geneORGANizer by carmelab Hebrew University of Jerusalem


Download links are near the bottom of this page

Gene-Body Part association tables

Here you can download the data sets representing the links between genes and body parts. Each file is an Excel workbook, within which there are four worksheets, one for each of the four annotation levels: organs, systems, regions and germ layers.

The two leftmost columns contain the gene symbol and the ENTREZ uid. The next columns mark associations between the body part whose name appears in the column heading.  links are marked by "1" (the gene affects the body part) or "0" (the gene is not known to affect the body part). The example figure shows the topmost rows of the Gene ORGANizer Confident Typical table. The table version is in the worksheet header.


GeneORGANizer headings v7


Gene-Disease-Phenotype-Body Part association tables

The next set of tables describes the associations between a gene, a body part, and diseases or phenotypes according to the literature. These cross tabulations are the source for generating the gene-phenotype links in the tables above. Again one table for each annotation level: organs, systems, and germ layers. These are compressed comma-delimited files.

A phenotype that is associated with a gene and a body part will appear under the columns HPOTermName and HPOTermID. HPO, the Human Phenotype Ontology, is a vocabulary of human phenotype abnormalities. Each phenotype is identified by a code, and this code is listed alongside its human-readable term. If a disease is further associated with this triplet of gene-organ-phenotype, according to OMIM, the Online Mendelian Inheritance in Man or ORPHANET, the catalog of rare diseases, the disease's code and convention will appear under the columns OMIMID and diseaseName. A disease may however be directly associated with a gene-organ pair, in which case no phenotype is found to describe it. In such case the disease identifier begins with umls, a prefix that signifies a DisGeNET origin. The top rows of the table for organ annotations is shown in the screenshot below

DiseaseORGANizer headings v11


Files for download

Gene-Body Part associations

Gene-Disease-Phenotype-Body Part associations


Database revisions

Current version is Ver 12 (published Sep 18, 2016)
Older versions are located here  


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Database last updated on 18 September 2016, 22:49 by moc.balemrac@rezinagroeneg (v12)