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Phenotypic Abnormality (PA): Abnormal oral cavity morphology 
(show info)
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).
Jump to [ Top · Hierarchy · Annotations ]
Root: HP Hierarchy (human phenotype with 3 sub-ontologies PA, MI, ON)
Jump to [ Top · Hierarchy ]
Supra-domain (Single)( show details)
Highlighted in gray are those with FDR>0.001
LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm
Jump to [ Top · Hierarchy ]
Supra-domain (Duplex) in N- to C-terminal order( show details)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
54452,48726
54452 - MHC antigen-recognition domain
48726 - Immunoglobulin | 1 | INHERITED FROM: Aphthous ulcer || Recurrent aphthous stomatitis |
55486,82895
55486 - Metalloproteases ("zincins"), catalytic domain
82895 - TSP-1 type 1 repeat | 1 | INHERITED FROM: Abnormality of dental morphology |
50978,50978
50978 - WD40 repeat-like
50978 - WD40 repeat-like | 1 | INHERITED FROM: Widely spaced teeth |
141072,141072
141072 - CalX-like
141072 - CalX-like | 1 | INHERITED FROM: Abnormality of the dentition |
48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin | 1 | INHERITED FROM: Abnormal parotid gland morphology |
48092,47655
48092 - Transcription factor STAT-4 N-domain
47655 - STAT | 1 | INHERITED FROM: Stomatitis |
57903,57903
57903 - FYVE/PHD zinc finger
57903 - FYVE/PHD zinc finger | 1 | INHERITED FROM: Cleft palate || Thin upper lip vermilion || Abnormal lip morphology || Abnormal palate morphology |
47655,49417
47655 - STAT
49417 - p53-like transcription factors | 1 | INHERITED FROM: Stomatitis |
57889,48350
57889 - Cysteine-rich domain
48350 - GTPase activation domain, GAP | 1 | INHERITED FROM: Abnormal palate morphology |
57184,57581
57184 - Growth factor receptor domain
57581 - TB module/8-cys domain | 1 | INHERITED FROM: Long philtrum |
51445,51011
51445 - (Trans)glycosidases
51011 - Glycosyl hydrolase domain | 1 | INHERITED FROM: Abnormality of lower lip |
81995,81811
81995 - beta-sandwich domain of Sec23/24
81811 - Helical domain of Sec23/24 | 1 | INHERITED FROM: High palate || Abnormal palate morphology |
64268,50044
64268 - PX domain
50044 - SH3-domain | 1 | INHERITED FROM: Abnormality of the gingiva || Abnormal oral mucosa morphology |
49417,55550
49417 - p53-like transcription factors
55550 - SH2 domain | 1 | INHERITED FROM: Stomatitis |
53300,81995
53300 - vWA-like
81995 - beta-sandwich domain of Sec23/24 | 1 | INHERITED FROM: High palate || Abnormal palate morphology |
57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin | 1 | INHERITED FROM: Oral mucosal blisters || Ankyloglossia || Abnormality of dental enamel |
81811,82754
81811 - Helical domain of Sec23/24
82754 - C-terminal, gelsolin-like domain of Sec23/24 | 1 | INHERITED FROM: Abnormality of dental structure || Abnormal palate morphology |
47986,52540
47986 - DEATH domain
52540 - P-loop containing nucleoside triphosphate hydrolases | 1 | INHERITED FROM: Aphthous ulcer || Recurrent aphthous stomatitis || Stomatitis || Abnormal oral mucosa morphology |
82919,53300
82919 - Zn-finger domain of Sec23/24
53300 - vWA-like | 1 | INHERITED FROM: Abnormal palate morphology |
64593,64593
64593 - Intermediate filament protein, coiled coil region
64593 - Intermediate filament protein, coiled coil region | 1 | INHERITED FROM: White lesion of the oral mucosa |
50447,50465
50447 - Translation proteins
50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 1 | INHERITED FROM: Abnormality of mouth shape |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
54452,48726
54452 - MHC antigen-recognition domain
48726 - Immunoglobulin | 1 | Inherited |
55486,82895
55486 - Metalloproteases ("zincins"), catalytic domain
82895 - TSP-1 type 1 repeat | 1 | Inherited |
50978,50978
50978 - WD40 repeat-like
50978 - WD40 repeat-like | 1 | Inherited |
141072,141072
141072 - CalX-like
141072 - CalX-like | 1 | Inherited |
48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin | 1 | Inherited |
48092,47655
48092 - Transcription factor STAT-4 N-domain
47655 - STAT | 1 | Inherited |
57903,57903
57903 - FYVE/PHD zinc finger
57903 - FYVE/PHD zinc finger | 1 | Inherited |
47655,49417
47655 - STAT
49417 - p53-like transcription factors | 1 | Inherited |
57889,48350
57889 - Cysteine-rich domain
48350 - GTPase activation domain, GAP | 1 | Inherited |
57184,57581
57184 - Growth factor receptor domain
57581 - TB module/8-cys domain | 1 | Inherited |
51445,51011
51445 - (Trans)glycosidases
51011 - Glycosyl hydrolase domain | 1 | Inherited |
81995,81811
81995 - beta-sandwich domain of Sec23/24
81811 - Helical domain of Sec23/24 | 1 | Inherited |
64268,50044
64268 - PX domain
50044 - SH3-domain | 1 | Inherited |
49417,55550
49417 - p53-like transcription factors
55550 - SH2 domain | 1 | Inherited |
53300,81995
53300 - vWA-like
81995 - beta-sandwich domain of Sec23/24 | 1 | Inherited |
57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin | 1 | Inherited |
81811,82754
81811 - Helical domain of Sec23/24
82754 - C-terminal, gelsolin-like domain of Sec23/24 | 1 | Inherited |
47986,52540
47986 - DEATH domain
52540 - P-loop containing nucleoside triphosphate hydrolases | 1 | Inherited |
82919,53300
82919 - Zn-finger domain of Sec23/24
53300 - vWA-like | 1 | Inherited |
64593,64593
64593 - Intermediate filament protein, coiled coil region
64593 - Intermediate filament protein, coiled coil region | 1 | Inherited |
50447,50465
50447 - Translation proteins
50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 1 | Inherited |
LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm
Jump to [ Top · Hierarchy ]
Supra-domain (Triple) in N- to C-terminal order( show details)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
48092,47655,49417
48092 - Transcription factor STAT-4 N-domain
47655 - STAT
49417 - p53-like transcription factors | 1 | INHERITED FROM: Stomatitis |
57196,57581,57196
57196 - EGF/Laminin
57581 - TB module/8-cys domain
57196 - EGF/Laminin | 1 | INHERITED FROM: High palate || Abnormal palate morphology |
57196,57581,57184
57196 - EGF/Laminin
57581 - TB module/8-cys domain
57184 - Growth factor receptor domain | 1 | INHERITED FROM: High palate || Abnormal palate morphology |
57184,57196,57184
57184 - Growth factor receptor domain
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 1 | INHERITED FROM: Misalignment of teeth || High palate || Abnormal palate morphology || Long philtrum |
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 | 1 | INHERITED FROM: High palate || Abnormal palate morphology |
57196,57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin
57196 - EGF/Laminin | 1 | INHERITED FROM: Oral mucosal blisters || Ankyloglossia || Abnormal oral frenulum morphology |
57196,57196,57581
57196 - EGF/Laminin
57196 - EGF/Laminin
57581 - TB module/8-cys domain | 1 | INHERITED FROM: High palate || Abnormal palate morphology |
63825,57196,63825
63825 - YWTD domain
57196 - EGF/Laminin
63825 - YWTD domain | 1 | INHERITED FROM: Abnormality of the dentition |
47655,49417,55550
47655 - STAT
49417 - p53-like transcription factors
55550 - SH2 domain | 1 | INHERITED FROM: Stomatitis |
57184,57184,57581
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain
57581 - TB module/8-cys domain | 1 | INHERITED FROM: Long philtrum |
141072,141072,141072
141072 - CalX-like
141072 - CalX-like
141072 - CalX-like | 1 | INHERITED FROM: Abnormality of the dentition |
57184,57581,57196
57184 - Growth factor receptor domain
57581 - TB module/8-cys domain
57196 - EGF/Laminin | 1 | INHERITED FROM: Long philtrum |
52540,50447,50465
52540 - P-loop containing nucleoside triphosphate hydrolases
50447 - Translation proteins
50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 1 | INHERITED FROM: Abnormality of mouth shape |
53300,81995,81811
53300 - vWA-like
81995 - beta-sandwich domain of Sec23/24
81811 - Helical domain of Sec23/24 | 1 | INHERITED FROM: High palate || Abnormal palate morphology |
48726,48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin
48726 - Immunoglobulin | 1 | INHERITED FROM: Abnormal parotid gland morphology |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
48092,47655,49417
48092 - Transcription factor STAT-4 N-domain
47655 - STAT
49417 - p53-like transcription factors | 1 | Inherited |
57196,57581,57196
57196 - EGF/Laminin
57581 - TB module/8-cys domain
57196 - EGF/Laminin | 1 | Inherited |
57196,57581,57184
57196 - EGF/Laminin
57581 - TB module/8-cys domain
57184 - Growth factor receptor domain | 1 | Inherited |
57184,57196,57184
57184 - Growth factor receptor domain
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 1 | Inherited |
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 | 1 | Inherited |
57196,57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin
57196 - EGF/Laminin | 1 | Inherited |
57196,57196,57581
57196 - EGF/Laminin
57196 - EGF/Laminin
57581 - TB module/8-cys domain | 1 | Inherited |
63825,57196,63825
63825 - YWTD domain
57196 - EGF/Laminin
63825 - YWTD domain | 1 | Inherited |
47655,49417,55550
47655 - STAT
49417 - p53-like transcription factors
55550 - SH2 domain | 1 | Inherited |
57184,57184,57581
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain
57581 - TB module/8-cys domain | 1 | Inherited |
141072,141072,141072
141072 - CalX-like
141072 - CalX-like
141072 - CalX-like | 1 | Inherited |
57184,57581,57196
57184 - Growth factor receptor domain
57581 - TB module/8-cys domain
57196 - EGF/Laminin | 1 | Inherited |
52540,50447,50465
52540 - P-loop containing nucleoside triphosphate hydrolases
50447 - Translation proteins
50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 1 | Inherited |
53300,81995,81811
53300 - vWA-like
81995 - beta-sandwich domain of Sec23/24
81811 - Helical domain of Sec23/24 | 1 | Inherited |
48726,48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin
48726 - Immunoglobulin | 1 | Inherited |
LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm
Plot distribution on species Tree Of Life (sTOL) for Superfamily and/or Family domains annotated by this HP term
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Plot tree as:
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Download Newick format tree:
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( show help)
Trees by TreeVector
A presence/absence matrix is generated using protein domain
architecture data for all genomes in SUPERFAMILY. The PAUP
software is used to produce a single, large tree topology using
heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as
if individual trees had been produced. However, this data is extracted from the single
large tree. This produces a higher quality topology than if the trees had been produced
on their own, and allows the trees to be displayed instantly.
Plot distribution on species Tree Of Life (sTOL) for single supra-domains annotated by this HP term
|
Plot tree as:
| |
Download Newick format tree:
| |
Browsing in TREE OF LIFE:
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( show help)
Trees by TreeVector
A presence/absence matrix is generated using protein domains and supradomains
for all genomes in SUPERFAMILY. The RAxML
software is used to produce a single, large tree topology using
heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as
if individual trees had been produced. However, this data is extracted from the single
large tree. This produces a higher quality topology than if the trees had been produced
on their own, and allows the trees to be displayed instantly.
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> BO Hierarchy > Abnormal oral cavity morphology
