Category Genomics>Genetic Data Analysis/Tools

Abstract CIPHER (Correlating protein Interaction networks and PHEnotype networks to pRedict disease genes) is a software tool that can be used to predict and prioritize disease genes.

Deciphering the genetic basis of human diseases is an important goal of biomedical research.

On the basis of the assumption that similar diseases are caused by functionally related genes, the manufacturer proposes a computational framework (CIPHER) that integrates human protein-protein interactions, disease phenotype similarities, and known gene-phenotype associations in order to capture the complex relationships between phenotypes and genotypes.

The manufacturer shows that the global concordance between the human protein network and the phenotype network reliably predicts disease genes.

Their method is applicable to genetically uncharacterized phenotypes, effective in the genome-wide scan of disease genes, and also extendable to explore gene cooperativity in complex diseases.

The predicted genetic landscape of over 1,000 human phenotypes reveals the modular organization of phenotype-genotype relationships and contributes to the understanding of how genotype may determine phenotype.

The genome-wide prioritization of candidate genes for over 5,000 human phenotypes, including those with under-characterized disease loci or even those lacking known association, is publicly released to facilitate the future discovery of disease genes.

The manufacturer's website hosts two (2) versions of the predicted genetic landscape of human disease.

One is predicted using a highly reliable protein interaction network, the Human Protein Reference Database (HPRD - see below).

The other version is predicted on an extended network which combines several high quality protein interaction databases.

According to the manufacturer, the results based on the HPRD network may be more reliable, while the other one based on the extended network may be more advanced in discovering novel disease genes.

Human Protein Reference Database (HPRD) --

The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.

All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data.

HPRD has been created using an object oriented database in Zope, an open source web application server, which provides versatility in query functions and allows data to be displayed dynamically.

A Predicted Genetic Landscape of Human Disease --

The manufacturer has performed in silico genome-wide screen of disease genes for almost all human diseases.

The pair-wise associations between 5,080 human disease phenotypes and 14,433 human genes are calculated by their novel disease gene prediction program CIPHER.

Their website provides a search interface of the top 1,000 candidate genes for each disease phenotype. The whole dataset can also be downloaded.

Please refer to the following paper for additional details:

Wu X, Jiang R, Zhang MQ, Li S (2008) Network-based global inference of human disease genes. Molecular Systems Biology, 4:18

Note: The manufacturer intends to update their website to make it more user-friendly for biologists.

They will also integrate gene annotations, map the scores onto the genome, visualize the results onto protein interaction networks, provide tools for retrieving a specific disease or gene, etc.

Contact their web-site for additional data on "The predicted genetic landscape of human disease".

System Requirements



Manufacturer Web Site CIPHER

Price Contact manufacturer.

G6G Abstract Number 20415

G6G Manufacturer Number 104044