmental stages, cell types, and potential roles in disease.

Conclusions:

• TEDD provides a valuable resource for researchers to investigate gene functions during development and in disease contexts.
• The database enables detailed analysis of cell-type/tissue-type specific and temporal gene expression and chromatin profiles.
• TEDD facilitates the association of genes with unknown biological functions in development and disease through comprehensive data integration and analysis.