This tutorial describes an example of the usage of PhenPathTOOL. We used the study case of Tourette syndrome, that is also reported in PhenPath paper (actually under review). The aims of this tutorial are:
i) to explain how to retrieve a characterized disease starting from a list of phenotypes;
ii) to show the possibility to enrich the annotation of the phentoypes in input with biological functions.

Tourette syndrome is a neurobehavioral disorder that causes motor and vocal tics associated with behavioural abnormalities, like attention-deficit-hyperactivity disorder and obsessive-compulsive disorder.
Possible symptoms include involuntary or semi-voluntary movements or sounds, repetitive movements, blinking, nose twitching, throat clearing to echolalia or coprolalia.
We searched with PhenPathTOOL the typical phenotypic traits of the Tourette syndrome, using a plain list of phenotype names (motor tic, vocal tic, behavioral, attention, hyperactivity, obsessive compulsive, involuntary movements, involuntary sounds, repetitive movements, blink, nose twitch, throat clear, echolalia, coprolalia).
Phenotypes can be inputted with their common names and the interface presents a list of HPO identifiers for the different phenotype names, allowing the user to select the right official HPO in a user-friendly way (Figure 1).


Figure 1: Selection of phenotypes in PhenPathTOOL.
After searching with a list of different names, the web interface shows all the names that do not correspond to any HPO identifier and then a table with all the HPO terms matching the input.
The user may then select the most appropriate phenotypes to be analysed.

We find out that attention, hyperactivity, behavioral, echolalia, involuntary movements, motor tic, obsessive compulsive match 12 HPO identifiers.
Out of them, we selected 6 HPO to perform further analyses: attention deficit hyperactivity disorder (HP:0007018), behavioral abnormality (HP:0000708), echolalia (HP:0010529), involuntary movements (HP:00043059), motor tics (HP:0100034), obsessive-compulsive behavior (HP:0000722).
PhenPathTOOL returns the diseases and genes shared among the phenotypes, as long as the shared enriched pathways (GO terms, KEGG and REACTOME, Figure 2).


Figure 2: PhenPathTOOL results.
The figure shows the webpage of PhenPathTOOL after the analysis of 6 different HPO phenotypes. First, a list of the shared diseases and genes is reported.
Then, a general table collects data on diseases and genes associated with each phenotype, allowing direct comparisons.
The last section reports the links to the analysis of GO terms, KEGG and Reactome pathways.

PhenPathTOOL correctly recognizes that the concomitance of phenotypes points to the Tourette syndrome, and to two genes (SLITRK1, HDC) that are associated to the disease in eDGAR.
Interestingly enough, while the enrichment procedure on the two genes does not retrieve any significant results (see the eDGAR page corresponding to the Tourette syndrome), the intersection of functional terms shared by different phenotypes is able to retrieve relevant annotations. No GO terms for biological process is shared among the 6 phenotypes.
Nevertheless, 30 terms are shared by at least 4 phenotypes.
Among them, besides the general annotations like behavior, cognition or learning or memory, there are interesting clues on more specific pathways such as catecholamine metabolic process.
Interestingly, symptomatic therapies for the Tourette syndrome involve the control of neurotransmission from dopamine and adrenaline, that are member of the catecholamine family.
Moreover, although the pathogenesis of the disorder remains obscure, this pathway has already been studied in relation to Tourette syndrome.