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Levels of gene network representation
Compartmentalization is a characteristic feature of the processes occurring in the gene network. The components of the gene network are scattered throughout organs, tissues, cells, and cell compartments. Three main hierarchical levels are considered in the description of the gene network:
The entities described at this level are organs, tissues, particular types of cells, and secreted proteins and substances affecting other organs, tissues, and cells. The description at this level enables the scattering of the gene network components throughout organs, tissues, and cells to be taken into account.
The entities described at this level are different cell compartments (for example citoplasm, nucles, mitochondria organs, tissues) proteins, RNAs, genes and substances. The description at this level enables the scattering of the gene network components throughout the cell compartments and different molecular levels of the gene network regulation (for example, transcription, translation, active membrane transport, etc.) to be considered.
The regulation of gene transcription is described at this level in detail employing the information from the TRRD database. The TRRD format allows the description of the modular structure of transcription regulatory regions and the hierarchy of their constituent regulatory units: 1) regulatory regions (for example, the 5’- or 3’-flanking regions); 2) promoters, enhancers, silencers, and other extended regulatory units; 3) composite elements ; and 4) transcription factor binding sites.