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Table 3 Overview of Human Phenotype Ontology (HPO) terms across the rare disorder spectrum

From: Rare disorders have many faces: in silico characterization of rare disorder spectrum

Category

Overall

Borderline-common

Rare

Ultra-rare

Da

Measuresb

Prop, %

Prop, %

Adj. p-valuec

Prop, %

Adj. p-valuec

Prop, %

 

Top 15 HPO terms for the RD spectrum

       

Seizures

22.92

16.79d

NS

23.77d

NS

23.17d

–

Intellectual disability

21.98

6.87

8.49 × 10–05

17.31d

2.85 × 10–02

23.95d

↑

Short stature

21.40

10.69d

1.14 × 10–02

17.31d

NS

22.96d

↑

Global developmental delay

20.04

6.87

4.41 × 10–04

13.44d

1.02 × 10–03

22.28d

↑

Microcephaly

15.68

2.29

1.06 × 10–05

6.20

1.32 × 10–08

18.51d

↑

Hypertelorism

15.06

3.82

3.22 × 10–04

6.72

6.05 × 10–07

17.52d

↑

Scoliosis

14.94

8.40d

NS

16.28d

NS

15.12d

–

Muscular hypotonia

13.09

6.87

NS

14.21d

NS

13.28d

–

Strabismus

12.76

4.58

1.75 × 10–02

9.82d

NS

13.91d

↑

Micrognathia

12.67 

4.58

1.05 × 10–02

5.17

1.69 × 10–06

14.75d

↑

Cryptorchidism

11.28

4.58

4.48 × 10–02

8.27

NS

12.34d

↑

Nystagmus

9.75

3.82

NS

9.82d

NS

10.15d

–

Hearing impairment

9.38

8.40d

NS

13.18d

4.32 × 10–02

8.68

–

Cleft palate

9.26

6.87

NS

7.24

NS

9.83d

–

Failure to thrive

8.97

3.82

NS

11.89d

NS

8.73

–

Top 15 HPO terms for the borderline-common disorders

       

Seizures

22.92d

16.79

NS

23.77d

NS

23.17d

–

Arthralgia

3.33

12.21

2.22 × 10–06

9.82d

7.92 × 10–12

1.41

↓

Depressivity

2.72

10.69

1.06 × 10–05

6.98

2.88 × 10–07

1.31

↓

Short stature

21.40d

10.69

1.14 × 10–02

17.31d

NS

22.96d

↑

Abdominal pain

2.84

9.92

2.07 × 10–05

8.53

2.25 × 10–10

1.20

↓

Fatigue

3.87

9.92

8.42 × 10–04

10.34d

1.13 × 10–09

2.14

–

Headache

2.35

9.92

4.11 × 10–05

4.65

1.68 × 10–03

1.36

↓

Hypertension

3.74

9.92

1.36 × 10–03

8.79

7.87 × 10–07

2.30

↓

Hepatomegaly

5.64

9.16

NS

11.11d

2.64 × 10–05

4.29

–

Renal insufficiency

3.13

9.16

8.77 × 10–04

7.49

2.62 × 10–06

1.83

↓

Attention deficit hyperactivity disorder

3.00

8.40

1.17 × 10–02

4.13

NS

2.41

↓

Constipation

3.54

8.40

4.88 × 10–02

8.27

2.98 × 10–06

2.25

↓

Diarrhea

2.51

8.40

1.37 × 10–03

4.91

3.82 × 10–03

1.62

↓

Hearing impairment

9.38d

8.40

NS

13.18d

4.32 × 10–02

8.68

–

Jaundice

1.85

8.40

2.34 × 10–05

4.91

7.99 × 10–06

0.78

↓

Muscle weakness

4.20

8.40

3.34 × 10–02

8.79

5.18 × 10–05

2.98

↓

Scoliosis

14.94d

8.40

NS

16.28d

NS

15.12d

–

Sleep disturbance

3.17

8.40

1.79 × 10–02

4.13

NS

2.62

↓

Splenomegaly

4.16

8.40

4.02 × 10–02

8.01

6.32 × 10–04

3.09

↓

  1. Here, we focus on the top 15 HPO terms for the rare disorder (RD) spectrum and borderline-common disorders of which 2430 out of 3,524 RDs and 131 out of 145 RDs hold phenotypic information (equivalent to 69.0% and 90.3%), respectively. For the rare disorder category, 387 out of 412 RDs hold phenotypic information (93.9%), and for the ultra-rare disorder category, 1,912 out of 2,967 RDs hold phenotypic information (64.4%). The proportions within the borderline-common and rare disorder categories were compared with those within the ultra-rare disorder category
  2. aDirection of change of proportions from borderline-common to ultra-rare (D)
  3. bProportion (prop) was calculated based on the number of RDs with phenotypic information within disorder category
  4. cFDR-adjusted p < 0.05 was considered statistically significant; NS refers to not significant
  5. dmarks the HPO terms in top 15 within the disorder category