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Xenopus ANatomical entity (XAN): sensory system
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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: XA Hierarchy (Xenopus anatomy and development from Xenbase frog anatomy ontology)
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 XA term (SDXA level: Moderately Informative)
Highlighted in gray are those with FDR_all>0.001
| SCOP term | FDR (all) | Annotation (direct or inherited) |
| Hedgehog (development protein), N-terminal signaling domain | 0 | DIRECT |
| PAS domain of steroid receptor coactivator 1A, NCo-A1 | 0 | DIRECT |
| Homeodomain | 0 | DIRECT |
| 14-3-3 protein | 0 | DIRECT |
| Guanido kinase catalytic domain | 0 | DIRECT |
| Guanido kinase N-terminal domain | 0 | DIRECT |
| Alanine racemase-like, N-terminal domain | 0 | DIRECT |
| Arrestin/Vps26-like | 0 | DIRECT |
| Noggin | 0 | DIRECT |
| Eukaryotic ODC-like | 0 | DIRECT |
| 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain | 0 | DIRECT |
| Nop domain | 0 | DIRECT |
| Fibroblast growth factors (FGF) | 0 | DIRECT |
| Synuclein | 0 | DIRECT |
| 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain | 0 | DIRECT |
| HLH, helix-loop-helix DNA-binding domain | 0.0000000000006914 | DIRECT |
| Frizzled cysteine-rich domain | 0.0000006083 | DIRECT |
| Forkhead DNA-binding domain | 0.000001033 | DIRECT |
| ets domain | 0.000001303 | DIRECT |
| Sema domain | 0.000002344 | DIRECT |
| HMG-box | 0.0001223 | DIRECT |
| Transducin (alpha subunit), insertion domain | 0.0001261 | DIRECT |
| SMAD domain | 0.0001402 | DIRECT |
| Plexin repeat | 0.0001823 | DIRECT |
| T-box | 0.0002398 | DIRECT |
| Canonical RBD | 0.000325 | DIRECT |
| Growth factor receptor domain | 0.0004414 | DIRECT |
| SMAD MH1 domain | 0.0004973 | DIRECT |
| Hairy Orange domain | 0.0009062 | DIRECT |
| Extracellular domain of cell surface receptors | 0.001729 | INHERITED FROM: visual system |
| P4 origin-binding domain-like | 0.001729 | INHERITED FROM: optic vesicle || otic placode || visual system |
| L domain | 0.001729 | INHERITED FROM: vestibuloauditory system || otic vesicle |
| BRK domain-like | 0.005811 | INHERITED FROM: vestibuloauditory system || otic vesicle |
| I set domains | 0.01213 | INHERITED FROM: retinal inner nuclear layer || optic vesicle || retinal ganglion cell layer |
| Link domain | 0.01715 | INHERITED FROM: vestibuloauditory system |
| Hypoxia-inducible factor Hif2a, C-terminal domain | 0.01761 | INHERITED FROM: otic vesicle |
| POU-specific domain | 0.02295 | INHERITED FROM: retinal ganglion cell layer |
| Tubulin, GTPase domain | 0.03501 | INHERITED FROM: glossopharyngeal nerve || vagus nerve || facial nerve |
| Tubulin, C-terminal domain | 0.03501 | INHERITED FROM: glossopharyngeal nerve || vagus nerve || facial nerve |
| Intermediate filament protein, coiled coil region | 0.04707 | INHERITED FROM: retinal ganglion cell || retinal inner nuclear layer || retinal ganglion cell layer || retinal inner plexiform layer || optic nerve || gustatory system || vestibulocochlear nerve |
| Glutathione peroxidase-like | 0.05028 | INHERITED FROM: eye primordium |
| Crystallins/Ca-binding development proteins | 0.06509 | INHERITED FROM: lens |
| Arginine methyltransferase | 0.1267 | INHERITED FROM: optic vesicle |
| Tandem AAA-ATPase domain | 0.1536 | INHERITED FROM: vestibuloauditory system || otic vesicle |
| Higher-molecular-weight phosphotyrosine protein phosphatases | 0.2672 | INHERITED FROM: retinal inner nuclear layer || retinal ganglion cell layer |
| Fibronectin type III | 0.4045 | INHERITED FROM: retinal ganglion cell layer || retinal neural layer |
| Tetramerization domain of potassium channels | 0.4943 | INHERITED FROM: retinal outer plexiform layer || retinal ganglion cell layer || retinal inner plexiform layer || optic disc || optic nerve |
| Voltage-gated potassium channels | 0.5098 | INHERITED FROM: retinal inner plexiform layer || optic disc || optic nerve |
| G proteins | 0.6161 | INHERITED FROM: olfactory epithelium || olfactory sensory neuron |
| Spectrin repeat | 0.6807 | INHERITED FROM: auditory hair cell || inner ear || auditory ossicle || auditory apparatus |
| Rhodopsin-like | 1 | INHERITED FROM: eye photoreceptor cell || granule cell layer of the olfactory bulb |
| SCOP term | FDR (all) | Annotation (direct or inherited) |
| Hedgehog (development protein), N-terminal signaling domain | 0 | Direct |
| PAS domain of steroid receptor coactivator 1A, NCo-A1 | 0 | Direct |
| Homeodomain | 0 | Direct |
| 14-3-3 protein | 0 | Direct |
| Guanido kinase catalytic domain | 0 | Direct |
| Guanido kinase N-terminal domain | 0 | Direct |
| Alanine racemase-like, N-terminal domain | 0 | Direct |
| Arrestin/Vps26-like | 0 | Direct |
| Noggin | 0 | Direct |
| Eukaryotic ODC-like | 0 | Direct |
| 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain | 0 | Direct |
| Nop domain | 0 | Direct |
| Fibroblast growth factors (FGF) | 0 | Direct |
| Synuclein | 0 | Direct |
| 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain | 0 | Direct |
| HLH, helix-loop-helix DNA-binding domain | 0.0000000000006914 | Direct |
| Frizzled cysteine-rich domain | 0.0000006083 | Direct |
| Forkhead DNA-binding domain | 0.000001033 | Direct |
| ets domain | 0.000001303 | Direct |
| Sema domain | 0.000002344 | Direct |
| HMG-box | 0.0001223 | Direct |
| Transducin (alpha subunit), insertion domain | 0.0001261 | Direct |
| SMAD domain | 0.0001402 | Direct |
| Plexin repeat | 0.0001823 | Direct |
| T-box | 0.0002398 | Direct |
| Canonical RBD | 0.000325 | Direct |
| Growth factor receptor domain | 0.0004414 | Direct |
| SMAD MH1 domain | 0.0004973 | Direct |
| Hairy Orange domain | 0.0009062 | Direct |
| Extracellular domain of cell surface receptors | 0.001729 | Inherited |
| P4 origin-binding domain-like | 0.001729 | Inherited |
| L domain | 0.001729 | Inherited |
| BRK domain-like | 0.005811 | Inherited |
| I set domains | 0.01213 | Inherited |
| Link domain | 0.01715 | Inherited |
| Hypoxia-inducible factor Hif2a, C-terminal domain | 0.01761 | Inherited |
| POU-specific domain | 0.02295 | Inherited |
| Tubulin, GTPase domain | 0.03501 | Inherited |
| Tubulin, C-terminal domain | 0.03501 | Inherited |
| Intermediate filament protein, coiled coil region | 0.04707 | Inherited |
| Glutathione peroxidase-like | 0.05028 | Inherited |
| Crystallins/Ca-binding development proteins | 0.06509 | Inherited |
| Arginine methyltransferase | 0.1267 | Inherited |
| Tandem AAA-ATPase domain | 0.1536 | Inherited |
| Higher-molecular-weight phosphotyrosine protein phosphatases | 0.2672 | Inherited |
| Fibronectin type III | 0.4045 | Inherited |
| Tetramerization domain of potassium channels | 0.4943 | Inherited |
| Voltage-gated potassium channels | 0.5098 | Inherited |
| G proteins | 0.6161 | Inherited |
| Spectrin repeat | 0.6807 | Inherited |
| Rhodopsin-like | 1 | 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)
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Supra-domains annotated to this XA term (SPXA level: Moderately Informative)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
52540,53254
52540 - P-loop containing nucleoside triphosphate hydrolases
53254 - Phosphoglycerate mutase-like | 0 | DIRECT |
51419,50621
51419 - PLP-binding barrel
50621 - Alanine racemase C-terminal domain-like | 0 | DIRECT |
56436,57535
56436 - C-type lectin-like
57535 - Complement control module/SCR domain | 0 | DIRECT |
57184,49265
57184 - Growth factor receptor domain
49265 - Fibronectin type III | 0 | DIRECT |
48034,55931
48034 - Guanido kinase N-terminal domain
55931 - Glutamine synthetase/guanido kinase | 0 | DIRECT |
49899,48726
49899 - Concanavalin A-like lectins/glucanases
48726 - Immunoglobulin | 0 | DIRECT |
50044,50156
50044 - SH3-domain
50156 - PDZ domain-like | 0 | DIRECT |
48726,56436
48726 - Immunoglobulin
56436 - C-type lectin-like | 0 | DIRECT |
101912,103575
101912 - Sema domain
103575 - Plexin repeat | 0.00002506 | DIRECT |
47895,52540
47895 - Transducin (alpha subunit), insertion domain
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.00007447 | DIRECT |
57716,57716
57716 - Glucocorticoid receptor-like (DNA-binding domain)
57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.000488 | DIRECT |
47459,158457
47459 - HLH, helix-loop-helix DNA-binding domain
158457 - Orange domain-like | 0.0006155 | DIRECT |
52058,57184
52058 - L domain-like
57184 - Growth factor receptor domain | 0.00128 | INHERITED FROM: vestibuloauditory system || otic vesicle |
57184,52058
57184 - Growth factor receptor domain
52058 - L domain-like | 0.00128 | INHERITED FROM: vestibuloauditory system || otic vesicle |
47459,55785
47459 - HLH, helix-loop-helix DNA-binding domain
55785 - PYP-like sensor domain (PAS domain) | 0.001965 | INHERITED FROM: visual system || eye |
55785,55785
55785 - PYP-like sensor domain (PAS domain)
55785 - PYP-like sensor domain (PAS domain) | 0.00224 | INHERITED FROM: visual system |
54928,54928
54928 - RNA-binding domain, RBD
54928 - RNA-binding domain, RBD | 0.004209 | INHERITED FROM: visual system |
52799,52799
52799 - (Phosphotyrosine protein) phosphatases II
52799 - (Phosphotyrosine protein) phosphatases II | 0.008843 | INHERITED FROM: retinal inner nuclear layer || retinal neural layer || retinal ganglion cell layer |
52490,55307
52490 - Tubulin nucleotide-binding domain-like
55307 - Tubulin C-terminal domain-like | 0.02497 | INHERITED FROM: facial nerve || gustatory system || glossopharyngeal nerve || vagus nerve |
47413,46689
47413 - lambda repressor-like DNA-binding domains
46689 - Homeodomain-like | 0.04581 | INHERITED FROM: retinal ganglion cell layer |
57850,49599
57850 - RING/U-box
49599 - TRAF domain-like | 0.04589 | INHERITED FROM: optic vesicle |
49265,49265
49265 - Fibronectin type III
49265 - Fibronectin type III | 0.06444 | INHERITED FROM: retinal inner nuclear layer |
48726,49265
48726 - Immunoglobulin
49265 - Fibronectin type III | 0.08653 | INHERITED FROM: retinal inner nuclear layer || retinal neural layer || retinal ganglion cell layer |
47954,47954
47954 - Cyclin-like
47954 - Cyclin-like | 0.2869 | INHERITED FROM: eye primordium |
46966,46966
46966 - Spectrin repeat
46966 - Spectrin repeat | 0.5067 | INHERITED FROM: auditory hair cell || auditory apparatus || inner ear || auditory ossicle |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
52540,53254
52540 - P-loop containing nucleoside triphosphate hydrolases
53254 - Phosphoglycerate mutase-like | 0 | Direct |
51419,50621
51419 - PLP-binding barrel
50621 - Alanine racemase C-terminal domain-like | 0 | Direct |
56436,57535
56436 - C-type lectin-like
57535 - Complement control module/SCR domain | 0 | Direct |
57184,49265
57184 - Growth factor receptor domain
49265 - Fibronectin type III | 0 | Direct |
48034,55931
48034 - Guanido kinase N-terminal domain
55931 - Glutamine synthetase/guanido kinase | 0 | Direct |
49899,48726
49899 - Concanavalin A-like lectins/glucanases
48726 - Immunoglobulin | 0 | Direct |
50044,50156
50044 - SH3-domain
50156 - PDZ domain-like | 0 | Direct |
48726,56436
48726 - Immunoglobulin
56436 - C-type lectin-like | 0 | Direct |
101912,103575
101912 - Sema domain
103575 - Plexin repeat | 0.00002506 | Direct |
47895,52540
47895 - Transducin (alpha subunit), insertion domain
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.00007447 | Direct |
57716,57716
57716 - Glucocorticoid receptor-like (DNA-binding domain)
57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.000488 | Direct |
47459,158457
47459 - HLH, helix-loop-helix DNA-binding domain
158457 - Orange domain-like | 0.0006155 | Direct |
52058,57184
52058 - L domain-like
57184 - Growth factor receptor domain | 0.00128 | Inherited |
57184,52058
57184 - Growth factor receptor domain
52058 - L domain-like | 0.00128 | Inherited |
47459,55785
47459 - HLH, helix-loop-helix DNA-binding domain
55785 - PYP-like sensor domain (PAS domain) | 0.001965 | Inherited |
55785,55785
55785 - PYP-like sensor domain (PAS domain)
55785 - PYP-like sensor domain (PAS domain) | 0.00224 | Inherited |
54928,54928
54928 - RNA-binding domain, RBD
54928 - RNA-binding domain, RBD | 0.004209 | Inherited |
52799,52799
52799 - (Phosphotyrosine protein) phosphatases II
52799 - (Phosphotyrosine protein) phosphatases II | 0.008843 | Inherited |
52490,55307
52490 - Tubulin nucleotide-binding domain-like
55307 - Tubulin C-terminal domain-like | 0.02497 | Inherited |
47413,46689
47413 - lambda repressor-like DNA-binding domains
46689 - Homeodomain-like | 0.04581 | Inherited |
57850,49599
57850 - RING/U-box
49599 - TRAF domain-like | 0.04589 | Inherited |
49265,49265
49265 - Fibronectin type III
49265 - Fibronectin type III | 0.06444 | Inherited |
48726,49265
48726 - Immunoglobulin
49265 - Fibronectin type III | 0.08653 | Inherited |
47954,47954
47954 - Cyclin-like
47954 - Cyclin-like | 0.2869 | Inherited |
46966,46966
46966 - Spectrin repeat
46966 - Spectrin repeat | 0.5067 | Inherited |
(show details)
Supra-domains annotated to this XA term (SPXA level: Moderately Informative)
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 |
48726,56436,56436
48726 - Immunoglobulin
56436 - C-type lectin-like
56436 - C-type lectin-like | 0 | DIRECT |
49899,48726,49265
49899 - Concanavalin A-like lectins/glucanases
48726 - Immunoglobulin
49265 - Fibronectin type III | 0 | DIRECT |
50044,55550,56112
50044 - SH3-domain
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.000183 | DIRECT |
47459,55785,55785
47459 - HLH, helix-loop-helix DNA-binding domain
55785 - PYP-like sensor domain (PAS domain)
55785 - PYP-like sensor domain (PAS domain) | 0.0006155 | DIRECT |
52058,57184,52058
52058 - L domain-like
57184 - Growth factor receptor domain
52058 - L domain-like | 0.004556 | INHERITED FROM: vestibuloauditory system || otic vesicle |
48726,48726,49265
48726 - Immunoglobulin
48726 - Immunoglobulin
49265 - Fibronectin type III | 0.03114 | INHERITED FROM: retinal inner nuclear layer || retinal ganglion cell layer |
48726,49265,49265
48726 - Immunoglobulin
49265 - Fibronectin type III
49265 - Fibronectin type III | 0.03645 | INHERITED FROM: optic vesicle |
57196,57196,49899
57196 - EGF/Laminin
57196 - EGF/Laminin
49899 - Concanavalin A-like lectins/glucanases | 0.05272 | INHERITED FROM: retina || retinal neural layer |
46966,46966,46966
46966 - Spectrin repeat
46966 - Spectrin repeat
46966 - Spectrin repeat | 0.4026 | INHERITED FROM: auditory hair cell || auditory apparatus || inner ear || auditory ossicle |
| 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 |
48726,56436,56436
48726 - Immunoglobulin
56436 - C-type lectin-like
56436 - C-type lectin-like | 0 | Direct |
49899,48726,49265
49899 - Concanavalin A-like lectins/glucanases
48726 - Immunoglobulin
49265 - Fibronectin type III | 0 | Direct |
50044,55550,56112
50044 - SH3-domain
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.000183 | Direct |
47459,55785,55785
47459 - HLH, helix-loop-helix DNA-binding domain
55785 - PYP-like sensor domain (PAS domain)
55785 - PYP-like sensor domain (PAS domain) | 0.0006155 | Direct |
52058,57184,52058
52058 - L domain-like
57184 - Growth factor receptor domain
52058 - L domain-like | 0.004556 | Inherited |
48726,48726,49265
48726 - Immunoglobulin
48726 - Immunoglobulin
49265 - Fibronectin type III | 0.03114 | Inherited |
48726,49265,49265
48726 - Immunoglobulin
49265 - Fibronectin type III
49265 - Fibronectin type III | 0.03645 | Inherited |
57196,57196,49899
57196 - EGF/Laminin
57196 - EGF/Laminin
49899 - Concanavalin A-like lectins/glucanases | 0.05272 | Inherited |
46966,46966,46966
46966 - Spectrin repeat
46966 - Spectrin repeat
46966 - Spectrin repeat | 0.4026 | Inherited |
Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term
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(show help)
Trees by TreeVector
A presence/absence matrix is generated using protein domains and supradomains
for all genomes in SUPERFAMILY. The RAxML
software is used to produce a single, large tree topology using
heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as
if individual trees had been produced. However, this data is extracted from the single
large tree. This produces a higher quality topology than if the trees had been produced
on their own, and allows the trees to be displayed instantly.
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