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Mammalian Phenotype (MP): abnormal blood vessel morphology  
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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: MP Hierarchy (mammalian/mouse phenotype from MGI_4.41)
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) |
57196,90193 57196 - EGF/Laminin 90193 - Notch domain | 0 | DIRECT |
90193,90193 90193 - Notch domain 90193 - Notch domain | 0 | DIRECT |
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.000000639 | DIRECT |
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain | 0.00000118 | DIRECT |
57440,57440 57440 - Kringle-like 57440 - Kringle-like | 0.000002153 | DIRECT |
55550,50044 55550 - SH2 domain 50044 - SH3-domain | 0.0002654 | DIRECT |
53300,69179 53300 - vWA-like 69179 - Integrin domains | 0.0004063 | DIRECT |
57603,57603 57603 - FnI-like domain 57603 - FnI-like domain | 0.0004063 | DIRECT |
57196,69687 57196 - EGF/Laminin 69687 - Integrin beta tail domain | 0.0004063 | DIRECT |
57440,50494 57440 - Kringle-like 50494 - Trypsin-like serine proteases | 0.001156 | INHERITED FROM: choroidal neovascularization || decreased susceptibility to induced choroidal neovascularization || abnormal choroid vasculature morphology |
57196,57581 57196 - EGF/Laminin 57581 - TB module/8-cys domain | 0.001888 | INHERITED FROM: abnormal systemic artery morphology || abnormal aorta morphology || abnormal artery morphology || abnormal aorta tunica media morphology |
57581,57196 57581 - TB module/8-cys domain 57196 - EGF/Laminin | 0.001888 | INHERITED FROM: abnormal systemic artery morphology || abnormal aorta morphology || abnormal artery morphology || abnormal aorta tunica media morphology |
49785,57184 49785 - Galactose-binding domain-like 57184 - Growth factor receptor domain | 0.002577 | INHERITED FROM: abnormal angiogenesis |
63825,57196 63825 - YWTD domain 57196 - EGF/Laminin | 0.002577 | INHERITED FROM: abnormal systemic artery morphology || abnormal aorta morphology || abnormal descending aorta morphology |
57424,57184 57424 - LDL receptor-like module 57184 - Growth factor receptor domain | 0.0047 | INHERITED FROM: abnormal systemic artery morphology || abnormal aorta morphology |
57184,63825 57184 - Growth factor receptor domain 63825 - YWTD domain | 0.0047 | INHERITED FROM: abnormal systemic artery morphology || abnormal aorta morphology |
47459,55785 47459 - HLH, helix-loop-helix DNA-binding domain 55785 - PYP-like sensor domain (PAS domain) | 0.005207 | INHERITED FROM: abnormal vascular regression |
57184,57196 57184 - Growth factor receptor domain 57196 - EGF/Laminin | 0.01013 | INHERITED FROM: abnormal aorta morphology || abnormal blood vessel elastic tissue morphology || abnormal aorta elastic fiber morphology || abnormal aorta tunica media morphology |
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.02137 | INHERITED FROM: abnormal aorta morphology || abnormal aorta elastic fiber morphology || abnormal aorta tunica media morphology |
57716,48508 57716 - Glucocorticoid receptor-like (DNA-binding domain) 48508 - Nuclear receptor ligand-binding domain | 0.055 | INHERITED FROM: absent fetal ductus arteriosus || abnormal stapedial artery morphology || abnormal pharyngeal arch artery morphology || right aortic arch || persistent right dorsal aorta |
47090,55486 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain | 0.06338 | INHERITED FROM: abnormal induced retinal neovascularization || retinal neovascularization || aortic aneurysm || decreased angiogenesis |
48065,50729 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like | 0.07711 | INHERITED FROM: abnormal vascular endothelial cell migration |
49854,49854 49854 - Spermadhesin, CUB domain 49854 - Spermadhesin, CUB domain | 0.128 | INHERITED FROM: abnormal dorsal aorta morphology |
57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module | 0.2297 | INHERITED FROM: abnormal systemic artery morphology || abnormal aorta morphology |
48726,49265 48726 - Immunoglobulin 49265 - Fibronectin type III | 0.2524 | INHERITED FROM: absent organized vascular network |
49265,49265 49265 - Fibronectin type III 49265 - Fibronectin type III | 0.2741 | INHERITED FROM: absent organized vascular network |
52540,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases | 0.7511 | INHERITED FROM: abnormal inferior vena cava morphology |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57196,90193 57196 - EGF/Laminin 90193 - Notch domain | 0 | Direct |
90193,90193 90193 - Notch domain 90193 - Notch domain | 0 | Direct |
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.000000639 | Direct |
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain | 0.00000118 | Direct |
57440,57440 57440 - Kringle-like 57440 - Kringle-like | 0.000002153 | Direct |
55550,50044 55550 - SH2 domain 50044 - SH3-domain | 0.0002654 | Direct |
53300,69179 53300 - vWA-like 69179 - Integrin domains | 0.0004063 | Direct |
57603,57603 57603 - FnI-like domain 57603 - FnI-like domain | 0.0004063 | Direct |
57196,69687 57196 - EGF/Laminin 69687 - Integrin beta tail domain | 0.0004063 | Direct |
57440,50494 57440 - Kringle-like 50494 - Trypsin-like serine proteases | 0.001156 | Inherited |
57196,57581 57196 - EGF/Laminin 57581 - TB module/8-cys domain | 0.001888 | Inherited |
57581,57196 57581 - TB module/8-cys domain 57196 - EGF/Laminin | 0.001888 | Inherited |
49785,57184 49785 - Galactose-binding domain-like 57184 - Growth factor receptor domain | 0.002577 | Inherited |
63825,57196 63825 - YWTD domain 57196 - EGF/Laminin | 0.002577 | Inherited |
57424,57184 57424 - LDL receptor-like module 57184 - Growth factor receptor domain | 0.0047 | Inherited |
57184,63825 57184 - Growth factor receptor domain 63825 - YWTD domain | 0.0047 | Inherited |
47459,55785 47459 - HLH, helix-loop-helix DNA-binding domain 55785 - PYP-like sensor domain (PAS domain) | 0.005207 | Inherited |
57184,57196 57184 - Growth factor receptor domain 57196 - EGF/Laminin | 0.01013 | Inherited |
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.02137 | Inherited |
57716,48508 57716 - Glucocorticoid receptor-like (DNA-binding domain) 48508 - Nuclear receptor ligand-binding domain | 0.055 | Inherited |
47090,55486 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain | 0.06338 | Inherited |
48065,50729 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like | 0.07711 | Inherited |
49854,49854 49854 - Spermadhesin, CUB domain 49854 - Spermadhesin, CUB domain | 0.128 | Inherited |
57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module | 0.2297 | Inherited |
48726,49265 48726 - Immunoglobulin 49265 - Fibronectin type III | 0.2524 | Inherited |
49265,49265 49265 - Fibronectin type III 49265 - Fibronectin type III | 0.2741 | Inherited |
52540,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases | 0.7511 | 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) |
57184,57196,57184 57184 - Growth factor receptor domain 57196 - EGF/Laminin 57184 - Growth factor receptor domain | 0 | DIRECT |
57196,90193,90193 57196 - EGF/Laminin 90193 - Notch domain 90193 - Notch domain | 0 | DIRECT |
57196,57184,57196 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57196 - EGF/Laminin | 0.0000108 | DIRECT |
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.00008416 | DIRECT |
57603,57603,57603 57603 - FnI-like domain 57603 - FnI-like domain 57603 - FnI-like domain | 0.00008416 | DIRECT |
57184,57196,57196 57184 - Growth factor receptor domain 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.00008611 | DIRECT |
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.0001403 | DIRECT |
57184,57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.0004063 | DIRECT |
57184,57184,57196 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57196 - EGF/Laminin | 0.0004063 | DIRECT |
57196,57196,69687 57196 - EGF/Laminin 57196 - EGF/Laminin 69687 - Integrin beta tail domain | 0.0004063 | DIRECT |
57440,57440,50494 57440 - Kringle-like 57440 - Kringle-like 50494 - Trypsin-like serine proteases | 0.0004738 | DIRECT |
57440,57440,57440 57440 - Kringle-like 57440 - Kringle-like 57440 - Kringle-like | 0.0004738 | DIRECT |
57196,57196,57581 57196 - EGF/Laminin 57196 - EGF/Laminin 57581 - TB module/8-cys domain | 0.0004738 | DIRECT |
57581,57196,57196 57581 - TB module/8-cys domain 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.0004738 | DIRECT |
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain | 0.0007164 | DIRECT |
57424,57424,57184 57424 - LDL receptor-like module 57424 - LDL receptor-like module 57184 - Growth factor receptor domain | 0.001888 | INHERITED FROM: abnormal systemic artery morphology || abnormal aorta morphology |
57424,57184,63825 57424 - LDL receptor-like module 57184 - Growth factor receptor domain 63825 - YWTD domain | 0.001888 | INHERITED FROM: abnormal systemic artery morphology || abnormal aorta morphology |
57196,57581,57184 57196 - EGF/Laminin 57581 - TB module/8-cys domain 57184 - Growth factor receptor domain | 0.002481 | INHERITED FROM: abnormal systemic artery morphology || abnormal aorta morphology || abnormal artery morphology |
57581,57196,57581 57581 - TB module/8-cys domain 57196 - EGF/Laminin 57581 - TB module/8-cys domain | 0.008207 | INHERITED FROM: abnormal systemic artery morphology || abnormal aorta morphology || abnormal artery morphology |
63825,57196,63825 63825 - YWTD domain 57196 - EGF/Laminin 63825 - YWTD domain | 0.01758 | INHERITED FROM: abnormal systemic artery morphology || abnormal aorta morphology |
48726,49265,49265 48726 - Immunoglobulin 49265 - Fibronectin type III 49265 - Fibronectin type III | 0.1807 | INHERITED FROM: absent organized vascular network |
57424,57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module 57424 - LDL receptor-like module | 0.2297 | INHERITED FROM: abnormal systemic artery morphology || abnormal aorta morphology |
52540,52540,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases | 0.2544 | INHERITED FROM: abnormal systemic artery morphology || abnormal aorta morphology || abnormal inferior vena cava morphology || abnormal vein morphology || abnormal vena cava morphology |
57716,57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.6377 | INHERITED FROM: vasculature congestion || visceral vascular congestion |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57184,57196,57184 57184 - Growth factor receptor domain 57196 - EGF/Laminin 57184 - Growth factor receptor domain | 0 | Direct |
57196,90193,90193 57196 - EGF/Laminin 90193 - Notch domain 90193 - Notch domain | 0 | Direct |
57196,57184,57196 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57196 - EGF/Laminin | 0.0000108 | Direct |
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.00008416 | Direct |
57603,57603,57603 57603 - FnI-like domain 57603 - FnI-like domain 57603 - FnI-like domain | 0.00008416 | Direct |
57184,57196,57196 57184 - Growth factor receptor domain 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.00008611 | Direct |
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.0001403 | Direct |
57184,57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.0004063 | Direct |
57184,57184,57196 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57196 - EGF/Laminin | 0.0004063 | Direct |
57196,57196,69687 57196 - EGF/Laminin 57196 - EGF/Laminin 69687 - Integrin beta tail domain | 0.0004063 | Direct |
57440,57440,50494 57440 - Kringle-like 57440 - Kringle-like 50494 - Trypsin-like serine proteases | 0.0004738 | Direct |
57440,57440,57440 57440 - Kringle-like 57440 - Kringle-like 57440 - Kringle-like | 0.0004738 | Direct |
57196,57196,57581 57196 - EGF/Laminin 57196 - EGF/Laminin 57581 - TB module/8-cys domain | 0.0004738 | Direct |
57581,57196,57196 57581 - TB module/8-cys domain 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.0004738 | Direct |
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain | 0.0007164 | Direct |
57424,57424,57184 57424 - LDL receptor-like module 57424 - LDL receptor-like module 57184 - Growth factor receptor domain | 0.001888 | Inherited |
57424,57184,63825 57424 - LDL receptor-like module 57184 - Growth factor receptor domain 63825 - YWTD domain | 0.001888 | Inherited |
57196,57581,57184 57196 - EGF/Laminin 57581 - TB module/8-cys domain 57184 - Growth factor receptor domain | 0.002481 | Inherited |
57581,57196,57581 57581 - TB module/8-cys domain 57196 - EGF/Laminin 57581 - TB module/8-cys domain | 0.008207 | Inherited |
63825,57196,63825 63825 - YWTD domain 57196 - EGF/Laminin 63825 - YWTD domain | 0.01758 | Inherited |
48726,49265,49265 48726 - Immunoglobulin 49265 - Fibronectin type III 49265 - Fibronectin type III | 0.1807 | Inherited |
57424,57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module 57424 - LDL receptor-like module | 0.2297 | 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 | 0.2544 | Inherited |
57716,57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.6377 | 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 MP 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 MP term
 |
Plot tree as:
| |
Download Newick format tree:
| |
Browsing in TREE OF LIFE:
|
( 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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