Phenotypic Abnormality (PA): Growth abnormality

Biomedical Ontology
Like Gene Ontology (GO), biomedical ontology such as phenotype ontology classifies and organizes gene-mutant/null phenotypic information from the very general at the top to more specific terms in the directed acyclic graph (DAG) by viewing an individual term as a node and its relations to parental terms (allowing for multiple parents) as directed edges. To navigate this hierarchy, we display all parental phenotypic terms to the current phenotypic term of interest ordered by their shortest distances to the current term. Also, only direct children phenotypic terms of the current phenotypic term are listed. Biomedical ontologies we have incorporated are as follows:

Disease Ontology (DO) Ontology
DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM.
Human Phenotype (HP) Ontology
HP captures phenotypic abnormalities that are described in OMIM, along with the corresponding disease-causing genes. It includes three complementary biological concepts: Mode_of_Inheritance (MI), ONset_and_clinical_course (ON), and Phenotypic_Abnormality (PA).
Mouse Phenotype (MP) Ontology
MP describes phenotypes of the mouse after a specific gene is genetically disrupted. Using it, Mouse Genome Informatics (MGI) provides high-coverate gene-level phenotypes for the mouse.
Worm Phenotype (WP) Ontology
WP classifies and organizes phenotype descriptions for C. elegans and other nematodes. Using it, WormBase provides primary resource for phenotype annotations for C. elegans.
Yeast Phenotype (YP) Ontology
Based on YP which is the major contributor to the ‘Ascomycete phenotype ontology’, Saccharomyces Genome Database (SGD) provides single mutant phenotypes for every gene in the yeast genome.
Fly Phenotype (FP) Ontology
FP refers to FlyBase controlled vocabulary. Specifically, a structured controlled vocabulary is used for the annotation of alleles (for their mutagen etc) in FlyBase.
Fly Anatomy (FA) Ontology
FA is a structured controlled vocabulary of the anatomy of Drosophila melanogaster, used for the description of phenotypes and where a gene is expressed.
Zebrafish Anatomy (ZA) Ontology
ZA displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
Xenopus Anatomy (XA) Ontology
XA represents the lineage of tissues and the timing of development for frogs (Xenopus laevis and Xenopus tropicalis). It is used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes.
Arabidopsis Plant Ontology (AP) Ontology
As a major contributor to Plant Ontology which describes plant anatomical and morphological structures (AN) and growth and developmental stages (DE), the Arabidopsis Information Resource (TAIR) provides arabidopsis plant ontology annotations for the model higher plant Arabidopsis thaliana.
Enzyme Commission (EC) Ontology
Each enzyme is allocated a four-digit EC number, the first three digits of which define the reaction catalysed and the fourth of which is a unique identifier (serial number). Each enzyme is also assigned a systematic name that uniquely defines the reaction catalysed.
UniProtKB KeyWords (KW) Ontology
Keywords in UniProtKB are controlled vocabulary, providing a summary of the entry content and are used to index UniProtKB/Swiss-Prot entries based on 10 categories (the category "Technical term" being excluded here). Each keyword is attributed manually to UniProtKB/Swiss-Prot entries and automatically to UniProtKB/TrEMBL entries (according to specific annotation rules).
CTD Diseases (CD) Ontology
CD is MEDIC disease vocabulary that is modified by CTD from the "Diseases" [C] branch of Medical Subject Headings (MeSH), combined with genetic disorders from the Online Mendelian Inheritance in OMIM database.
CTD Chemicals (CC) Ontology
CC is chemical vocabulary that is adapted by CTD from the "Chemicals and Drugs" category and Supplementary Concept Records of Medical Subject Headings (MeSH, a hierarchical vocabulary used to index articles for MEDLINE/PubMed).

Superfamily

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Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
Notch domain	0	Direct
C-terminal, gelsolin-like domain of Sec23/24	0	Direct
Tricorn protease domain 2	0	Direct
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0	Direct
Acyl-CoA N-acyltransferases (Nat)	0	Direct
Arginase/deacetylase	0	Direct
ADC-like	0	Direct
TB module/8-cys domain	0	Direct
RuvA domain 2-like	0	Direct
Plakin repeat	0	Direct
Isocitrate/Isopropylmalate dehydrogenase-like	0	Direct
Helical domain of Sec23/24	0	Direct
Glycerol-3-phosphate (1)-acyltransferase	0	Direct
Ribonuclease PH domain 2-like	0	Direct
Zn-finger domain of Sec23/24	0	Direct
CCCH zinc finger	0	Direct
JAB1/MPN domain	0	Direct
beta and beta-prime subunits of DNA dependent RNA-polymerase	0	Direct
BRK domain-like	0	Direct
Transcription factor STAT-4 N-domain	0.06341	Inherited
STAT	0.06341	Inherited
Bromodomain	0.1102	Inherited
Insulin-like	0.1625	Inherited
"Winged helix" DNA-binding domain	0.2084	Inherited
Homeodomain-like	0.3942	Inherited
Family A G protein-coupled receptor-like	0.4029	Inherited
MHC antigen-recognition domain	0.4164	Inherited
FnI-like domain	0.4417	Inherited
vWA-like	0.6064	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Family

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
CCCH zinc finger	0	Direct
Zn-finger domain of Sec23/24	0	Direct
Proteasome subunits	0	Direct
Ferredoxin domains from multidomain proteins	0	Direct
C-terminal, gelsolin-like domain of Sec23/24	0	Direct
Helical domain of Sec23/24	0	Direct
N-acetyl transferase, NAT	0	Direct
BRK domain-like	0	Direct
SWIRM domain	0	Direct
P4 origin-binding domain-like	0	Direct
Notch domain	0	Direct
XPF/Rad1/Mus81 nuclease	0	Direct
Histone deacetylase, HDAC	0	Direct
Erythroid transcription factor GATA-1	0	Direct
L-aspartase/fumarase	0	Direct
Ribonuclease PH domain 1-like	0	Direct
Long-chain cytokines	0	Direct
Plakin repeat	0	Direct
Biotin dependent carboxylase carboxyltransferase domain	0	Direct
Exostosin	0	Direct
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0	Direct
Inositol polyphosphate 5-phosphatase (IPP5)	0	Direct
HCDH C-domain-like	0	Direct
Ribonuclease PH domain 2-like	0	Direct
TB module/8-cys domain	0	Direct
Dimeric isocitrate & isopropylmalate dehydrogenases	0	Direct
beta-sandwich domain of Sec23/24	0	Direct
Trunk domain of Sec23/24	0	Direct
JAB1/MPN domain	0	Direct
Histone lysine methyltransferases	0.006024	Inherited
Hect, E3 ligase catalytic domain	0.03845	Inherited
Transcription factor STAT-4 N-domain	0.05148	Inherited
STAT DNA-binding domain	0.05148	Inherited
STAT	0.05148	Inherited
DNA gyrase/MutL, second domain	0.08526	Inherited
DNA gyrase/MutL, N-terminal domain	0.08526	Inherited
Bromodomain	0.09559	Inherited
ZZ domain	0.1394	Inherited
Insulin-like	0.1394	Inherited
GAF domain	0.1394	Inherited
Hypoxia-inducible factor Hif2a, C-terminal domain	0.1394	Inherited
C1 set domains (antibody constant domain-like)	0.3226	Inherited
Rhodopsin-like	0.3357	Inherited
Integrin A (or I) domain	0.3514	Inherited
MHC antigen-recognition domain	0.3911	Inherited
Homeodomain	0.4971	Inherited
Phosphotyrosine-binding domain (PTB)	0.8112	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Supra-domain (Single|Duplex|Triple)

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Supra-domain (Single)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Ribonuclease PH domain 2-like	0	Direct
Plakin repeat	0	Direct
TB module/8-cys domain	0	Direct
BRK domain-like	0	Direct
Arginase/deacetylase	0	Direct
JAB1/MPN domain	0	Direct
Helical domain of Sec23/24	0	Direct
beta and beta-prime subunits of DNA dependent RNA-polymerase	0	Direct
Notch domain	0	Direct
ADC-like	0	Direct
Isocitrate/Isopropylmalate dehydrogenase-like	0	Direct
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0	Direct
C-terminal, gelsolin-like domain of Sec23/24	0	Direct
Zn-finger domain of Sec23/24	0	Direct
RuvA domain 2-like	0	Direct
Tricorn protease domain 2	0	Direct
Glycerol-3-phosphate (1)-acyltransferase	0	Direct
CCCH zinc finger	0	Direct
Acyl-CoA N-acyltransferases (Nat)	0	Direct
Hect, E3 ligase catalytic domain	0.03497	Inherited
STAT	0.04789	Inherited
Transcription factor STAT-4 N-domain	0.04789	Inherited
Bromodomain	0.08694	Inherited
Concanavalin A-like lectins/glucanases	0.09868	Inherited
Restriction endonuclease-like	0.1332	Inherited
GAF domain-like	0.1332	Inherited
Insulin-like	0.1332	Inherited
"Winged helix" DNA-binding domain	0.1751	Inherited
SET domain	0.1975	Inherited
Homeodomain-like	0.3509	Inherited
Family A G protein-coupled receptor-like	0.3595	Inherited
MHC antigen-recognition domain	0.3728	Inherited
FnI-like domain	0.3978	Inherited
vWA-like	0.5641	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

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

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
57581,57184 57581 - TB module/8-cys domain 57184 - Growth factor receptor domain	0	Direct
52980,47781 52980 - Restriction endonuclease-like 47781 - RuvA domain 2-like	0	Direct
54211,55666 54211 - Ribosomal protein S5 domain 2-like 55666 - Ribonuclease PH domain 2-like	0	Direct
-7,56112 -7 - CATH 56112 - Protein kinase-like (PK-like)	0	Direct
57581,57196 57581 - TB module/8-cys domain 57196 - EGF/Laminin	0	Direct
57903,57903 57903 - FYVE/PHD zinc finger 57903 - FYVE/PHD zinc finger	0	Direct
81811,82754 81811 - Helical domain of Sec23/24 82754 - C-terminal, gelsolin-like domain of Sec23/24	0	Direct
103575,48726 103575 - Plexin repeat 48726 - Immunoglobulin	0	Direct
50447,50465 50447 - Translation proteins 50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0	Direct
47095,47095 47095 - HMG-box 47095 - HMG-box	0	Direct
52096,52096 52096 - ClpP/crotonase 52096 - ClpP/crotonase	0	Direct
57196,90193 57196 - EGF/Laminin 90193 - Notch domain	0	Direct
75399,75399 75399 - Plakin repeat 75399 - Plakin repeat	0	Direct
82919,53300 82919 - Zn-finger domain of Sec23/24 53300 - vWA-like	0	Direct
81995,81811 81995 - beta-sandwich domain of Sec23/24 81811 - Helical domain of Sec23/24	0	Direct
57184,57581 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain	0	Direct
53300,81995 53300 - vWA-like 81995 - beta-sandwich domain of Sec23/24	0	Direct
57196,57581 57196 - EGF/Laminin 57581 - TB module/8-cys domain	0	Direct
49417,55550 49417 - p53-like transcription factors 55550 - SH2 domain	0.04789	Inherited
47655,49417 47655 - STAT 49417 - p53-like transcription factors	0.04789	Inherited
48092,47655 48092 - Transcription factor STAT-4 N-domain 47655 - STAT	0.04789	Inherited
55874,54211 55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 54211 - Ribosomal protein S5 domain 2-like	0.08023	Inherited
47459,55785 47459 - HLH, helix-loop-helix DNA-binding domain 55785 - PYP-like sensor domain (PAS domain)	0.1332	Inherited
55781,109604 55781 - GAF domain-like 109604 - HD-domain/PDEase-like	0.1332	Inherited
55781,55781 55781 - GAF domain-like 55781 - GAF domain-like	0.1332	Inherited
53300,53300 53300 - vWA-like 53300 - vWA-like	0.2895	Inherited
54452,48726 54452 - MHC antigen-recognition domain 48726 - Immunoglobulin	0.3728	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

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

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
52540,50447,50465 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins 50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0	Direct
81995,81811,82754 81995 - beta-sandwich domain of Sec23/24 81811 - Helical domain of Sec23/24 82754 - C-terminal, gelsolin-like domain of Sec23/24	0	Direct
57184,57581,57196 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain 57196 - EGF/Laminin	0	Direct
57184,57184,57581 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain	0	Direct
57184,57581,57184 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain 57184 - Growth factor receptor domain	0	Direct
57184,57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor 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
57184,57196,57184 57184 - Growth factor receptor domain 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0	Direct
101912,103575,48726 101912 - Sema domain 103575 - Plexin repeat 48726 - Immunoglobulin	0	Direct
57196,57196,57581 57196 - EGF/Laminin 57196 - EGF/Laminin 57581 - TB module/8-cys domain	0	Direct
57196,57581,57196 57196 - EGF/Laminin 57581 - TB module/8-cys domain 57196 - EGF/Laminin	0	Direct
57196,57196,90193 57196 - EGF/Laminin 57196 - EGF/Laminin 90193 - Notch domain	0	Direct
57184,57184,57196 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57196 - EGF/Laminin	0	Direct
57581,57196,57196 57581 - TB module/8-cys domain 57196 - EGF/Laminin 57196 - EGF/Laminin	0	Direct
57581,57184,57581 57581 - TB module/8-cys domain 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain	0	Direct
57196,57581,57184 57196 - EGF/Laminin 57581 - TB module/8-cys domain 57184 - Growth factor receptor domain	0	Direct
53300,81995,81811 53300 - vWA-like 81995 - beta-sandwich domain of Sec23/24 81811 - Helical domain of Sec23/24	0	Direct
49899,49899,57196 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases 57196 - EGF/Laminin	0	Direct
48092,47655,49417 48092 - Transcription factor STAT-4 N-domain 47655 - STAT 49417 - p53-like transcription factors	0.04789	Inherited
47655,49417,55550 47655 - STAT 49417 - p53-like transcription factors 55550 - SH2 domain	0.04789	Inherited
55781,55781,109604 55781 - GAF domain-like 55781 - GAF domain-like 109604 - HD-domain/PDEase-like	0.1332	Inherited