Mammalian Phenotype (MP): craniofacial phenotype

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)
p53 tetramerization domain	0	Direct
Homeodomain-like	0	Direct
SMAD MH1 domain	0.000002294	Direct
p53-like transcription factors	0.00001009	Direct
Cystine-knot cytokines	0.0001074	Direct
Growth factor receptor domain	0.0001078	Direct
EGF/Laminin	0.001271	Inherited
FnI-like domain	0.004652	Inherited
Intermediate filament protein, coiled coil region	0.005165	Inherited
TB module/8-cys domain	0.01008	Inherited
Bromodomain	0.03366	Inherited
Metalloproteases ("zincins"), catalytic domain	0.03969	Inherited
PGBD-like	0.06893	Inherited
Nuclear receptor ligand-binding domain	0.08602	Inherited
Hemopexin-like domain	0.1146	Inherited
lambda repressor-like DNA-binding domains	0.1693	Inherited
(Trans)glycosidases	0.1887	Inherited
Transducin (alpha subunit), insertion domain	0.2292	Inherited
4-helical cytokines	0.3236	Inherited
Family A G protein-coupled receptor-like	1	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)
p53 DNA-binding domain-like	0	Direct
p53 tetramerization domain	0	Direct
Retinoblastoma tumor suppressor domains	0	Direct
Homeodomain	0.000000000000007869	Direct
SMAD MH1 domain	0.000001554	Direct
SMAD domain	0.000001554	Direct
Paired domain	0.00001036	Direct
Forkhead DNA-binding domain	0.0001754	Direct
T-box	0.0007699	Direct
Transforming growth factor (TGF)-beta	0.0008853	Direct
CalX-beta domain	0.0009039	Direct
Growth factor receptor domain	0.001261	Inherited
Arylsulfatase	0.002029	Inherited
Multidrug efflux transporter AcrB transmembrane domain	0.002133	Inherited
TNF receptor-like	0.002544	Inherited
Rel/Dorsal transcription factors, DNA-binding domain	0.003901	Inherited
Intermediate filament protein, coiled coil region	0.004576	Inherited
Laminin-type module	0.005624	Inherited
TB module/8-cys domain	0.007795	Inherited
Pyridoxal-dependent decarboxylase	0.01529	Inherited
VWC domain	0.01539	Inherited
Extracellular domain of cell surface receptors	0.02087	Inherited
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0.02162	Inherited
Neutral endopeptidase (neprilysin)	0.02673	Inherited
Ephrin ectodomain	0.02673	Inherited
Bromodomain	0.02964	Inherited
MMP N-terminal domain	0.06036	Inherited
Nuclear receptor	0.065	Inherited
I set domains	0.06939	Inherited
Matrix metalloproteases, catalytic domain	0.07359	Inherited
Nuclear receptor ligand-binding domain	0.08139	Inherited
Hemopexin-like domain	0.104	Inherited
DEATH domain, DD	0.128	Inherited
Transducin (alpha subunit), insertion domain	0.2124	Inherited
G proteins	0.4179	Inherited
Rhodopsin-like	1	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)
p53 tetramerization domain	0	Direct
Homeodomain-like	0	Direct
SMAD MH1 domain	0.0000009563	Direct
p53-like transcription factors	0.000004429	Direct
Cystine-knot cytokines	0.00005219	Direct
Growth factor receptor domain	0.00005242	Direct
CalX-like	0.0006932	Direct
EGF/Laminin	0.0007056	Direct
Protein kinase-like (PK-like)	0.0008914	Direct
FnI-like domain	0.00277	Inherited
Intermediate filament protein, coiled coil region	0.003096	Inherited
TB module/8-cys domain	0.006299	Inherited
Orange domain-like	0.02285	Inherited
Bromodomain	0.02309	Inherited
Metalloproteases ("zincins"), catalytic domain	0.02754	Inherited
PGBD-like	0.05036	Inherited
Nuclear receptor ligand-binding domain	0.06399	Inherited
Snake toxin-like	0.0659	Inherited
Hemopexin-like domain	0.08803	Inherited
lambda repressor-like DNA-binding domains	0.1355	Inherited
(Trans)glycosidases	0.153	Inherited
Transducin (alpha subunit), insertion domain	0.1903	Inherited
4-helical cytokines	0.2794	Inherited
Family A G protein-coupled receptor-like	1	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)
49417,47719 49417 - p53-like transcription factors 47719 - p53 tetramerization domain	0	Direct
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.0004336	Direct
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0.0005473	Direct
57196,63825 57196 - EGF/Laminin 63825 - YWTD domain	0.001224	Inherited
46579,64593 46579 - Prefoldin 64593 - Intermediate filament protein, coiled coil region	0.001744	Inherited
57184,57196 57184 - Growth factor receptor domain 57196 - EGF/Laminin	0.002007	Inherited
49417,81296 49417 - p53-like transcription factors 81296 - E set domains	0.00304	Inherited
57603,57603 57603 - FnI-like domain 57603 - FnI-like domain	0.003134	Inherited
64593,64593 64593 - Intermediate filament protein, coiled coil region 64593 - Intermediate filament protein, coiled coil region	0.0083	Inherited
57196,57581 57196 - EGF/Laminin 57581 - TB module/8-cys domain	0.01279	Inherited
57581,57196 57581 - TB module/8-cys domain 57196 - EGF/Laminin	0.01279	Inherited
141072,141072 141072 - CalX-like 141072 - CalX-like	0.01279	Inherited
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like	0.02285	Inherited
57716,48508 57716 - Glucocorticoid receptor-like (DNA-binding domain) 48508 - Nuclear receptor ligand-binding domain	0.03312	Inherited
47090,55486 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain	0.05036	Inherited
47413,46689 47413 - lambda repressor-like DNA-binding domains 46689 - Homeodomain-like	0.07426	Inherited
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0.1632	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)
57196,57184,57196 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57196 - EGF/Laminin	0.00007578	Direct
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin	0.0005652	Direct
63825,57196,63825 63825 - YWTD domain 57196 - EGF/Laminin 63825 - YWTD domain	0.001224	Inherited
57184,57196,57196 57184 - Growth factor receptor domain 57196 - EGF/Laminin 57196 - EGF/Laminin	0.002474	Inherited
57184,57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0.003134	Inherited
57196,57196,57581 57196 - EGF/Laminin 57196 - EGF/Laminin 57581 - TB module/8-cys domain	0.005905	Inherited
57581,57196,57196 57581 - TB module/8-cys domain 57196 - EGF/Laminin 57196 - EGF/Laminin	0.005905	Inherited
57603,57603,57603 57603 - FnI-like domain 57603 - FnI-like domain 57603 - FnI-like domain	0.01279	Inherited
48726,48726,49265 48726 - Immunoglobulin 48726 - Immunoglobulin 49265 - Fibronectin type III	0.02277	Inherited
52540,52540,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0.03572	Inherited