Homer

The Human Organ-specific Molecule Electronic Repository (Homer) is a comprehensive database covering about 22809 proteins, 52 organs, and 4290 diseases integrated and filtered from organ-specific protein/genes and disease databases like dbEST[1], TiSGeD[2], HPA[3], CTD[4], and Disease Ontology[5]. It is the first comprehensive database that can be used to analyze, identify, and characterize organ-specific biomarkers in association with disease-organ and disease-protein relationships. The database has a web user interface that allows users to query organ-specific genes/proteins by gene, protein, organ, or disease, to browse organ-specific genes/proteins by human organ system and disease ontology, to explore a histogram of each organ-specific gene/protein, and to identify disease-related genes or disease-related organs.
The Homer is created based on four criteria: 1) organ-specific gene expression; 2) gene/protein-disease association; 3) specificity and abundance of genes/proteins across multiple target organs; and 4) disease-organ association. As of the current release, Hommer contains 22809 proteins (IPI IDs), 5703 genes (gene IDs), 52 organs, and 4290 diseases (Mesh IDs) of which 4492 are disease-related organ-specific genes (gene IDs) and 2000 are identified as organ-specific markers (gene IDs) (Table 1). A comparison of organ-specific biomarkers in Homer against several common human tissue/organ-specific data sources is shown in Table 2.

Table 1 - Current Statistics of Database

Table 2 - A Comparison of Human Organ-Specific Biomarkers in Hommer against Several Common Human Tissue/Organ-Specific Data Sources

*1359 gene IDs was filtered out from 54, 576 human unigene IDs with TissueSpecificityIndex = 1. We used TissueSpecificityIndex = 1 as the website doesn¡¯t recommend any criteria for us to derive organ-specific genes.
** 1494 of 6698 Unigene IDs were retired.
*** 957 gene IDs was filtered out from 2423 gene IDs with SPM 0.9. We used SPM 0.9 as the website doesn¡¯t recommend any criteria for us to derive organ-specific genes.

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