TY - JOUR
T1 - HOMER
T2 - A human organ-specific molecular electronic repository
AU - Zhang, Fan
AU - Chen, Jake Y.
N1 - Funding Information:
This work was supported by a grant from the National Cancer Institute (U24CA126480-01), which is a part of NCI’s Clinical Proteomic Technologies Initiative (http://proteomics.cancer.gov). The grant was awarded to Dr. Fred Regnier (PI) and Dr. Jake Chen (co-PI). We thank for their support the Indiana Center for Systems Biology and Personalized Medicine. We thank Sumit Makashir and Hrishikesh Lokhande for help with data analysis, data collection, and web development. We especially thank David Michael Grobe from UITS at Indiana University for thoroughly proofreading the manuscript. We also thank three anonymous reviewers for comments that helped us improve this manuscript. This article has been published as part of BMC Bioinformatics Volume 12 Supplement 10, 2011: Proceedings of the Eighth Annual MCBIOS Conference. Computational Biology and Bioinformatics for a New Decade. The full contents of the supplement are available online at http://www. biomedcentral.com/1471-2105/12?issue=S10.
PY - 2011/10/18
Y1 - 2011/10/18
N2 - 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 Human Organ-specific Molecular Electronic Repository (HOMER, http://bio.informatics.iupui.edu/homer), 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.
AB - 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 Human Organ-specific Molecular Electronic Repository (HOMER, http://bio.informatics.iupui.edu/homer), 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.
UR - http://www.scopus.com/inward/record.url?scp=80054103029&partnerID=8YFLogxK
U2 - 10.1186/1471-2105-12-S10-S4
DO - 10.1186/1471-2105-12-S10-S4
M3 - Article
C2 - 22165817
AN - SCOPUS:80054103029
SN - 1471-2105
VL - 12
JO - BMC Bioinformatics
JF - BMC Bioinformatics
IS - SUPPL. 10
M1 - S4
ER -