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Mammalian Phenotype (MP): abnormal somatic nervous system 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: MP Hierarchy (mammalian/mouse phenotype from MGI_4.41)
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Superfamily(show details)
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Family(show details)
Family domains annotated to this MP term (Not in SDMP)
Highlighted in gray are those with FDR_all>0.001
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 MP term (Not in SPMP)
Highlighted in gray are those with FDR>0.001
(show details)
Supra-domains annotated to this MP term (Not in SPMP)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
64593,74853
64593 - Intermediate filament protein, coiled coil region
74853 - Lamin A/C globular tail domain | 0 | DIRECT |
52058,57184
52058 - L domain-like
57184 - Growth factor receptor domain | 0.0001255 | DIRECT |
57184,52058
57184 - Growth factor receptor domain
52058 - L domain-like | 0.0001255 | DIRECT |
49417,81296
49417 - p53-like transcription factors
81296 - E set domains | 0.00172 | INHERITED FROM: abnormal trigeminal nerve morphology || abnormal sensory neuron innervation pattern |
56112,55073
56112 - Protein kinase-like (PK-like)
55073 - Nucleotide cyclase | 0.001927 | INHERITED FROM: abnormal sensory neuron morphology || abnormal somatic sensory system morphology |
57716,48508
57716 - Glucocorticoid receptor-like (DNA-binding domain)
48508 - Nuclear receptor ligand-binding domain | 0.005405 | INHERITED FROM: optic disc coloboma || abnormal optic nerve morphology || abnormal optic disc morphology |
57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.02153 | INHERITED FROM: abnormal cochlear hair cell number || abnormal cochlear inner hair cell number || short photoreceptor inner segment || increased cochlear inner hair cell number || abnormal cochlear outer hair cell number |
101912,103575
101912 - Sema domain
103575 - Plexin repeat | 0.04423 | INHERITED FROM: abnormal trochlear nerve morphology || abnormal amacrine cell morphology |
57196,57184
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.04681 | INHERITED FROM: increased sensory neuron number || abnormal cochlear hair cell number || abnormal cochlear inner hair cell number || abnormal cochlear hair cell morphology || abnormal cochlear outer hair cell morphology || abnormal cochlear inner hair cell morphology || increased cochlear inner hair cell number || abnormal cochlear outer hair cell number |
47413,46689
47413 - lambda repressor-like DNA-binding domains
46689 - Homeodomain-like | 0.04681 | INHERITED FROM: abnormal retinal ganglion cell morphology || cochlear outer hair cell degeneration |
57184,49265
57184 - Growth factor receptor domain
49265 - Fibronectin type III | 0.05228 | INHERITED FROM: abnormal sensory neuron morphology || abnormal sensory neuron innervation pattern |
55781,55781
55781 - GAF domain-like
55781 - GAF domain-like | 0.05228 | INHERITED FROM: abnormal retinal photoreceptor morphology || decreased sensory neuron number || retinal photoreceptor degeneration || decreased retinal photoreceptor cell number |
55781,109604
55781 - GAF domain-like
109604 - HD-domain/PDEase-like | 0.05228 | INHERITED FROM: abnormal retinal photoreceptor morphology || decreased sensory neuron number || retinal photoreceptor degeneration || decreased retinal photoreceptor cell number |
63712,90112
63712 - Nicotinic receptor ligand binding domain-like
90112 - Neurotransmitter-gated ion-channel transmembrane pore | 0.06761 | INHERITED FROM: abnormal cochlear hair cell morphology || abnormal cochlear outer hair cell morphology || abnormal cochlear inner hair cell morphology || abnormal cochlear OHC efferent innervation pattern || abnormal hair cell morphology || cochlear ganglion degeneration |
52058,48726
52058 - L domain-like
48726 - Immunoglobulin | 0.07058 | INHERITED FROM: abnormal dorsal root ganglion morphology |
81296,81296
81296 - E set domains
81296 - E set domains | 0.0802 | INHERITED FROM: abnormal amacrine cell morphology |
57184,57196
57184 - Growth factor receptor domain
57196 - EGF/Laminin | 0.0802 | INHERITED FROM: increased sensory neuron number || abnormal cochlear hair cell number || increased cochlear hair cell number || abnormal cochlear inner hair cell number || increased cochlear inner hair cell number || abnormal cochlear outer hair cell number |
47459,158457
47459 - HLH, helix-loop-helix DNA-binding domain
158457 - Orange domain-like | 0.1325 | INHERITED FROM: increased sensory neuron number |
47473,57850
47473 - EF-hand
57850 - RING/U-box | 0.1325 | INHERITED FROM: abnormal somatic motor system morphology || abnormal neuromuscular synapse morphology |
49313,49313
49313 - Cadherin-like
49313 - Cadherin-like | 0.2291 | INHERITED FROM: abnormal orientation of outer hair cell stereociliary bundles || abnormal outer hair cell stereociliary bundle morphology || abnormal cochlear hair cell stereociliary bundle morphology || abnormal cochlear hair cell morphology || abnormal orientation of cochlear hair cell stereociliary bundles || abnormal cochlear outer hair cell morphology |
46785,144074
46785 - "Winged helix" DNA-binding domain
144074 - E2F-DP heterodimerization region | 0.3332 | INHERITED FROM: decreased sensory neuron number || abnormal retinal ganglion cell morphology || abnormal retinal bipolar cell morphology || decreased retinal ganglion cell number |
46966,46966
46966 - Spectrin repeat
46966 - Spectrin repeat | 0.3899 | INHERITED FROM: abnormal somatic motor system morphology || abnormal neuromuscular synapse morphology |
50156,50156
50156 - PDZ domain-like
50156 - PDZ domain-like | 0.5286 | INHERITED FROM: abnormal outer hair cell stereociliary bundle morphology || abnormal cochlear hair cell stereociliary bundle morphology || abnormal cochlear outer hair cell morphology |
47473,47473
47473 - EF-hand
47473 - EF-hand | 0.5323 | INHERITED FROM: abnormal somatic motor system morphology |
57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 0.5712 | INHERITED FROM: abnormal olfactory nerve morphology |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
64593,74853
64593 - Intermediate filament protein, coiled coil region
74853 - Lamin A/C globular tail domain | 0 | Direct |
52058,57184
52058 - L domain-like
57184 - Growth factor receptor domain | 0.0001255 | Direct |
57184,52058
57184 - Growth factor receptor domain
52058 - L domain-like | 0.0001255 | Direct |
49417,81296
49417 - p53-like transcription factors
81296 - E set domains | 0.00172 | Inherited |
56112,55073
56112 - Protein kinase-like (PK-like)
55073 - Nucleotide cyclase | 0.001927 | Inherited |
57716,48508
57716 - Glucocorticoid receptor-like (DNA-binding domain)
48508 - Nuclear receptor ligand-binding domain | 0.005405 | Inherited |
57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.02153 | Inherited |
101912,103575
101912 - Sema domain
103575 - Plexin repeat | 0.04423 | Inherited |
57196,57184
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.04681 | Inherited |
47413,46689
47413 - lambda repressor-like DNA-binding domains
46689 - Homeodomain-like | 0.04681 | Inherited |
57184,49265
57184 - Growth factor receptor domain
49265 - Fibronectin type III | 0.05228 | Inherited |
55781,55781
55781 - GAF domain-like
55781 - GAF domain-like | 0.05228 | Inherited |
55781,109604
55781 - GAF domain-like
109604 - HD-domain/PDEase-like | 0.05228 | Inherited |
63712,90112
63712 - Nicotinic receptor ligand binding domain-like
90112 - Neurotransmitter-gated ion-channel transmembrane pore | 0.06761 | Inherited |
52058,48726
52058 - L domain-like
48726 - Immunoglobulin | 0.07058 | Inherited |
81296,81296
81296 - E set domains
81296 - E set domains | 0.0802 | Inherited |
57184,57196
57184 - Growth factor receptor domain
57196 - EGF/Laminin | 0.0802 | Inherited |
47459,158457
47459 - HLH, helix-loop-helix DNA-binding domain
158457 - Orange domain-like | 0.1325 | Inherited |
47473,57850
47473 - EF-hand
57850 - RING/U-box | 0.1325 | Inherited |
49313,49313
49313 - Cadherin-like
49313 - Cadherin-like | 0.2291 | Inherited |
46785,144074
46785 - "Winged helix" DNA-binding domain
144074 - E2F-DP heterodimerization region | 0.3332 | Inherited |
46966,46966
46966 - Spectrin repeat
46966 - Spectrin repeat | 0.3899 | Inherited |
50156,50156
50156 - PDZ domain-like
50156 - PDZ domain-like | 0.5286 | Inherited |
47473,47473
47473 - EF-hand
47473 - EF-hand | 0.5323 | Inherited |
57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 0.5712 | Inherited |
(show details)
Supra-domains annotated to this MP term (Not in SPMP)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57184,52058,57184
57184 - Growth factor receptor domain
52058 - L domain-like
57184 - Growth factor receptor domain | 0 | DIRECT |
52058,48726,48726
52058 - L domain-like
48726 - Immunoglobulin
48726 - Immunoglobulin | 0 | DIRECT |
52058,57184,52058
52058 - L domain-like
57184 - Growth factor receptor domain
52058 - L domain-like | 0.0001255 | DIRECT |
57196,57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.0006755 | DIRECT |
57184,49899,49899
57184 - Growth factor receptor domain
49899 - Concanavalin A-like lectins/glucanases
49899 - Concanavalin A-like lectins/glucanases | 0.02416 | INHERITED FROM: abnormal somatic sensory system morphology |
57184,57196,57196
57184 - Growth factor receptor domain
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.03652 | INHERITED FROM: abnormal cochlear hair cell number || increased cochlear hair cell number || abnormal cochlear inner hair cell number || abnormal cochlear hair cell morphology || abnormal cochlear outer hair cell morphology || abnormal cochlear inner hair cell morphology || increased cochlear inner hair cell number || abnormal cochlear outer hair cell number |
55781,55781,109604
55781 - GAF domain-like
55781 - GAF domain-like
109604 - HD-domain/PDEase-like | 0.05228 | INHERITED FROM: abnormal retinal photoreceptor morphology || decreased sensory neuron number || retinal photoreceptor degeneration || decreased retinal photoreceptor cell number |
57196,57184,57196
57196 - EGF/Laminin
57184 - Growth factor receptor domain
57196 - EGF/Laminin | 0.07058 | INHERITED FROM: increased sensory neuron number || abnormal cochlear hair cell number || abnormal mechanoreceptor morphology || increased cochlear hair cell number || abnormal cochlear inner hair cell number || abnormal cochlear hair cell morphology || abnormal cochlear outer hair cell morphology || abnormal cochlear inner hair cell morphology || increased cochlear inner hair cell number || abnormal cochlear outer hair cell number |
57196,57196,57184
57196 - EGF/Laminin
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.0802 | INHERITED FROM: increased sensory neuron number || abnormal cochlear hair cell number || abnormal cochlear inner hair cell number || abnormal cochlear hair cell morphology || increased cochlear outer hair cell number || abnormal cochlear outer hair cell morphology || abnormal cochlear inner hair cell morphology || abnormal somatic sensory system morphology || increased cochlear inner hair cell number || abnormal cochlear outer hair cell number |
81296,81296,81296
81296 - E set domains
81296 - E set domains
81296 - E set domains | 0.0802 | INHERITED FROM: abnormal amacrine cell morphology |
49313,49313,49313
49313 - Cadherin-like
49313 - Cadherin-like
49313 - Cadherin-like | 0.1221 | INHERITED FROM: abnormal orientation of outer hair cell stereociliary bundles || abnormal outer hair cell stereociliary bundle morphology || abnormal cochlear hair cell stereociliary bundle morphology || abnormal cochlear hair cell morphology || abnormal orientation of cochlear hair cell stereociliary bundles || abnormal cochlear outer hair cell morphology |
47473,47473,57850
47473 - EF-hand
47473 - EF-hand
57850 - RING/U-box | 0.1325 | INHERITED FROM: abnormal somatic motor system morphology || abnormal neuromuscular synapse morphology |
49899,57196,57196
49899 - Concanavalin A-like lectins/glucanases
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.1362 | INHERITED FROM: abnormal retinal bipolar cell morphology || abnormal amacrine cell morphology |
46966,46966,46966
46966 - Spectrin repeat
46966 - Spectrin repeat
46966 - Spectrin repeat | 0.2742 | INHERITED FROM: abnormal somatic motor system morphology || abnormal neuromuscular synapse morphology |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57184,52058,57184
57184 - Growth factor receptor domain
52058 - L domain-like
57184 - Growth factor receptor domain | 0 | Direct |
52058,48726,48726
52058 - L domain-like
48726 - Immunoglobulin
48726 - Immunoglobulin | 0 | Direct |
52058,57184,52058
52058 - L domain-like
57184 - Growth factor receptor domain
52058 - L domain-like | 0.0001255 | Direct |
57196,57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.0006755 | Direct |
57184,49899,49899
57184 - Growth factor receptor domain
49899 - Concanavalin A-like lectins/glucanases
49899 - Concanavalin A-like lectins/glucanases | 0.02416 | Inherited |
57184,57196,57196
57184 - Growth factor receptor domain
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.03652 | Inherited |
55781,55781,109604
55781 - GAF domain-like
55781 - GAF domain-like
109604 - HD-domain/PDEase-like | 0.05228 | Inherited |
57196,57184,57196
57196 - EGF/Laminin
57184 - Growth factor receptor domain
57196 - EGF/Laminin | 0.07058 | Inherited |
57196,57196,57184
57196 - EGF/Laminin
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.0802 | Inherited |
81296,81296,81296
81296 - E set domains
81296 - E set domains
81296 - E set domains | 0.0802 | Inherited |
49313,49313,49313
49313 - Cadherin-like
49313 - Cadherin-like
49313 - Cadherin-like | 0.1221 | Inherited |
47473,47473,57850
47473 - EF-hand
47473 - EF-hand
57850 - RING/U-box | 0.1325 | Inherited |
49899,57196,57196
49899 - Concanavalin A-like lectins/glucanases
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.1362 | Inherited |
46966,46966,46966
46966 - Spectrin repeat
46966 - Spectrin repeat
46966 - Spectrin repeat | 0.2742 | Inherited |
Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term
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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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