Downloads Disease-Associated Genes

predictions

Predictions

Predicted probabilities of association between all genes (rows) and diseases (columns).

predictions.txt.gz

Features

The features (columns) computed for each gene-disease pair (rows). Column names with beginning with 'XB' refer to standardized features.

features.txt.gz

Model Coefficients

Standardized and unstandardized coefficients from the ridge and lasso logistic regression models.

coefficients.txt


resources

Protein-coding Genes

Information on the included protein-coding genes, derived from the HGNC database.

genes.txt

Complex Diseases

All diseases with at least one GWAS-Catalog-extracted association. The manual pathophysiology classification is included.

diseases.txt

Tissue-specific Gene Expression

A processed version of the GNF BodyMap providing a gene's (row, HGNC symbols) expression value for each of 77 tissues (columns, BRENDA Tissue Ontology IDs).

expression.txt.gz

Gene-Disease Associations

All gene-disease associations extracted from the GWAS catalog for the four categories of association.

gene-associations.txt

Processed GWAS Catalog Loci

The associated gene-disease loci (regions) derived from the GWAS Catalog.

loci-associations.txt

Disease Localization

Literature co-occurrence between diseases and tissues calculated using CoPub 5.0.

disease-localization.txt

Protein-Protein Interactions

Protein-protein interactions processed from iRefIndex using ppiTrim. ppiTrim converts to gene space, consolidates duplicate interactions, and removes complexes.

protein-interactions.txt.gz


network

Serialized Network

A JSON formatted text file storing the complete network. The top level is an JSON object with four pairs (metanodes, metaedges, nodes, edges). The value for each pair is a JSON array containing the corresponding items.

network.json.gz

Network Tables

A table of network edges (sif format) and a table of node attributes.

network-tables.zip


vizualization

Vector Images

PDF formatted versions of the figures.

figures.zip