TRED: a transcriptional regulatory element database, new entries and other development

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Transcriptional factors (TFs) and target genes are crucial for gene regulation.
• Understanding transcriptional regulatory elements is key to deciphering gene regulatory networks (GRNs).
• TRED serves as a curated resource for mammalian gene regulation and function studies.

Purpose of the Study:

• To update and expand the TRED database with new mammalian cis- and trans-regulatory elements.
• To incorporate 36 TF families involved in cancer, increasing the dataset's relevance for cancer research.
• To facilitate the construction and analysis of gene regulatory networks.

Main Methods:

• Curating mammalian cis- and trans-regulatory elements and experimental evidence.
• Mapping regulatory elements to assembled genomes.
• Integrating TF families, target promoters, and target genes into the TRED database.
• Constructing GRNs by connecting TF-target gene pairs.

Main Results:

• The TRED database now includes 36 TF families implicated in cancer.
• A significant increase in the number of target genes (11,660) and target promoters (14,908) across human, mouse, and rat.
• GRNs were constructed for each TF family, providing interaction data.

Conclusions:

• The expanded TRED database offers a comprehensive resource for gene regulation studies, particularly in cancer.
• The integrated GRNs provide valuable insights into TF-target gene interactions.
• This resource will aid in detailed functional studies and understanding complex GRNs in cancer research.