Example

Still not understand how to use Phenolyzer? Not a big deal, try some exciting examples here!

Some pregenerated examples could be found below
(Caution: they might not be updated!)

Disease name

Autism

Amyotrophic lateral sclerosis

Phenotype terms as free texts

a list of clinical phenotype terms such as Hypoplasia of the corpus callosum, Bulbous nose and Retrognathia for the same patient below with HPO IDs

a list of clinical phenotype terms such as Bilateral single transverse palmar creases, Brachydactyly, Macrodontia and Myoclonic seizures for a patient

Phenotype terms as HPO IDs

a list of HPO IDs for the same patient above with phenotype terms

Sample commands for Phenolyzer command line tools:

Help:

perl disease_annotation.pl --help
Prioritize 'sleep' genes:

perl disease_annotation.pl sleep -p -ph -logistic -out out/sleep/out
Use the terms in 'disease' file:

perl disease_annotation.pl disease -f -p -ph -logistic -out out/disease/out
Use the cnv.bed region:

perl disease_annotation.pl alzheimer -bedfile cnv.bed -p -ph -logistic -out out/alzheimer/out
Use the Mentha gene-gene interaction database as Addon

perl disease_annotation.pl alzheimer -p -ph -logistic -out out/alzheimer_addon/out -addon_gg DB_MENTHA_GENE_GENE_INTERACTION -addon_gg_weight 0.05

All Rights Reserved @Wang Genomics Lab 2010-