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RegulonDB is a database the shows the gene regulatory network in Escherichia coli K12. [1] Specifically it contains information on how transcription factors interact with genes in E. coli, allowing researches to clearly map out the web of gene to gene interactions in the entire E. coli genome.

History Edit

RegulonDB was a project funded by the Center of Genomic Sciences at the University of Mexico and the National Institute of Health in the United States. It was started in 1997 and at the time only described 542 genes, 300 promoters and 533 regulatory interactions. Since then, the database has been expanded to contain, among other things, 4,639 genes, 8,555 promoters and 3,148 regulatory interactions in E. coli. [2]

Usage Edit

RegulonDB

Search field for RegulonDB.

The database is free for everyone to use and is hosted online here. On the website, users can search by gene, operon, regulon, etc. For example, if a search for a gene returns a number of results the appropriate one should be selected by the user. RegulonDB will show the positioning of the gene in the genome, synonyms, DNA sequence, as well as any interactions the gene has with other genes in E. coli.

Importance Edit

The Model Organism Edit

E. coli is known in the microbiology community as a model organism for gram-negative bacteria. The scientific community has agreed that basic concepts of biology can learned and demonstrated in E. coli first and then those ideas can be applied to other organisms. RegulonDB is the result of the cooperation of many scientists which allows easy access for anyone else doing research in the field of microbiology.

Network Motifs Edit

RegulonDB has been extremely important in understanding patterns in genetic networks. Since the early 2000s, Dr. Uri Alon has been a pioneer in area of network motifs. [3] Dr. Alon's research has been instrumental in understanding why organisms have evolved to contain some the same genetic regulatory patterns (e.g. feedforward loop). This work is extremely important in gaining a greater understanding of genetics in general. Dr. Alon's research on network motifs used RegulonDB to identify the genes within E. Coli that were influenced by transcription regulation.[3]

References Edit

  1. http://regulondb.ccg.unam.mx/
  2. http://regulondb.ccg.unam.mx/menu/about_regulondb/regulondb_history/database_summary.jsp
  3. 3.0 3.1 Shen-Orr, Shai S., et al. "Network motifs in the transcriptional regulation network of Escherichia coli." Nature genetics 31.1 (2002): 64-68.