Phenolyzer stands for Phenotype Based Gene Analyzer, a tool focusing on discovering genes based on user-specific disease/phenotype terms.

Get Started Post result

Please use semicolon or enter as separators. Like "alzheimer;brain".
Try to use multiple terms instead of a super long term
OMIM IDs are also accepted, like 114480 for 'Breast cancer'
Please enter 'HP:0002459;HP:0010522;HP:0001662' as HPO IDs.
Please separate genes by semicolon or enter. Entrez IDs are also accepted here.
Bed File


OMIM database is now updated to 2016-08-04 version!


OMIM database is now updated to 2016-01-24 version!


Due to copyright issues, GeneCards database is no longer provided in Phenolyzer.


Dear all, you might have experienced some changes in your result. Don't panic! There's been several big updates in NCBI's Biosystem database. We recently noticed it and updated the database in Phenolyzer! Toast!


1) OMIM database was updated to 2015-11-19

2) We added a functionality specifically for Chinese, now you can entern chinese and click 'Translate' to translate your disease into English!


1) We really apologize for a tricky server bug! The submission ID jumps back to 1 suddenly. NOTICE: It's been fixed now but the submissions with ID smaller than 150 won't be processed. Please submit your disease again.
2) OMIM database was updated again.


OK, it's really bad to have a server failure. Due to our environment re-setup, I just found the wordcloud is not working. We have just fixed it!


Due to a recent server failure and server environment re-setup, the result from 2015-09-28 to 2015-10-05 is not correct! Please rerun your analysis!


Please notice you can now post your findings on Phenolyzer!

Phenolyzer 0.1.4 was released! A bug in Bioperl dependency was fixed. Now it is strictly required to install Bioperl before you can use Phenolyzer.'.


Now the HPO Identifiers are supported. For example, please enter 'HP:0002459; HP:0010522; HP:0001662'.


The addon databases only contribute 25% now as they are not confident as original databases!


Finally, Phenolyzer is published in Nature Methods!


The HPO ontology and anotation, DO ontology, and OMIM disease synonyms are updated to the newest version!


The OMIM,GWAS Catalog, ClinVar databases are updated to the newest version!


Two additional gene scores were added into Phenolyzer as annotations: Gene Haploinsufficiency Score for dominant disease genes, and Gene Intolerance Score for severe disease genes


A minor bug in '' script was fixed.


The Phenolyzer v0.1.1 is released. A script named '' for integrating ANNOVAR result and Phenolyzer result is available! A detailed user mannual is provided in Tutorial!


The Phenolyzer v0.1.0 is released.Now no R packages need to be installed by the user for the utility of command line wordcloud function.

The HPO terms corresponding to each term (if existing) are also available in the result!.


The GeneReview score has been recalculated, for each GeneReview book, the score will not be repeatedly calculated for different specific OMIM diseases.


The 'Regulates' relations are now penalized to a quarter, which does not affect the performance and prevents the general transcription factors to show up on top.


Several important databases are integrated as the form of plugins: Mentha protein-protein interaction database for gene-gene mapping, , DisGenet gene-disease database, Genetic Association Database, GeneCards for disease-gene mapping!

Now the database for disease-gene relations have more than 100000 records!

The Addon Databases could be found and selected below!