This document discusses using computational approaches to integrate animal and human phenotype data to identify candidate genes for orphan diseases and enable drug repurposing. It describes using ontologies to make phenotypes comparable across species and using semantic similarity to measure phenotypic similarity. Animal mutant phenotypes are compared to human disease phenotypes to find candidate genes. Pharmacogenomic databases are integrated to enable queries about drugs, genes, genotypes, diseases and pathways. Disease and drug pathways are identified using ontology enrichment analysis. The approach is evaluated using known gene-disease associations, showing it can prioritize candidate genes and predict drug-disease relationships.

1. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Integrative and translational analysis of the
phenome
Robert Hoehndorf
Department of Physiology, Development and Neuroscience
University of Cambridge
26 September 2012

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3. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Translational research
National Cancer Institute:
Translational research transforms scientific discoveries arising from
laboratory, clinical, or population studies into clinical applications
to reduce [disease] incidence, morbidity, and mortality.

6. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Genetic diseases
Almost 4,000 genetic diseases in OMIM have an unknown molecular basis.

7. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Genetic diseases
OrphaNet
5,917 orphan diseases
2,543 genes linked to 2,544 diseases
2,700 diseases indexed with clinical signs

8. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Genetic diseases
Animal models have been shown to be highly successful in studying human disease

9. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Approach
Can we use phenotypes of mutant animal organisms to find
candidate genes for orphan diseases?

10. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Approach
Can we use phenotypes of mutant animal organisms to find
candidate genes for orphan diseases?
1 make animal and human phenotypes comparable
2 systematically analyze the phenome for possible causative
mutations
3 evaluate using real biomedical data

11. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Genetic diseases
PATO and the EQ method enable the integration of phenotype ontologies across species.
use of Entity-Quality definitions
homologous anatomical structures
integration based on species-independent ontologies
Gene Ontology
ChEBI, Protein ontology, Celltype ontology

12. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Genetic diseases
Integration of phenotypes enables direct comparison between species
Proximal fibular overgrowth
Abnormal fibula morphology
(HPO):
(MP):
E: Proximal epiphysis of
E: fibula (MA)
fibula (FMA)
Q: morphology (abnormal)
Q: hypertrophic
UBERON: fibula (MA) orthologous to Fibula (FMA)
FMA: Proximal epiphysis of fibula part-of Fibula
PATO: hypertrophic is-a morphology
Proximal fibular overgrowth is-a Abnormal fibula morphology

13. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Genetic diseases
Experimental data can be integrated through ontologies and explored using automated
reasoning.
integration of phenotype ontologies
yeast, fly, slime mold, worm, fish, mouse, rat, human
ontology-based integration of phenotypes
mutant phenotypes for yeast, fly, slime mold, worm, fish,
mouse, rat
human disease phenotypes from OMIM and OrphaNet
OWL ontology with more than 500,000 classes
OWL reasoner reveals connections between phenotypes

14. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Genetic diseases
Semantic similarity over phenotype ontologies measures phenotypic similarity.
semantic similarity: metric based on information contained in
the axioms of an ontology
pairwise comparison of disease and animal phenotypes
IC (x)
x∈Cl(P)∩Cl(D)
sim(P, D) =
IC (y )
y ∈Cl(P)∪Cl(D)

15. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Genetic diseases
Similarity-based comparison
Evaluation against known gene–disease associations:
OMIM
MGI
OrphaNet

16. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Genetic diseases
OMIM phenotypes
AUC (OMIM): 0.78
AUC (MGI): 0.87

17. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Genetic diseases
OrphaNet phenotypes
AUC (OrphaNet):
0.73
AUC (OMIM): 0.76
AUC (MGI): 0.80

18. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Genetic diseases
Ontology-based integration and analysis can reveal disease genes for orphan diseases.
Adam19 and Fgf15 in mice are strong candidates for
Tetralogy of Fallot
Gene disease associations for orphan diseases
Slc34a1 (MGI:1345284) and Fanconi renotubular syndrome 1
(OMIM:134600)
Disease pathways
Cytokine-cytokine receptor interaction pathway (ko04060) is
significantly correlated with Tetralogy of Fallot (p = 5 · 10−7 ,
Wilcoxon signed-rank test)

19. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Bassoe Syndrome
Signs and symptoms
skeletal:
kyphosis, hypertensible joints, cubitus valgus
muscular:
hypotonia, muscle hypotrophy, amyotrophy
behavior:
abnormal gait, amimia
visual:
cataract, strabismus
reproductive:
hypogonadism, hypogenitalism, abnormal ovaries, hypoplastic
testis, reduced fertility

20. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Bassoe Syndrome
http://phenomebrowser.net

21. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Bassoe Syndrome
HIP1 knockout mice

22. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Bassoe Syndrome
HIP1 mouse phenotypes
Bassoe Syndrome: Mouse phenotypes:
kyphosis, hypertensible kyphosis, abnormal spine curvature,
joints, cubitus valgus lordosis
amyotrophy, hypotonia, abnormal muscle morphology
muscle hypotrophy
abnormal gait, amimia abnormal gait, hypoactivity, tremors
cataract, strabismus
nuclear cataracts, microphthalmia
testicular atrophy,
hypogonadism, testicular atrophy, male infertility
hypogenitalism,
abnormal ovaries,
reduced fertility

23. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Bassoe Syndrome
HIP1 mouse phenotypes
Bassoe Syndrome: Mouse phenotypes:
kyphosis, hypertensible kyphosis, abnormal spine curvature,
joints, cubitus valgus lordosis
amyotrophy, hypotonia, abnormal muscle morphology, muscle
muscle hypotrophy hypotrophy, muscle wasting
abnormal gait, amimia abnormal gait, hypoactivity, tremors,
failure to thrive, ataxia
cataract, strabismus
nuclear cataracts, microphthalmia
testicular atrophy,
hypogonadism, testicular atrophy, male infertility,
hypogenitalism, ovarian abnormalities, testicular
abnormal ovaries, degeneration, increased apoptosis of
reduced fertility postmeiotic spermatids, oligospermia

24. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Bassoe Syndrome
Computational analysis of mouse phenotypes provides a strong
indication that HIP1 may be involved in Bassoe syndrome.

25. Genetic diseases
ROC analysis quantifies the performance of the approach.

27. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Question
Is there a similarity between a knock-out/knock-down of a gene
(through targeted mutation) and the inhibition/negative regulation
of a gene (through a drug action)?

29. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
PhenomeNET compares phenotypes across species

30. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Statistical testing to rank drug–disease pairs
one-sided Wilcoxon signed rank test
result: ranking of drugs for each disease based on p-value

31. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Phenotype-based comparison can provide some information
about drug indications
PhenomeDrug improved
1
0.9
0.8
0.7
AUC (CTD): 0.61
True Positive Rate
0.6
AUC (FDA): 0.67
0.5
0.4
0.3
0.2
0.1 x
original
latest
0
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
False Positive Rate

32. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Future: phenotype-based drug repurposing
similarity between inhibition (drug action) and
knock-out/knock-down (mutation)
effects
indications
targets
combination with interaction networks
D inhibits G1 and G1 positively regulated G2 ⇒ D inhibits G2 .
drug pathways
pharmacodynamics
pharmacokinetics
physiological pathways

33. Pharmacogenomics databases

34. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Aims: queries and integrated analysis
integrate and query knowledge in pharmacogenomics
identify aberrant pathways and patho-physiology underlying
disease
identify drug pathways (pharmacokinetics and
pharmacodynamics)
personalized treatment and dosage guidelines

35. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Approach to data integration in pharmacogenomics
integration of databases containing drug, gene, genotype,
disease and pathway information
DrugBank: drugs and drugs targets
PharmGKB: genotype and drug response
Pathway Interaction Database: biological pathways
CTD: toxicogenomics information (chemical–gene–disease)

36. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Queries
What drugs can be used to treat parasitic infectious diseases
(DOID:1398)?
Chloroquine
Arthemeter
...

37. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Queries
What drugs are effective for diseases affecting the joints
(FMA:7490)?
Folic acid (for arthritis)
Chloroquine (for Chikungunya virus)
...

38. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Queries
What genotypes are related to diseases affecting the joints
(FMA:7490)?
RSID:rs70991108 (with arthritis)
RSID:rs1207421 (Osteoarthritis, Knee)
...

39. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Queries
What genotypes are related to response to steroids
(CHEBI:35341)?
RSID:rs45566039 (with estrogen)
RSID:rs1042713 (with budesonide)
...

40. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Disease and drug pathways
Ontology enrichment analysis can identify over-represented ontology classes.
ontology-based, statistical approach to identify drug and
disease pathways
use graph structure of ontology to identify statistically over-
and under-represented ontology classes
aims:
identify over-represented disease classes (in disease ontology)
for genes in a pathway (disease pathways)
identify over-represented chemical classes (from chemical
ontology) for genes in a pathway (drug pathways)

41. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Disease and drug pathways
OntoFUNC enables enrichment analyses over OWL ontologies.
OntoFUNC: http://ontofunc.googlecode.com
based on FUNC (http://func.eva.mpg.de)
supports
hypergeometric test
Wilcoxon rank test
binomial test
McDonaldKreitman (2x2 contingency) test
correction for multiple testing (FWER, FDR)

42. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Disease and drug pathways
OntoFUNC identifies disease classes that are enriched in pathways.
hypergeometric test over Disease Ontology
genes participating in pathway P vs. all other genes
carcinosarcoma (DOID:4236) and Zidovudine Pathway
(PharmGKB:PA165859361) (p < 10−10 ).
mood disorder (DOID:3324) and Zidovudine Pathway
(PharmGKB:PA165859361) (p < 0.01).
(All results at http://pharmgkb-owl.googlecode.com)

46. Species Inferred p-value
Fish 1717 0.240
Yeast 14047 0.162
Fly 1633 0.041
Worm 9221 0.003
Mouse 15693 7 · 10−5
D. dario D. melanogaster S. cerevisiae
1 1 1
0.9 0.9 0.9
0.8 0.8 0.8
0.7 0.7 0.7
True Positive Rate
True Positive Rate
True Positive Rate
0.6 0.6 0.6
0.5 0.5 0.5
0.4 0.4 0.4
0.3 0.3 0.3
0.2 0.2 0.2
0.1 original 0.1 original 0.1 original
new new new
x x x
0 0 0
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
False Positive Rate False Positive Rate False Positive Rate
M. musculus C. elegans
1 1
0.9 0.9
0.8 0.8
0.7 0.7
True Positive Rate
True Positive Rate
0.6 0.6
0.5 0.5
0.4 0.4
0.3 0.3
0.2 0.2
0.1 original 0.1 original
new new
x x
0 0
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
False Positive Rate False Positive Rate

48. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Summary
Ontologies can be used to enable integrative biology.
1 integration of ontologies
2 integration of data through ontologies
3 ontology-based data analysis
semantic similarity
statistical tests
graph-/network-based algorithms
4 quantitative evaluation on real biological data

49. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Acknowledgements
George Gkoutos
Pierre Grenon
Paul Schofield
Midori Harris
Michel Dumontier
Pascal Hitzler
Heinrich Herre
Simon Jupp
Janet Kelso
Frank Loebe
Dietrich
Kay Pruefer
Rebholz-Schuhmann
Gabrielle Rustici
Dan Cook
Stefan Schulz
John Gennari
Robert Stevens
Anika Oellrich
Sarala Wimalaratne
Nico Adams
...
Bernard de Bono

50. Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary
Thank you!
http://phenomebrowser.net