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Phenotypic Abnormality (PA): Abnormality of brain morphology
(show info)
Phenotype Ontology
Like Gene Ontology (GO), phenotypy 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. Phenotype ontologies we have incorporated are as follows:
- Disease Ontology (DO) Ontology (DO) DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI thesaurus, SNOMED and OMIM.
- Human Phenotype (HP) Ontology (HP) 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) 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) 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 (YP) 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) 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) 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) ZA displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
- Xenopus Anatomy (XA) Ontology (XA) 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 (AP) 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 (EC) 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.
- DrugBank ATC (DB) Ontology (DB) In the Anatomical Therapeutic Chemical (ATC) classification system, drugs are classified in groups at five different levels according to the organ or system (1st level, anatomical main group) on which they act and their therapeutic (2nd level, therapeutic subgroup), pharmacological (3rd level, pharmacological subgroup) and chemical properties (4th level, chemical subgroup; 5th level, chemical substance). Only drugs in DrugBank are considered.
- UniProtKB KeyWords (KW) Ontology (KW) 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).
- UniProtKB UniPathway (UP) Ontology (UP) UP is a fully manually curated resource for the representation and annotation of metabolic pathways, being used as controlled vocabulary for pathway annotation in UniProtKB.
Structural Domain Phenotype Ontology and its Annotations
Structural Classification of Proteins (SCOP) classifies evolutionary-related domains into Superfamily level and Family level. Using the phenotype ontologies above, we have generated the domain-centric phenotype annotations, and further identified those phenotype terms which are the most informative to annotate SCOP domains. Promisingly, domain-centric phenotypic annotations can serve as an alternative starting point to explore genotype-phenotype relationships. We provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.
- Structural Domain Disease Ontology (DO) Ontology (SDDO) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DO.txt, and the corresponding ontology:SDDO.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Human Phenotype (HP) Ontology (SDHP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2HP.txt, and the corresponding ontology:SDHP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Mouse Phenotype (MP) Ontology (SDMP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2MP.txt, and the corresponding ontology:SDMP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Worm Phenotype (WP) Ontology (SDWP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2WP.txt, and the corresponding ontology:SDWP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Yeast Phenotype (YP) Ontology (SDYP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2YP.txt, and the corresponding ontology:SDYP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Fly Phenotype (FP) Ontology (SDFP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FP.txt, and the corresponding ontology:SDFP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Fly Anatomy (FA) Ontology (SDFA) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FA.txt, and the corresponding ontology:SDFA.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Zebrafish Anatomy (ZA) Ontology (SDZA) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2ZA.txt, and the corresponding ontology:SDZA.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Xenopus Anatomy (XA) Ontology (SDXA) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2XA.txt, and the corresponding ontology:SDXA.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Arabidopsis Plant Ontology (AP) Ontology (SDAP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2AP.txt, and the corresponding ontology:SDAP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Enzyme Commission (EC) Ontology (SDEC) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2EC.txt, and the corresponding ontology:SDEC.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain DrugBank ATC (DB) Ontology (SDDB) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DB.txt, and the corresponding ontology:SDDB.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain UniProtKB KeyWords (KW) Ontology (SDKW) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2KW.txt, and the corresponding ontology:SDKW.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain UniProtKB UniPathway (UP) Ontology (SDUP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2UP.txt, and the corresponding ontology:SDUP.txt) and mysql tables (Domain2PO.sql.gz).
Supra-domain Phenotype Ontology and its Annotations
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are interested in domain combinations. Also, we provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.
- Supra-domain Domain Disease Ontology (DO) Ontology (SPDO) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DO.txt, and the corresponding ontology:SPDO.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Human Phenotype (HP) Ontology (SPHO) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2HP.txt, and the corresponding ontology:SPHO.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Mouse Phenotype (MP) Ontology (SPMP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2MP.txt, and the corresponding ontology:SPMP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Worm Phenotype (WP) Ontology (SPWP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2WP.txt, and the corresponding ontology:SPWP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Yeast Phenotype (YP) Ontology (SPYP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2YP.txt, and the corresponding ontology:SPYP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Fly Phenotype (FP) Ontology (SPFP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FP.txt, and the corresponding ontology:SPFP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Fly Anatomy (FA) Ontology (SPFA) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FA.txt, and the corresponding ontology:SPFA.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Zebrafish Anatomy (ZA) Ontology (SPZA) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2ZA.txt, and the corresponding ontology:SPZA.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Xenopus Anatomy (XA) Ontology (SPXA) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2XA.txt, and the corresponding ontology:SPXA.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Arabidopsis Plant Ontology (AP) Ontology (SPAP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2AP.txt, and the corresponding ontology:SPAP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Enzyme Commission (EC) Ontology (SPEC) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2EC.txt, and the corresponding ontology:SPEC.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain DrugBank ATC (DB) Ontology (SPDB) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DB.txt, and the corresponding ontology:SPDB.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain UniProtKB KeyWords (KW) Ontology (SPKW) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2KW.txt, and the corresponding ontology:SPKW.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain UniProtKB UniPathway (UP) Ontology (SPUP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2UP.txt, and the corresponding ontology:SPUP.txt) and mysql tables (SP2PO.sql.gz).
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Root: HP Hierarchy (human phenotype with 3 sub-ontologies PA, MI, ON)
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Superfamily(show details)
Superfamily domains annotated to this HP term (Not in SDHP)
Highlighted in gray are those with FDR_all>0.001
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Family(show details)
Family domains annotated to this HP term (Not in SDHP)
Highlighted in gray are those with FDR_all>0.001
| SCOP term | FDR (all) | Annotation (direct or inherited) |
| CCCH zinc finger | 0 | DIRECT |
| Translational machinery components | 0 | DIRECT |
| Ferredoxin domains from multidomain proteins | 0 | DIRECT |
| Protein serine/threonine phosphatase | 0 | DIRECT |
| Multidrug efflux transporter AcrB transmembrane domain | 0 | DIRECT |
| N-acetyl transferase, NAT | 0 | DIRECT |
| Elongation factors | 0 | DIRECT |
| alpha-Amylases, C-terminal beta-sheet domain | 0 | DIRECT |
| Clathrin adaptor core protein | 0 | DIRECT |
| Lamin A/C globular tail domain | 0 | DIRECT |
| SWIRM domain | 0 | DIRECT |
| tRNA-intron endonuclease catalytic domain-like | 0 | DIRECT |
| Smc hinge domain | 0 | DIRECT |
| CAT-like | 0 | DIRECT |
| XPF/Rad1/Mus81 nuclease | 0 | DIRECT |
| Branched-chain alpha-keto acid dehydrogenase PP module | 0 | DIRECT |
| Histone deacetylase, HDAC | 0 | DIRECT |
| L-aspartase/fumarase | 0 | DIRECT |
| Ribonuclease PH domain 1-like | 0 | DIRECT |
| Long-chain cytokines | 0 | DIRECT |
| C5 cytosine-specific DNA methylase, DCM | 0 | DIRECT |
| Exostosin | 0 | DIRECT |
| EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0 | DIRECT |
| Putative glucosidase YicI, domain 3 | 0 | DIRECT |
| EF-G/eEF-2 domains III and V | 0 | DIRECT |
| Ribonuclease PH domain 2-like | 0 | DIRECT |
| Fibrinogen coiled-coil and central regions | 0 | DIRECT |
| IF2B-like | 0 | DIRECT |
| Histone lysine methyltransferases | 0.003456 | INHERITED FROM: Ventriculomegaly || Abnormality of forebrain morphology || Abnormality of the cerebrum |
| Phosphate binding protein-like | 0.006485 | INHERITED FROM: Hypoplasia of the corpus callosum || Abnormality of the cerebral white matter || Abnormal corpus callosum morphology |
| Class I aminoacyl-tRNA synthetases (RS), catalytic domain | 0.008686 | INHERITED FROM: Hypoplasia of the corpus callosum || Cerebral atrophy || Abnormality of forebrain morphology || Abnormality of the cerebrum |
| G proteins | 0.01731 | INHERITED FROM: Abnormal corpus callosum morphology || Abnormality of the cerebrum |
| GLA-domain | 0.02147 | INHERITED FROM: Abnormality of the cerebral vasculature |
| ARID domain | 0.03827 | INHERITED FROM: Dandy-Walker malformation || Partial agenesis of the corpus callosum || Microcephaly || Hypoplasia of the corpus callosum || Abnormality of the fourth ventricle || Dilated fourth ventricle || Abnormality of the cerebellar vermis || Cerebellar cyst || Aplasia/Hypoplasia of the cerebellar vermis || Cerebellar vermis hypoplasia |
| Medium chain acyl-CoA dehydrogenase-like, C-terminal domain | 0.04187 | INHERITED FROM: Intracranial hemorrhage |
| Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains | 0.04187 | INHERITED FROM: Intracranial hemorrhage |
| DNA gyrase/MutL, second domain | 0.06731 | INHERITED FROM: Neoplasm of the anterior pituitary || Pituitary adenoma || Abnormality of the pituitary gland || Abnormality of the anterior pituitary |
| DNA gyrase/MutL, N-terminal domain | 0.06731 | INHERITED FROM: Neoplasm of the anterior pituitary || Pituitary adenoma || Abnormality of the pituitary gland || Abnormality of the anterior pituitary |
| Phoshoinositide 3-kinase (PI3K), catalytic domain | 0.06799 | INHERITED FROM: Abnormality of the cerebral cortex || Abnormal cortical gyration |
| T-box | 0.08904 | INHERITED FROM: Anencephaly |
| Fibrinogen C-terminal domain-like | 0.09114 | INHERITED FROM: Abnormality of the cerebral vasculature |
| Tetramerization domain of potassium channels | 0.1102 | INHERITED FROM: Cerebellar atrophy |
| Tyrosine-dependent oxidoreductases | 0.1107 | INHERITED FROM: Hyperpituitarism |
| Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain | 0.1107 | INHERITED FROM: Hypoplasia of the corpus callosum || Abnormality of the cerebral white matter || Cerebellar atrophy |
| Ypt/Rab-GAP domain of gyp1p | 0.1157 | INHERITED FROM: Hypoplasia of the corpus callosum |
| beta-glycanases | 0.1157 | INHERITED FROM: Hydrocephalus |
| PHD domain | 0.2664 | INHERITED FROM: Microcephaly |
| Integrin domains | 0.3054 | INHERITED FROM: Subarachnoid hemorrhage || Intracranial hemorrhage |
| Transforming growth factor (TGF)-beta | 0.3858 | INHERITED FROM: Transient ischemic attack |
| Crotonase-like | 0.4052 | INHERITED FROM: Abnormality of the basal ganglia |
| Transducin (alpha subunit), insertion domain | 0.4172 | INHERITED FROM: Cerebral calcification |
| Bromodomain | 0.4454 | INHERITED FROM: Microcephaly |
| Tubulin, GTPase domain | 0.479 | INHERITED FROM: Aplasia/Hypoplasia of the brainstem || Abnormality of the cerebral cortex || Abnormal cortical gyration || Abnormality of brainstem morphology || Abnormality of lateral ventricle |
| Tubulin, C-terminal domain | 0.5148 | INHERITED FROM: Aplasia/Hypoplasia of the brainstem || Abnormality of the cerebral cortex || Abnormal cortical gyration || Abnormality of brainstem morphology || Abnormality of lateral ventricle |
| MIR domain | 0.5406 | INHERITED FROM: Cerebellar hypoplasia || Aplasia/Hypoplasia of the cerebellar vermis |
| Second domain of FERM | 0.5921 | INHERITED FROM: Cerebral hemorrhage |
| Actin/HSP70 | 0.5975 | INHERITED FROM: Cerebral ischemia || Stroke || Transient ischemic attack |
| Myosin rod fragments | 0.6368 | INHERITED FROM: Cerebral ischemia |
| Nuclear receptor ligand-binding domain | 0.6798 | INHERITED FROM: Hyperpituitarism |
| Nuclear receptor | 0.693 | INHERITED FROM: Hyperpituitarism |
| PDZ domain | 0.798 | INHERITED FROM: Subcortical cerebral atrophy |
| Homeodomain | 0.8275 | INHERITED FROM: Anterior pituitary dysgenesis || Ectopic anterior pituitary gland || Holoprosencephaly || Posterior pituitary dysgenesis || Pituitary dwarfism || Septo-optic dysplasia || Agenesis of corpus callosum |
| Cytochrome P450 | 0.9071 | INHERITED FROM: Adrenocorticotropic hormone excess |
| SCOP term | FDR (all) | Annotation (direct or inherited) |
| CCCH zinc finger | 0 | Direct |
| Translational machinery components | 0 | Direct |
| Ferredoxin domains from multidomain proteins | 0 | Direct |
| Protein serine/threonine phosphatase | 0 | Direct |
| Multidrug efflux transporter AcrB transmembrane domain | 0 | Direct |
| N-acetyl transferase, NAT | 0 | Direct |
| Elongation factors | 0 | Direct |
| alpha-Amylases, C-terminal beta-sheet domain | 0 | Direct |
| Clathrin adaptor core protein | 0 | Direct |
| Lamin A/C globular tail domain | 0 | Direct |
| SWIRM domain | 0 | Direct |
| tRNA-intron endonuclease catalytic domain-like | 0 | Direct |
| Smc hinge domain | 0 | Direct |
| CAT-like | 0 | Direct |
| XPF/Rad1/Mus81 nuclease | 0 | Direct |
| Branched-chain alpha-keto acid dehydrogenase PP module | 0 | Direct |
| Histone deacetylase, HDAC | 0 | Direct |
| L-aspartase/fumarase | 0 | Direct |
| Ribonuclease PH domain 1-like | 0 | Direct |
| Long-chain cytokines | 0 | Direct |
| C5 cytosine-specific DNA methylase, DCM | 0 | Direct |
| Exostosin | 0 | Direct |
| EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0 | Direct |
| Putative glucosidase YicI, domain 3 | 0 | Direct |
| EF-G/eEF-2 domains III and V | 0 | Direct |
| Ribonuclease PH domain 2-like | 0 | Direct |
| Fibrinogen coiled-coil and central regions | 0 | Direct |
| IF2B-like | 0 | Direct |
| Histone lysine methyltransferases | 0.003456 | Inherited |
| Phosphate binding protein-like | 0.006485 | Inherited |
| Class I aminoacyl-tRNA synthetases (RS), catalytic domain | 0.008686 | Inherited |
| G proteins | 0.01731 | Inherited |
| GLA-domain | 0.02147 | Inherited |
| ARID domain | 0.03827 | Inherited |
| Medium chain acyl-CoA dehydrogenase-like, C-terminal domain | 0.04187 | Inherited |
| Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains | 0.04187 | Inherited |
| DNA gyrase/MutL, second domain | 0.06731 | Inherited |
| DNA gyrase/MutL, N-terminal domain | 0.06731 | Inherited |
| Phoshoinositide 3-kinase (PI3K), catalytic domain | 0.06799 | Inherited |
| T-box | 0.08904 | Inherited |
| Fibrinogen C-terminal domain-like | 0.09114 | Inherited |
| Tetramerization domain of potassium channels | 0.1102 | Inherited |
| Tyrosine-dependent oxidoreductases | 0.1107 | Inherited |
| Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain | 0.1107 | Inherited |
| Ypt/Rab-GAP domain of gyp1p | 0.1157 | Inherited |
| beta-glycanases | 0.1157 | Inherited |
| PHD domain | 0.2664 | Inherited |
| Integrin domains | 0.3054 | Inherited |
| Transforming growth factor (TGF)-beta | 0.3858 | Inherited |
| Crotonase-like | 0.4052 | Inherited |
| Transducin (alpha subunit), insertion domain | 0.4172 | Inherited |
| Bromodomain | 0.4454 | Inherited |
| Tubulin, GTPase domain | 0.479 | Inherited |
| Tubulin, C-terminal domain | 0.5148 | Inherited |
| MIR domain | 0.5406 | Inherited |
| Second domain of FERM | 0.5921 | Inherited |
| Actin/HSP70 | 0.5975 | Inherited |
| Myosin rod fragments | 0.6368 | Inherited |
| Nuclear receptor ligand-binding domain | 0.6798 | Inherited |
| Nuclear receptor | 0.693 | Inherited |
| PDZ domain | 0.798 | Inherited |
| Homeodomain | 0.8275 | Inherited |
| Cytochrome P450 | 0.9071 | Inherited |
Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term
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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.
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Supra-domain (including individual superfamily)
(show details)
Supra-domains annotated to this HP term (Not in SPHO)
Highlighted in gray are those with FDR>0.001
(show details)
Supra-domains annotated to this HP term (Not in SPHO)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
51206,51206
51206 - cAMP-binding domain-like
51206 - cAMP-binding domain-like | 0 | DIRECT |
52980,47781
52980 - Restriction endonuclease-like
47781 - RuvA domain 2-like | 0 | DIRECT |
47005,52777
47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
52777 - CoA-dependent acyltransferases | 0 | DIRECT |
57903,57903
57903 - FYVE/PHD zinc finger
57903 - FYVE/PHD zinc finger | 0 | DIRECT |
54897,52743
54897 - Protease propeptides/inhibitors
52743 - Subtilisin-like | 0 | DIRECT |
50447,54980
50447 - Translation proteins
54980 - EF-G C-terminal domain-like | 0 | DIRECT |
52540,46785
52540 - P-loop containing nucleoside triphosphate hydrolases
46785 - "Winged helix" DNA-binding domain | 0 | DIRECT |
54980,54211
54980 - EF-G C-terminal domain-like
54211 - Ribosomal protein S5 domain 2-like | 0 | DIRECT |
57196,90193
57196 - EGF/Laminin
90193 - Notch domain | 0 | DIRECT |
141072,141072
141072 - CalX-like
141072 - CalX-like | 0 | DIRECT |
50447,50465
50447 - Translation proteins
50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0 | DIRECT |
51230,47005
51230 - Single hybrid motif
47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 0 | DIRECT |
54211,55666
54211 - Ribosomal protein S5 domain 2-like
55666 - Ribonuclease PH domain 2-like | 0 | DIRECT |
50447,-8
50447 - Translation proteins
-8 - ECOD | 0 | DIRECT |
-8,54980
-8 - ECOD
54980 - EF-G C-terminal domain-like | 0 | DIRECT |
52540,50447
52540 - P-loop containing nucleoside triphosphate hydrolases
50447 - Translation proteins | 0 | DIRECT |
53822,53850
53822 - Periplasmic binding protein-like I
53850 - Periplasmic binding protein-like II | 0 | DIRECT |
57184,49899
57184 - Growth factor receptor domain
49899 - Concanavalin A-like lectins/glucanases | 0 | DIRECT |
54211,54980
54211 - Ribosomal protein S5 domain 2-like
54980 - EF-G C-terminal domain-like | 0 | DIRECT |
48371,48371
48371 - ARM repeat
48371 - ARM repeat | 0.01647 | INHERITED FROM: Lewy bodies || Cerebral inclusion bodies |
55874,54211
55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
54211 - Ribosomal protein S5 domain 2-like | 0.06927 | INHERITED FROM: Neoplasm of the anterior pituitary || Pituitary adenoma || Abnormality of the anterior pituitary || Abnormality of the pituitary gland |
47923,47923
47923 - Ypt/Rab-GAP domain of gyp1p
47923 - Ypt/Rab-GAP domain of gyp1p | 0.06927 | INHERITED FROM: Cerebellar vermis hypoplasia || Cerebellar malformation || Aplasia/Hypoplasia of the cerebellar vermis || Abnormality of the cerebellar vermis |
52374,47323
52374 - Nucleotidylyl transferase
47323 - Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 0.1121 | INHERITED FROM: Cerebellar hypoplasia |
50249,55681
50249 - Nucleic acid-binding proteins
55681 - Class II aaRS and biotin synthetases | 0.119 | INHERITED FROM: Hypoplasia of the corpus callosum |
57630,57196
57630 - GLA-domain
57196 - EGF/Laminin | 0.119 | INHERITED FROM: Abnormality of the cerebral vasculature |
55681,52954
55681 - Class II aaRS and biotin synthetases
52954 - Class II aaRS ABD-related | 0.2955 | INHERITED FROM: Hypoplasia of the corpus callosum |
47895,52540
47895 - Transducin (alpha subunit), insertion domain
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.4277 | INHERITED FROM: Cerebral calcification |
53067,53067
53067 - Actin-like ATPase domain
53067 - Actin-like ATPase domain | 0.5222 | INHERITED FROM: Transient ischemic attack || Subcortical cerebral atrophy |
52490,55307
52490 - Tubulin nucleotide-binding domain-like
55307 - Tubulin C-terminal domain-like | 0.5222 | INHERITED FROM: Abnormal cortical gyration || Abnormality of the cerebral cortex || Abnormality of brainstem morphology || Abnormality of lateral ventricle || Aplasia/Hypoplasia of the brainstem |
54452,48726
54452 - MHC antigen-recognition domain
48726 - Immunoglobulin | 0.6026 | INHERITED FROM: Cerebral ischemia |
50156,50156
50156 - PDZ domain-like
50156 - PDZ domain-like | 0.6471 | INHERITED FROM: Subcortical cerebral atrophy |
57716,57716
57716 - Glucocorticoid receptor-like (DNA-binding domain)
57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.919 | INHERITED FROM: Anterior pituitary dysgenesis |
57535,57535
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.9444 | INHERITED FROM: Cerebral hemorrhage |
48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.9467 | INHERITED FROM: Absent septum pellucidum |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
51206,51206
51206 - cAMP-binding domain-like
51206 - cAMP-binding domain-like | 0 | Direct |
52980,47781
52980 - Restriction endonuclease-like
47781 - RuvA domain 2-like | 0 | Direct |
47005,52777
47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
52777 - CoA-dependent acyltransferases | 0 | Direct |
57903,57903
57903 - FYVE/PHD zinc finger
57903 - FYVE/PHD zinc finger | 0 | Direct |
54897,52743
54897 - Protease propeptides/inhibitors
52743 - Subtilisin-like | 0 | Direct |
50447,54980
50447 - Translation proteins
54980 - EF-G C-terminal domain-like | 0 | Direct |
52540,46785
52540 - P-loop containing nucleoside triphosphate hydrolases
46785 - "Winged helix" DNA-binding domain | 0 | Direct |
54980,54211
54980 - EF-G C-terminal domain-like
54211 - Ribosomal protein S5 domain 2-like | 0 | Direct |
57196,90193
57196 - EGF/Laminin
90193 - Notch domain | 0 | Direct |
141072,141072
141072 - CalX-like
141072 - CalX-like | 0 | Direct |
50447,50465
50447 - Translation proteins
50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0 | Direct |
51230,47005
51230 - Single hybrid motif
47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 0 | Direct |
54211,55666
54211 - Ribosomal protein S5 domain 2-like
55666 - Ribonuclease PH domain 2-like | 0 | Direct |
50447,-8
50447 - Translation proteins
-8 - ECOD | 0 | Direct |
-8,54980
-8 - ECOD
54980 - EF-G C-terminal domain-like | 0 | Direct |
52540,50447
52540 - P-loop containing nucleoside triphosphate hydrolases
50447 - Translation proteins | 0 | Direct |
53822,53850
53822 - Periplasmic binding protein-like I
53850 - Periplasmic binding protein-like II | 0 | Direct |
57184,49899
57184 - Growth factor receptor domain
49899 - Concanavalin A-like lectins/glucanases | 0 | Direct |
54211,54980
54211 - Ribosomal protein S5 domain 2-like
54980 - EF-G C-terminal domain-like | 0 | Direct |
48371,48371
48371 - ARM repeat
48371 - ARM repeat | 0.01647 | Inherited |
55874,54211
55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
54211 - Ribosomal protein S5 domain 2-like | 0.06927 | Inherited |
47923,47923
47923 - Ypt/Rab-GAP domain of gyp1p
47923 - Ypt/Rab-GAP domain of gyp1p | 0.06927 | Inherited |
52374,47323
52374 - Nucleotidylyl transferase
47323 - Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 0.1121 | Inherited |
50249,55681
50249 - Nucleic acid-binding proteins
55681 - Class II aaRS and biotin synthetases | 0.119 | Inherited |
57630,57196
57630 - GLA-domain
57196 - EGF/Laminin | 0.119 | Inherited |
55681,52954
55681 - Class II aaRS and biotin synthetases
52954 - Class II aaRS ABD-related | 0.2955 | Inherited |
47895,52540
47895 - Transducin (alpha subunit), insertion domain
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.4277 | Inherited |
53067,53067
53067 - Actin-like ATPase domain
53067 - Actin-like ATPase domain | 0.5222 | Inherited |
52490,55307
52490 - Tubulin nucleotide-binding domain-like
55307 - Tubulin C-terminal domain-like | 0.5222 | Inherited |
54452,48726
54452 - MHC antigen-recognition domain
48726 - Immunoglobulin | 0.6026 | Inherited |
50156,50156
50156 - PDZ domain-like
50156 - PDZ domain-like | 0.6471 | Inherited |
57716,57716
57716 - Glucocorticoid receptor-like (DNA-binding domain)
57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.919 | Inherited |
57535,57535
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.9444 | Inherited |
48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.9467 | Inherited |
(show details)
Supra-domains annotated to this HP term (Not in SPHO)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
141072,141072,141072
141072 - CalX-like
141072 - CalX-like
141072 - CalX-like | 0 | DIRECT |
50447,-8,54980
50447 - Translation proteins
-8 - ECOD
54980 - EF-G C-terminal domain-like | 0 | DIRECT |
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 |
54980,54211,54980
54980 - EF-G C-terminal domain-like
54211 - Ribosomal protein S5 domain 2-like
54980 - EF-G C-terminal domain-like | 0 | DIRECT |
51230,47005,52777
51230 - Single hybrid motif
47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
52777 - CoA-dependent acyltransferases | 0 | DIRECT |
49899,57196,57196
49899 - Concanavalin A-like lectins/glucanases
57196 - EGF/Laminin
57196 - EGF/Laminin | 0 | DIRECT |
49899,49899,57196
49899 - Concanavalin A-like lectins/glucanases
49899 - Concanavalin A-like lectins/glucanases
57196 - EGF/Laminin | 0 | DIRECT |
57196,57196,90193
57196 - EGF/Laminin
57196 - EGF/Laminin
90193 - Notch domain | 0 | DIRECT |
52540,50447,54980
52540 - P-loop containing nucleoside triphosphate hydrolases
50447 - Translation proteins
54980 - EF-G C-terminal domain-like | 0 | DIRECT |
57184,49899,49899
57184 - Growth factor receptor domain
49899 - Concanavalin A-like lectins/glucanases
49899 - Concanavalin A-like lectins/glucanases | 0 | DIRECT |
52540,52540,52540
52540 - P-loop containing nucleoside triphosphate hydrolases
52540 - P-loop containing nucleoside triphosphate hydrolases
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.07105 | INHERITED FROM: Ventriculomegaly |
57184,57184,57196
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain
57196 - EGF/Laminin | 0.119 | INHERITED FROM: Hydrocephalus |
57184,57196,57184
57184 - Growth factor receptor domain
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.119 | INHERITED FROM: Cerebellar malformation || Arnold-Chiari malformation |
48726,48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.7581 | INHERITED FROM: Aqueductal stenosis || Abnormality of the septum pellucidum || Absent septum pellucidum |
57535,57535,57535
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.8306 | INHERITED FROM: Cerebral hemorrhage |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
141072,141072,141072
141072 - CalX-like
141072 - CalX-like
141072 - CalX-like | 0 | Direct |
50447,-8,54980
50447 - Translation proteins
-8 - ECOD
54980 - EF-G C-terminal domain-like | 0 | Direct |
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 |
54980,54211,54980
54980 - EF-G C-terminal domain-like
54211 - Ribosomal protein S5 domain 2-like
54980 - EF-G C-terminal domain-like | 0 | Direct |
51230,47005,52777
51230 - Single hybrid motif
47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
52777 - CoA-dependent acyltransferases | 0 | Direct |
49899,57196,57196
49899 - Concanavalin A-like lectins/glucanases
57196 - EGF/Laminin
57196 - EGF/Laminin | 0 | Direct |
49899,49899,57196
49899 - Concanavalin A-like lectins/glucanases
49899 - Concanavalin A-like lectins/glucanases
57196 - EGF/Laminin | 0 | Direct |
57196,57196,90193
57196 - EGF/Laminin
57196 - EGF/Laminin
90193 - Notch domain | 0 | Direct |
52540,50447,54980
52540 - P-loop containing nucleoside triphosphate hydrolases
50447 - Translation proteins
54980 - EF-G C-terminal domain-like | 0 | Direct |
57184,49899,49899
57184 - Growth factor receptor domain
49899 - Concanavalin A-like lectins/glucanases
49899 - Concanavalin A-like lectins/glucanases | 0 | Direct |
52540,52540,52540
52540 - P-loop containing nucleoside triphosphate hydrolases
52540 - P-loop containing nucleoside triphosphate hydrolases
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.07105 | Inherited |
57184,57184,57196
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain
57196 - EGF/Laminin | 0.119 | Inherited |
57184,57196,57184
57184 - Growth factor receptor domain
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.119 | Inherited |
48726,48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.7581 | Inherited |
57535,57535,57535
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.8306 | Inherited |
Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term
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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
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