Phenotypic Abnormality (PA): Aplasia/hypoplasia involving the skeleton 

Root: HP Hierarchy (human phenotype with 3 sub-ontologies PA, MI, ON)

Shortest distance to current term (+ for parents, - for children)	HP term [HP ID] <#Children>	#Domains (Superfamily|Family)	#Supra-domain (Single|Duplex|Triple)
+ + + 3:	Phenotypic abnormality [HP:0000118] <25>
+ + 2:	Abnormality of the skeletal system [HP:0000924] <7>	(88|98)	(93|55|34)
+ 1:	Abnormality of skeletal morphology [HP:0011842] <17>	(86|89)	(90|52|33)
0:	Aplasia/hypoplasia involving the skeleton [HP:0009115] <2>	(13|12)	(15|10|17)
- 1:	Aplasia/hypoplasia of the extremities [HP:0009815] <6>	(8|10)	(10|3|5)
- 1:	Aplasia/hypoplasia affecting bones of the axial skeleton [HP:0009122] <3>	(4|1)	(4|2|1)

Superfamily

Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
Notch domain	0	DIRECT
TB module/8-cys domain	0	DIRECT
RuvA domain 2-like	0	DIRECT
Arginase/deacetylase	0.01762	INHERITED FROM: Aplasia/hypoplasia involving bones of the lower limbs || Short foot || Aplasia/Hypoplasia involving bones of the feet
ARID-like	0.04023	INHERITED FROM: Aplasia/Hypoplasia of fingers || Aplasia/Hypoplasia of the distal phalanx of the 5th toe || Short distal phalanx of finger || Aplasia/hypoplasia involving bones of the lower limbs || Aplasia/Hypoplasia of the phalanges of the 5th toe || Aplasia/hypoplasia involving bones of the hand || Aplasia/Hypoplasia of the 5th toe || Aplasia/Hypoplasia of the distal phalanges of the toes || Absent toe || Short finger || Aplasia/Hypoplasia involving bones of the feet
WD40 repeat-like	0.05549	INHERITED FROM: Short ribs
Multidrug efflux transporter AcrB transmembrane domain	0.07811	INHERITED FROM: Short distal phalanx of finger || Short finger
BRK domain-like	0.07811	INHERITED FROM: Aplasia/hypoplasia involving bones of the lower limbs
Galactose-binding domain-like	0.1317	INHERITED FROM: Hypoplasia of the odontoid process
p53-like transcription factors	0.1443	INHERITED FROM: Hypoplastic scapulae || Absent hand
HMG-box	0.2195	INHERITED FROM: Aplasia/Hypoplasia of the distal phalanx of the 5th toe || Aplasia/Hypoplasia of the phalanges of the 5th toe
(Trans)glycosidases	0.5788	INHERITED FROM: Aplasia/Hypoplasia involving the vertebral column
Immunoglobulin	0.9391	INHERITED FROM: Short middle phalanx of toe

Family

Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
SWIRM domain	0	DIRECT
Notch domain	0	DIRECT
XPF/Rad1/Mus81 nuclease	0	DIRECT
Histone deacetylase, HDAC	0	DIRECT
TB module/8-cys domain	0	DIRECT
ARID domain	0.03027	INHERITED FROM: Aplasia/Hypoplasia of fingers || Aplasia/Hypoplasia of the distal phalanx of the 5th toe || Short distal phalanx of finger || Aplasia/hypoplasia involving bones of the lower limbs || Aplasia/Hypoplasia of the phalanges of the 5th toe || Aplasia/hypoplasia involving bones of the hand || Aplasia/Hypoplasia of the 5th toe || Aplasia/Hypoplasia of the distal phalanges of the toes || Absent toe || Short finger || Aplasia/hypoplasia involving bones of the upper limbs || Aplasia/Hypoplasia involving bones of the feet
Homeodomain	0.04017	INHERITED FROM: Aplasia/Hypoplasia of the 2nd finger
BRK domain-like	0.0627	INHERITED FROM: Aplasia/hypoplasia involving bones of the lower limbs || Aplasia/hypoplasia involving bones of the hand
RecA protein-like (ATPase-domain)	0.1576	INHERITED FROM: Hypoplasia of the ulna || Forearm undergrowth || Aplasia/Hypoplasia of the ulna || Aplasia/Hypoplasia of the radius
HMG-box	0.1925	INHERITED FROM: Aplasia/Hypoplasia of the distal phalanx of the 5th toe || Aplasia/Hypoplasia of the phalanges of the 5th toe
I set domains	0.3901	INHERITED FROM: Aplasia involving bones of the extremities || Short middle phalanx of toe || Aplasia involving bones of the upper limbs || Aplasia of the phalanges of the hand
Transforming growth factor (TGF)-beta	0.6704	INHERITED FROM: Short middle phalanx of finger

Supra-domain (Single|Duplex|Triple)

Supra-domain (Single)

Highlighted in gray are those with FDR>0.001

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
RuvA domain 2-like	0	DIRECT
Notch domain	0	DIRECT
TB module/8-cys domain	0	DIRECT
Protein kinase-like (PK-like)	0.0009853	DIRECT
Arginase/deacetylase	0.01183	INHERITED FROM: Aplasia/Hypoplasia involving bones of the feet || Aplasia/hypoplasia involving bones of the hand || Aplasia/hypoplasia involving bones of the lower limbs || Short foot
ARID-like	0.02894	INHERITED FROM: Aplasia/Hypoplasia of the phalanges of the 5th toe || Aplasia/Hypoplasia involving bones of the feet || Aplasia/Hypoplasia of fingers || Absent toe || Aplasia/Hypoplasia of the distal phalanx of the 5th toe || Aplasia/hypoplasia involving bones of the upper limbs || Aplasia/hypoplasia involving bones of the hand || Aplasia/Hypoplasia of the distal phalanges of the toes || Aplasia/Hypoplasia of the 5th toe || Aplasia/hypoplasia involving bones of the lower limbs || Short finger || Aplasia/Hypoplasia of the patella || Short distal phalanx of finger
WD40 repeat-like	0.04131	INHERITED FROM: Short ribs
Multidrug efflux transporter AcrB transmembrane domain	0.06005	INHERITED FROM: Aplasia/Hypoplasia of fingers || Short finger || Short distal phalanx of finger
BRK domain-like	0.06005	INHERITED FROM: Aplasia/hypoplasia involving bones of the hand || Aplasia/hypoplasia involving bones of the lower limbs
Galactose-binding domain-like	0.1062	INHERITED FROM: Hypoplasia of the odontoid process
p53-like transcription factors	0.1174	INHERITED FROM: Hypoplastic scapulae || Short clavicles || Absent hand
HMG-box	0.1852	INHERITED FROM: Aplasia/Hypoplasia of the phalanges of the 5th toe || Aplasia/Hypoplasia of the distal phalanx of the 5th toe
(Trans)glycosidases	0.536	INHERITED FROM: Aplasia/Hypoplasia involving the vertebral column
Cystine-knot cytokines	0.6827	INHERITED FROM: Short hallux || Aplasia/Hypoplasia of the hallux
Immunoglobulin	0.9127	INHERITED FROM: Short middle phalanx of toe

Supra-domain (Duplex) in N- to C-terminal order

Highlighted in gray are those with FDR>0.001

Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
57184,57581 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain	0	DIRECT
57581,57196 57581 - TB module/8-cys domain 57196 - EGF/Laminin	0	DIRECT
52980,47781 52980 - Restriction endonuclease-like 47781 - RuvA domain 2-like	0	DIRECT
57196,90193 57196 - EGF/Laminin 90193 - Notch domain	0	DIRECT
57196,57581 57196 - EGF/Laminin 57581 - TB module/8-cys domain	0	DIRECT
57581,57184 57581 - TB module/8-cys domain 57184 - Growth factor receptor domain	0	DIRECT
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.01616	INHERITED FROM: Absent toe || Short finger
81296,81296 81296 - E set domains 81296 - E set domains	0.02894	INHERITED FROM: Aplasia/Hypoplasia of the fibula || Aplasia/Hypoplasia involving the metacarpal bones
50978,50978 50978 - WD40 repeat-like 50978 - WD40 repeat-like	0.08163	INHERITED FROM: Short ribs || Aplasia/Hypoplasia of the ribs
48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin	0.672	INHERITED FROM: Short middle phalanx of toe

Supra-domain (Triple) in N- to C-terminal order

Highlighted in gray are those with FDR>0.001

Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
57184,57184,57581 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain	0	DIRECT
57196,57196,90193 57196 - EGF/Laminin 57196 - EGF/Laminin 90193 - Notch domain	0	DIRECT
57196,57581,57196 57196 - EGF/Laminin 57581 - TB module/8-cys domain 57196 - EGF/Laminin	0	DIRECT
57184,57581,57184 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain 57184 - Growth factor receptor domain	0	DIRECT
57184,57184,57196 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57196 - EGF/Laminin	0	DIRECT
57196,57196,57581 57196 - EGF/Laminin 57196 - EGF/Laminin 57581 - TB module/8-cys domain	0	DIRECT
57581,57196,57196 57581 - TB module/8-cys domain 57196 - EGF/Laminin 57196 - EGF/Laminin	0	DIRECT
57184,57196,57184 57184 - Growth factor receptor domain 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0	DIRECT
57184,57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0	DIRECT
57184,57581,57196 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain 57196 - EGF/Laminin	0	DIRECT
57196,57581,57184 57196 - EGF/Laminin 57581 - TB module/8-cys domain 57184 - Growth factor receptor domain	0	DIRECT
57581,57196,57581 57581 - TB module/8-cys domain 57196 - EGF/Laminin 57581 - TB module/8-cys domain	0	DIRECT
57581,57184,57581 57581 - TB module/8-cys domain 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain	0	DIRECT
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0.006272	INHERITED FROM: Short finger
81296,81296,81296 81296 - E set domains 81296 - E set domains 81296 - E set domains	0.02894	INHERITED FROM: Aplasia/Hypoplasia of the fibula || Aplasia/Hypoplasia involving the metacarpal bones
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.02943	INHERITED FROM: Absent toe || Short finger
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin	0.2512	INHERITED FROM: Short middle phalanx of toe