Phenotype/disease specific gene prioritization and gene network visualization.

Introduction

Phenolyzer is a software aimed at phenotype/disease specific gene prioritization and gene network visualization. It can be used alone to prioritize genes genome-widely, or from user-specified genomic regions or genes. It can also be used to further prioritize genes after the variant annotation and filtering step from other tools, like ANNOVAR.

Workflow

Phenolyzer can take any disease/phenotype related term as input, which makes it very different from most gene prioritization tools. It then interprets the term into a whole bunch of specific professional diseases, and tries to map these diseases into genes through multiple gene-disease relation databaes. Finally Phenolyzer integrates all the information together to assign each gene a score based on its association with the input term. 

Then Phenolyzer grows the seed genes in four different gene-gene relation databases, including most possible gene-gene interaction information, such as protein interaction, bio-pathway, gene complex, gene family and transcription interaction. 

Finally a robust logistic learning method was used to train the parameters for integrating the information of each relation and also the disease mapping. And finally a genome-wide gene ranking list and all the details are in the output.

 

 

Term Interpretation

The first step of Phenolyzer is to interpret each input term into a full set of specific disease names, by synonym and descendent searches. The result of the interpretation for term 'cancer' is used to generate a WordCloud.

 

 

 

Network Visualization

The network contains only top 50 genes with the information of their relative scores and different kinds of relations. The scores of genes are represented by the sizes of the gene ball. The blue gene balls are seed genes, and the yellow gene balls are discovered by relations with seed genes.

The mapping from terms into disease are represented by the pink lines between large term logo and the round rectangle disease names. The mapping from diseases into genes are represented by the pink lines between round rectangles into gene balls.  All the gene-gene interactions with seed genes are also represented in the plot by different colors of lines:

blue for protein interaction,

yellow for the same biosystem,

green for the same gene family,

black for transcription interaction, with arrows pointin to the transcription targets.

 

autism sq 

 

Availability

Phenolyzer is available at http://phenolyzer.usc.edu

Phenolyzer was developed by Hui Yang at Wang Genomics Lab.