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Mammalian Phenotype (MP): abnormal brain 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) |
51556,51338 51556 - Metallo-dependent hydrolases 51338 - Composite domain of metallo-dependent hydrolases | 0 | DIRECT |
51338,51556 51338 - Composite domain of metallo-dependent hydrolases 51556 - Metallo-dependent hydrolases | 0 | DIRECT |
57196,57424 57196 - EGF/Laminin 57424 - LDL receptor-like module | 0 | DIRECT |
48452,81901 48452 - TPR-like 81901 - HCP-like | 0.007257 | INHERITED FROM: abnormal telencephalon morphology |
49562,48350 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 48350 - GTPase activation domain, GAP | 0.0161 | INHERITED FROM: abnormal cerebellar cortex morphology || abnormal cerebellar layer morphology || abnormal hindbrain morphology |
57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module | 0.02519 | INHERITED FROM: abnormal cerebellum morphology |
63825,57196 63825 - YWTD domain 57196 - EGF/Laminin | 0.09964 | INHERITED FROM: abnormal forebrain morphology || abnormal metencephalon morphology || abnormal cerebellum morphology |
103575,48726 103575 - Plexin repeat 48726 - Immunoglobulin | 0.09964 | INHERITED FROM: abnormal olfactory lobe morphology |
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.1026 | INHERITED FROM: abnormal Rathke's pouch development || abnormal pituitary gland development || abnormal pituitary diverticulum morphology |
81296,81296 81296 - E set domains 81296 - E set domains | 0.1472 | INHERITED FROM: abnormal hippocampal mossy fiber morphology || abnormal cerebellar granule cell morphology || abnormal cerebellar foliation || ectopic cerebellar granule cells |
49785,49899 49785 - Galactose-binding domain-like 49899 - Concanavalin A-like lectins/glucanases | 0.1938 | INHERITED FROM: abnormal brain commissure morphology |
57196,63825 57196 - EGF/Laminin 63825 - YWTD domain | 0.1938 | INHERITED FROM: abnormal cerebellum morphology |
57184,63825 57184 - Growth factor receptor domain 63825 - YWTD domain | 0.1938 | INHERITED FROM: abnormal cerebellar cortex morphology || abnormal cerebral hemisphere morphology |
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain | 0.1938 | INHERITED FROM: abnormal cerebellar cortex morphology || abnormal cerebellar layer morphology |
57424,57184 57424 - LDL receptor-like module 57184 - Growth factor receptor domain | 0.1938 | INHERITED FROM: abnormal cerebellar cortex morphology || abnormal cerebral hemisphere morphology |
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like | 0.1938 | INHERITED FROM: abnormal cerebellar cortex morphology || abnormal cerebellar layer morphology |
101912,103575 101912 - Sema domain 103575 - Plexin repeat | 0.4133 | INHERITED FROM: abnormal hippocampal mossy fiber morphology || abnormal cerebellar cortex morphology || abnormal cerebellar granule layer morphology || abnormal cerebellum morphology || abnormal cerebellar granule cell morphology || abnormal telencephalon morphology || abnormal brain commissure morphology || ectopic cerebellar granule cells |
50044,50044 50044 - SH3-domain 50044 - SH3-domain | 0.4182 | INHERITED FROM: abnormal brain commissure morphology |
47413,46689 47413 - lambda repressor-like DNA-binding domains 46689 - Homeodomain-like | 0.4957 | INHERITED FROM: abnormal cerebellar foliation |
56112,47769 56112 - Protein kinase-like (PK-like) 47769 - SAM/Pointed domain | 0.5051 | INHERITED FROM: abnormal brain white matter morphology || abnormal optic tract morphology || decreased corpus callosum size |
89837,89837 89837 - Doublecortin (DC) 89837 - Doublecortin (DC) | 0.514 | INHERITED FROM: abnormal hippocampus layer morphology || abnormal hippocampus morphology || abnormal dentate gyrus morphology || abnormal temporal lobe morphology |
57184,49899 57184 - Growth factor receptor domain 49899 - Concanavalin A-like lectins/glucanases | 0.514 | INHERITED FROM: abnormal brain ventricular system morphology |
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.6078 | INHERITED FROM: abnormal Bergmann glial cell morphology || abnormal olfactory lobe morphology || abnormal rostral migratory stream morphology |
52058,48726 52058 - L domain-like 48726 - Immunoglobulin | 0.7039 | INHERITED FROM: abnormal telencephalon development |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
51556,51338 51556 - Metallo-dependent hydrolases 51338 - Composite domain of metallo-dependent hydrolases | 0 | Direct |
51338,51556 51338 - Composite domain of metallo-dependent hydrolases 51556 - Metallo-dependent hydrolases | 0 | Direct |
57196,57424 57196 - EGF/Laminin 57424 - LDL receptor-like module | 0 | Direct |
48452,81901 48452 - TPR-like 81901 - HCP-like | 0.007257 | Inherited |
49562,48350 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 48350 - GTPase activation domain, GAP | 0.0161 | Inherited |
57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module | 0.02519 | Inherited |
63825,57196 63825 - YWTD domain 57196 - EGF/Laminin | 0.09964 | Inherited |
103575,48726 103575 - Plexin repeat 48726 - Immunoglobulin | 0.09964 | Inherited |
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.1026 | Inherited |
81296,81296 81296 - E set domains 81296 - E set domains | 0.1472 | Inherited |
49785,49899 49785 - Galactose-binding domain-like 49899 - Concanavalin A-like lectins/glucanases | 0.1938 | Inherited |
57196,63825 57196 - EGF/Laminin 63825 - YWTD domain | 0.1938 | Inherited |
57184,63825 57184 - Growth factor receptor domain 63825 - YWTD domain | 0.1938 | Inherited |
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain | 0.1938 | Inherited |
57424,57184 57424 - LDL receptor-like module 57184 - Growth factor receptor domain | 0.1938 | Inherited |
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like | 0.1938 | Inherited |
101912,103575 101912 - Sema domain 103575 - Plexin repeat | 0.4133 | Inherited |
50044,50044 50044 - SH3-domain 50044 - SH3-domain | 0.4182 | Inherited |
47413,46689 47413 - lambda repressor-like DNA-binding domains 46689 - Homeodomain-like | 0.4957 | Inherited |
56112,47769 56112 - Protein kinase-like (PK-like) 47769 - SAM/Pointed domain | 0.5051 | Inherited |
89837,89837 89837 - Doublecortin (DC) 89837 - Doublecortin (DC) | 0.514 | Inherited |
57184,49899 57184 - Growth factor receptor domain 49899 - Concanavalin A-like lectins/glucanases | 0.514 | Inherited |
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.6078 | Inherited |
52058,48726 52058 - L domain-like 48726 - Immunoglobulin | 0.7039 | 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) |
51338,51556,51338 51338 - Composite domain of metallo-dependent hydrolases 51556 - Metallo-dependent hydrolases 51338 - Composite domain of metallo-dependent hydrolases | 0 | DIRECT |
57196,57424,57424 57196 - EGF/Laminin 57424 - LDL receptor-like module 57424 - LDL receptor-like module | 0 | DIRECT |
63825,57196,57424 63825 - YWTD domain 57196 - EGF/Laminin 57424 - LDL receptor-like module | 0 | DIRECT |
57424,57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module 57424 - LDL receptor-like module | 0.02519 | INHERITED FROM: abnormal metencephalon morphology || abnormal cerebellum morphology |
48726,48726,49265 48726 - Immunoglobulin 48726 - Immunoglobulin 49265 - Fibronectin type III | 0.03485 | INHERITED FROM: abnormal metencephalon morphology || abnormal telencephalon morphology || abnormal brain commissure morphology |
101912,103575,48726 101912 - Sema domain 103575 - Plexin repeat 48726 - Immunoglobulin | 0.09964 | INHERITED FROM: abnormal olfactory lobe morphology |
81296,81296,81296 81296 - E set domains 81296 - E set domains 81296 - E set domains | 0.1472 | INHERITED FROM: abnormal hippocampal mossy fiber morphology || abnormal cerebellar granule layer morphology || abnormal cerebral hemisphere morphology || abnormal cerebellar granule cell morphology || abnormal telencephalon morphology || abnormal cerebellar foliation || abnormal brain commissure morphology || ectopic cerebellar granule cells |
50044,50044,50044 50044 - SH3-domain 50044 - SH3-domain 50044 - SH3-domain | 0.1938 | INHERITED FROM: abnormal brain white matter morphology || abnormal brain commissure morphology |
57424,57184,63825 57424 - LDL receptor-like module 57184 - Growth factor receptor domain 63825 - YWTD domain | 0.1938 | INHERITED FROM: abnormal cerebellar cortex morphology || abnormal cerebral hemisphere morphology || abnormal cerebellum morphology || abnormal telencephalon morphology |
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like | 0.1938 | INHERITED FROM: abnormal cerebellar cortex morphology || abnormal cerebellar layer morphology |
57424,57424,57184 57424 - LDL receptor-like module 57424 - LDL receptor-like module 57184 - Growth factor receptor domain | 0.1938 | INHERITED FROM: abnormal cerebellar cortex morphology || abnormal cerebral hemisphere morphology || abnormal cerebellum morphology || abnormal telencephalon morphology |
57184,52058,57184 57184 - Growth factor receptor domain 52058 - L domain-like 57184 - Growth factor receptor domain | 0.2694 | INHERITED FROM: abnormal cerebellar cortex morphology || abnormal cerebellar layer morphology || abnormal metencephalon morphology || abnormal cerebellum morphology || abnormal hindbrain morphology |
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin | 0.3699 | INHERITED FROM: enlarged brain ventricles || abnormal brain ventricle size |
57184,49899,49899 57184 - Growth factor receptor domain 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases | 0.514 | INHERITED FROM: abnormal brain ventricular system morphology |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
51338,51556,51338 51338 - Composite domain of metallo-dependent hydrolases 51556 - Metallo-dependent hydrolases 51338 - Composite domain of metallo-dependent hydrolases | 0 | Direct |
57196,57424,57424 57196 - EGF/Laminin 57424 - LDL receptor-like module 57424 - LDL receptor-like module | 0 | Direct |
63825,57196,57424 63825 - YWTD domain 57196 - EGF/Laminin 57424 - LDL receptor-like module | 0 | Direct |
57424,57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module 57424 - LDL receptor-like module | 0.02519 | Inherited |
48726,48726,49265 48726 - Immunoglobulin 48726 - Immunoglobulin 49265 - Fibronectin type III | 0.03485 | Inherited |
101912,103575,48726 101912 - Sema domain 103575 - Plexin repeat 48726 - Immunoglobulin | 0.09964 | Inherited |
81296,81296,81296 81296 - E set domains 81296 - E set domains 81296 - E set domains | 0.1472 | Inherited |
50044,50044,50044 50044 - SH3-domain 50044 - SH3-domain 50044 - SH3-domain | 0.1938 | Inherited |
57424,57184,63825 57424 - LDL receptor-like module 57184 - Growth factor receptor domain 63825 - YWTD domain | 0.1938 | Inherited |
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like | 0.1938 | Inherited |
57424,57424,57184 57424 - LDL receptor-like module 57424 - LDL receptor-like module 57184 - Growth factor receptor domain | 0.1938 | Inherited |
57184,52058,57184 57184 - Growth factor receptor domain 52058 - L domain-like 57184 - Growth factor receptor domain | 0.2694 | Inherited |
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin | 0.3699 | Inherited |
57184,49899,49899 57184 - Growth factor receptor domain 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases | 0.514 | 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:
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Download Newick format tree:
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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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