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Bioinformatics Advance Access published online on January 29, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth010
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received September 11, 2003
Revised October 15, 2003
Accepted October 16, 2003

Article

The Hera database and its use in the characterization of endoplasmic reticulum proteins

M. Scott 1, G. Lu 2, M. Hallett 1, D. Y. Thomas 3*

1 McGill Center for Bioinformatics, Duff Medical Building, McGill University, 3755 University Street, Montreal, Quebec, Canada, H3A 2B4
2 Center for Biotechnology and School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
3 Biochemistry Department, Faculty of Medicine, McGill University, McIntyre Medical Sciences Building, 3655 Promenade Sir William Osler, Montreal, Quebec, Canada, H3G 1Y6

* To whom correspondence should be addressed. E-mail: david.thomas{at}mcgill.ca.


  Abstract

Motivation: Information concerning endoplasmic reticulum (ER) proteins is widely dispersed and cannot be easily and rapidly processed by the biological community. We present a comprehensive database of human ER proteins, called Hera (Human ER Aperçu). The Hera database was constructed by exhaustively searching through public databases and the scientific literature for ER proteins.

Results: Hera was used for the analysis of characteristics common to all human ER proteins. Our results show that a high proportion of ER proteins (59%) have at least one transmembrane domain and display physical characteristics consistent with this observation. In addition, one third of ER proteins contain known ER retrieval or retention signals and 70% of ER proteins contain a signal peptide or anchor. Finally, 85% percent of ER proteins contain at least one InterPro motif. The most abundant InterPro motifs in ER proteins represent many of the most well-characterized functions of the ER.

Availability: Hera is available at http://www.mcb.mcgill.ca/~hera


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