Cytomer -

A database on gene expression sources

Ellen Fricke, Xin Chen, Edgar Wingender
Biobase Biological Databases GmbH, Mascheroder Weg 1b, D-38124 Braunschweig
Gesellschaft für Biotechnologische Forschung mbH, Mascheroder Weg 1, D-38124 Braunschweig


Although only few relatively small genomes have been completely sequenced thus far, the end of the human genome sequencing poject is conceptually anticipated by the community in proclaiming the start of the "post-genomic era" or the period of "functional genomics". Systematic elucidation of gene function requires to link sequence data with information about molecular mechanisms, and also with histological, anatomical and even taxonomical data. As a consequence, even "classical" branches of biological and medical research gained interest when linked to genome-based information.

Content and structure of the database

We have developed a relational database system which is aiming at providing a comprehensive overview on all expression sources.  Gene expression sources are organs, tissues, cell types and developmental stages. Therefore CYTOMER is a database of physiological systems (Ssystem-table), developmental stages (Sstage-table), anatomical structures and substructures (Sorgan-table) and the constituting cell-types (Scell-table). The central table of CYTOMER is Hub which is a list that links entries of four other tables. The Hub-table represents anatomical / histological knowledge about which cells occur with what kind of function in which organs and at what stages.
The CYTOMER database is applied to map expression patterns as the TRANSFAC database gives. Therefore entries of the Hub-table have been linked with human transcription factor entries in the TRANSFAC factor table: 1) CP (Cytomer positive)-column for those expression sources where a certain factor has been shown to be expressed in and 2) CN (Cytomer negative)-column for those expression sources where no evidence of a certain factor has been published.
CYTOMER is first of all a TRANSFAC-complementing module which enables proper representation of expression patterns. However, CYTOMER is going to be extended to an independent database system which provides customers with specific aims.


The most extensive table of CYTOMER is the Sorgan-table. The Sorgan-table is itself hierarchically organized and is representing primary organs and their substructures:   respiratory system (you will find in the Ssystem-table) consists of  lung and bronchial tree (Sorgan-table)

Lungs in Situ: Anterior view

Bronchial Tree

Bronchial Tree

Abbreviations of S-organ-table: Organ-Acc (organ accession number),
A_H (number of anatomical hierarchies), A_Parent (anatomical parent)

*The alveolar epithelium consits of type I + II pneumocytes; these cell types you will find in the Cell-table