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This article is part of the supplement: Proceedings of the Eighth Annual MCBIOS Conference. Computational Biology and Bioinformatics for a New Decade

Open Access Proceedings

HOMER: a human organ-specific molecular electronic repository

Fan Zhang13 and Jake Y Chen123*

Author Affiliations

1 School of Informatics, Indiana University, Indianapolis, IN 46202, USA

2 Department of Computer and Information Science, School of Science, Purdue University, Indianapolis, IN 46202, USA

3 Indiana Center for Systems Biology and Personalized Medicine, Indianapolis, IN 46202, USA

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BMC Bioinformatics 2011, 12(Suppl 10):S4  doi:10.1186/1471-2105-12-S10-S4

Published: 18 October 2011

Abstract

Background

Each organ has a specific function in the body. “Organ-specificity” refers to differential expressions of the same gene across different organs. An organ-specific gene/protein is defined as a gene/protein whose expression is significantly elevated in a specific human organ. An “organ-specific marker” is defined as an organ-specific gene/protein that is also implicated in human diseases related to the organ. Previous studies have shown that identifying specificity for the organ in which a gene or protein is significantly differentially expressed, can lead to discovery of its function. Most currently available resources for organ-specific genes/proteins either allow users to access tissue-specific expression over a limited range of organs, or do not contain disease information such as disease-organ relationship and disease-gene relationship.

Results

We designed an integrated

    H
uman
    O
rgan-specific
    M
olecular
    E
lectronic
    R
epository (HOMER, http://bio.informatics.iupui.edu/homer webcite), defining human organ-specific genes/proteins, based on five criteria: 1) comprehensive organ coverage; 2) gene/protein to disease association; 3) disease-organ association; 4) quantification of organ-specificity; and 5) cross-linking of multiple available data sources.

HOMER is a comprehensive database covering about 22,598 proteins, 52 organs, and 4,290 diseases integrated and filtered from organ-specific proteins/genes and disease databases like dbEST, TiSGeD, HPA, CTD, and Disease Ontology. The database has a Web-based user interface that allows users to find organ-specific genes/proteins by gene, protein, organ or disease, to explore the histogram of an organ-specific gene/protein, and to identify disease-related organ-specific genes by browsing the disease data online.

Moreover, the quality of the database was validated with comparison to other known databases and two case studies: 1) an association analysis of organ-specific genes with disease and 2) a gene set enrichment analysis of organ-specific gene expression data.

Conclusions

HOMER is a new resource for analyzing, identifying, and characterizing organ-specific molecules in association with disease-organ and disease-gene relationships. The statistical method we developed for organ-specific gene identification can be applied to other organism. The current HOMER database can successfully answer a variety of questions related to organ specificity in human diseases and can help researchers in discovering and characterizing organ-specific genes/proteins with disease relevance.