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Xenopus ANatomical entity (XAN): musculoskeletal 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) |
| ADP-ribosylglycohydrolase | 0 | DIRECT |
| RUNT domain | 0 | DIRECT |
| gamma-adaptin C-terminal appendage domain-like | 0 | DIRECT |
| Group II chaperonin (CCT, TRIC), intermediate domain | 0 | DIRECT |
| F1F0 ATP synthase subunit C | 0 | DIRECT |
| SRF-like | 0 | DIRECT |
| GABARAP-like | 0 | DIRECT |
| alpha-ketoacid dehydrogenase kinase, N-terminal domain | 0 | DIRECT |
| Branched-chain alpha-keto acid dehydrogenase PP module | 0 | DIRECT |
| Noggin | 0 | DIRECT |
| HSP90 C-terminal domain | 0 | DIRECT |
| 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain | 0 | DIRECT |
| Heat shock protein 90, HSP90, N-terminal domain | 0 | DIRECT |
| A20-like zinc finger | 0 | DIRECT |
| alpha-ketoacid dehydrogenase kinase, C-terminal domain | 0 | DIRECT |
| Hsp90 middle domain | 0 | DIRECT |
| Troponin I | 0 | DIRECT |
| Mitochondrial cytochrome c oxidase subunit VIIa | 0 | DIRECT |
| Malic enzyme N-domain | 0 | DIRECT |
| DJ-1/PfpI | 0 | DIRECT |
| Noncollagenous (NC1) domain of collagen IV | 0 | DIRECT |
| Troponin T | 0 | DIRECT |
| DnaJ/Hsp40 cysteine-rich domain | 0 | DIRECT |
| 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain | 0 | DIRECT |
| GDI-like N domain | 0 | DIRECT |
| HLH, helix-loop-helix DNA-binding domain | 0.000004491 | DIRECT |
| Canonical RBD | 0.00001159 | DIRECT |
| Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains | 0.0000903 | DIRECT |
| Medium chain acyl-CoA dehydrogenase-like, C-terminal domain | 0.0000903 | DIRECT |
| Proteasome subunits | 0.0001108 | DIRECT |
| Hairy Orange domain | 0.0006149 | DIRECT |
| Group II chaperonin (CCT, TRIC), apical domain | 0.001583 | INHERITED FROM: muscular system || muscle || skeletal muscle |
| Group II chaperonin (CCT, TRIC), ATPase domain | 0.002712 | INHERITED FROM: muscular system || muscle || skeletal muscle |
| Glutathione peroxidase-like | 0.003543 | INHERITED FROM: bone element || splanchnocranium || skeletal tissue || bone tissue || cranium || presomitic mesoderm |
| Actin/HSP70 | 0.003875 | INHERITED FROM: cranial muscle || muscular system || head somite || muscle || myocyte || skeletal muscle || trunk somite || jaw muscle |
| Homeodomain | 0.00773 | INHERITED FROM: lower jaw || olfactory region || caudal presomitic mesoderm || cranium || cartilage element || rostral presomitic mesoderm || neurocranium || cartilage tissue || hindlimb digit || mandibular arch || skeletal subdivision || presomitic mesoderm |
| Fibroblast growth factors (FGF) | 0.007731 | INHERITED FROM: splanchnocranium || cranium || presomitic mesoderm |
| Parvalbumin | 0.009958 | INHERITED FROM: cranial muscle || somite |
| Thiolase-related | 0.01875 | INHERITED FROM: muscle || skeletal muscle |
| Translational machinery components | 0.01875 | INHERITED FROM: muscle || skeletal muscle |
| Paired domain | 0.01875 | INHERITED FROM: cranium |
| LIM domain | 0.02053 | INHERITED FROM: skeletal system |
| T-box | 0.02141 | INHERITED FROM: myocardium |
| LDH N-terminal domain-like | 0.02411 | INHERITED FROM: skeleton || bone element || skeletal tissue || bone tissue || skeletal element |
| Linker histone H1/H5 | 0.02411 | INHERITED FROM: skeleton || bone element || skeletal tissue || bone tissue || skeletal element |
| Lactate & malate dehydrogenases, C-terminal domain | 0.02411 | INHERITED FROM: skeleton || bone element || skeletal tissue || bone tissue || skeletal element |
| Frizzled cysteine-rich domain | 0.03545 | INHERITED FROM: somite || presomitic mesoderm |
| Spectrin repeat | 0.03545 | INHERITED FROM: auditory ossicle |
| Myosin rod fragments | 0.03917 | INHERITED FROM: musculature of face |
| Heat shock protein 70kD (HSP70), peptide-binding domain | 0.05558 | INHERITED FROM: skeletal muscle |
| HMG-box | 0.0696 | INHERITED FROM: splanchnocranium |
| Tropomyosin | 0.08136 | INHERITED FROM: myocyte || myotome || dermomyotome || myocardium |
| 14-3-3 protein | 0.08196 | INHERITED FROM: somite |
| L domain | 0.08196 | INHERITED FROM: somite |
| Hypoxia-inducible factor Hif2a, C-terminal domain | 0.1001 | INHERITED FROM: epaxial muscle || somite |
| Forkhead DNA-binding domain | 0.1704 | INHERITED FROM: olfactory region || cranium || myocardium || presomitic mesoderm |
| 28-residue LRR | 0.2675 | INHERITED FROM: epaxial muscle |
| Extracellular domain of cell surface receptors | 0.2854 | INHERITED FROM: splanchnocranium || cranium |
| Erythroid transcription factor GATA-1 | 0.3669 | INHERITED FROM: myocardium |
| Motor proteins | 0.678 | INHERITED FROM: musculature of face |
| SCOP term | FDR (all) | Annotation (direct or inherited) |
| ADP-ribosylglycohydrolase | 0 | Direct |
| RUNT domain | 0 | Direct |
| gamma-adaptin C-terminal appendage domain-like | 0 | Direct |
| Group II chaperonin (CCT, TRIC), intermediate domain | 0 | Direct |
| F1F0 ATP synthase subunit C | 0 | Direct |
| SRF-like | 0 | Direct |
| GABARAP-like | 0 | Direct |
| alpha-ketoacid dehydrogenase kinase, N-terminal domain | 0 | Direct |
| Branched-chain alpha-keto acid dehydrogenase PP module | 0 | Direct |
| Noggin | 0 | Direct |
| HSP90 C-terminal domain | 0 | Direct |
| 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain | 0 | Direct |
| Heat shock protein 90, HSP90, N-terminal domain | 0 | Direct |
| A20-like zinc finger | 0 | Direct |
| alpha-ketoacid dehydrogenase kinase, C-terminal domain | 0 | Direct |
| Hsp90 middle domain | 0 | Direct |
| Troponin I | 0 | Direct |
| Mitochondrial cytochrome c oxidase subunit VIIa | 0 | Direct |
| Malic enzyme N-domain | 0 | Direct |
| DJ-1/PfpI | 0 | Direct |
| Noncollagenous (NC1) domain of collagen IV | 0 | Direct |
| Troponin T | 0 | Direct |
| DnaJ/Hsp40 cysteine-rich domain | 0 | Direct |
| 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain | 0 | Direct |
| GDI-like N domain | 0 | Direct |
| HLH, helix-loop-helix DNA-binding domain | 0.000004491 | Direct |
| Canonical RBD | 0.00001159 | Direct |
| Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains | 0.0000903 | Direct |
| Medium chain acyl-CoA dehydrogenase-like, C-terminal domain | 0.0000903 | Direct |
| Proteasome subunits | 0.0001108 | Direct |
| Hairy Orange domain | 0.0006149 | Direct |
| Group II chaperonin (CCT, TRIC), apical domain | 0.001583 | Inherited |
| Group II chaperonin (CCT, TRIC), ATPase domain | 0.002712 | Inherited |
| Glutathione peroxidase-like | 0.003543 | Inherited |
| Actin/HSP70 | 0.003875 | Inherited |
| Homeodomain | 0.00773 | Inherited |
| Fibroblast growth factors (FGF) | 0.007731 | Inherited |
| Parvalbumin | 0.009958 | Inherited |
| Thiolase-related | 0.01875 | Inherited |
| Translational machinery components | 0.01875 | Inherited |
| Paired domain | 0.01875 | Inherited |
| LIM domain | 0.02053 | Inherited |
| T-box | 0.02141 | Inherited |
| LDH N-terminal domain-like | 0.02411 | Inherited |
| Linker histone H1/H5 | 0.02411 | Inherited |
| Lactate & malate dehydrogenases, C-terminal domain | 0.02411 | Inherited |
| Frizzled cysteine-rich domain | 0.03545 | Inherited |
| Spectrin repeat | 0.03545 | Inherited |
| Myosin rod fragments | 0.03917 | Inherited |
| Heat shock protein 70kD (HSP70), peptide-binding domain | 0.05558 | Inherited |
| HMG-box | 0.0696 | Inherited |
| Tropomyosin | 0.08136 | Inherited |
| 14-3-3 protein | 0.08196 | Inherited |
| L domain | 0.08196 | Inherited |
| Hypoxia-inducible factor Hif2a, C-terminal domain | 0.1001 | Inherited |
| Forkhead DNA-binding domain | 0.1704 | Inherited |
| 28-residue LRR | 0.2675 | Inherited |
| Extracellular domain of cell surface receptors | 0.2854 | Inherited |
| Erythroid transcription factor GATA-1 | 0.3669 | Inherited |
| Motor proteins | 0.678 | 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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(show details)
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) |
90257,90257
90257 - Myosin rod fragments
90257 - Myosin rod fragments | 0 | DIRECT |
52540,53254
52540 - P-loop containing nucleoside triphosphate hydrolases
53254 - Phosphoglycerate mutase-like | 0 | DIRECT |
46966,47473
46966 - Spectrin repeat
47473 - EF-hand | 0 | DIRECT |
48592,54849
48592 - GroEL equatorial domain-like
54849 - GroEL-intermediate domain like | 0 | DIRECT |
69012,55874
69012 - alpha-ketoacid dehydrogenase kinase, N-terminal domain
55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 0 | DIRECT |
48371,46785
48371 - ARM repeat
46785 - "Winged helix" DNA-binding domain | 0 | DIRECT |
54631,54631
54631 - CBS-domain pair
54631 - CBS-domain pair | 0 | DIRECT |
57938,49493
57938 - DnaJ/Hsp40 cysteine-rich domain
49493 - HSP40/DnaJ peptide-binding domain | 0 | DIRECT |
46565,57938
46565 - Chaperone J-domain
57938 - DnaJ/Hsp40 cysteine-rich domain | 0 | DIRECT |
54928,54928
54928 - RNA-binding domain, RBD
54928 - RNA-binding domain, RBD | 0.0001063 | DIRECT |
47459,158457
47459 - HLH, helix-loop-helix DNA-binding domain
158457 - Orange domain-like | 0.0004127 | DIRECT |
54849,52029
54849 - GroEL-intermediate domain like
52029 - GroEL apical domain-like | 0.001114 | INHERITED FROM: skeletal muscle || muscle || muscular system |
56645,47203
56645 - Acyl-CoA dehydrogenase NM domain-like
47203 - Acyl-CoA dehydrogenase C-terminal domain-like | 0.003021 | INHERITED FROM: skeletal muscle || muscle || muscular system |
46966,46966
46966 - Spectrin repeat
46966 - Spectrin repeat | 0.006729 | INHERITED FROM: bone element || skeletal system || auditory ossicle || skeleton |
57716,57716
57716 - Glucocorticoid receptor-like (DNA-binding domain)
57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.008383 | INHERITED FROM: cranium || skeletal system |
53067,53067
53067 - Actin-like ATPase domain
53067 - Actin-like ATPase domain | 0.01064 | INHERITED FROM: skeletal muscle || myocyte || cranial muscle || jaw muscle || muscle || head somite |
47095,47095
47095 - HMG-box
47095 - HMG-box | 0.01961 | INHERITED FROM: skeletal element || bone tissue || skeletal tissue || bone element |
51735,56327
51735 - NAD(P)-binding Rossmann-fold domains
56327 - LDH C-terminal domain-like | 0.01961 | INHERITED FROM: skeletal element || skeletal muscle || bone tissue || skeletal tissue || bone element || skeleton |
100920,100934
100920 - Heat shock protein 70kD (HSP70), peptide-binding domain
100934 - Heat shock protein 70kD (HSP70), C-terminal subdomain | 0.03206 | INHERITED FROM: skeletal muscle |
53901,53901
53901 - Thiolase-like
53901 - Thiolase-like | 0.03911 | INHERITED FROM: skeletal muscle |
53067,100920
53067 - Actin-like ATPase domain
100920 - Heat shock protein 70kD (HSP70), peptide-binding domain | 0.04263 | INHERITED FROM: skeletal muscle |
48726,56436
48726 - Immunoglobulin
56436 - C-type lectin-like | 0.04839 | INHERITED FROM: cranium |
52058,57184
52058 - L domain-like
57184 - Growth factor receptor domain | 0.06861 | INHERITED FROM: somite |
57184,52058
57184 - Growth factor receptor domain
52058 - L domain-like | 0.06861 | INHERITED FROM: somite |
57184,57184
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain | 0.07691 | INHERITED FROM: presomitic mesoderm |
47459,55785
47459 - HLH, helix-loop-helix DNA-binding domain
55785 - PYP-like sensor domain (PAS domain) | 0.1875 | INHERITED FROM: somite |
55785,55785
55785 - PYP-like sensor domain (PAS domain)
55785 - PYP-like sensor domain (PAS domain) | 0.221 | INHERITED FROM: somite |
57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 1 | INHERITED FROM: otic region |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
90257,90257
90257 - Myosin rod fragments
90257 - Myosin rod fragments | 0 | Direct |
52540,53254
52540 - P-loop containing nucleoside triphosphate hydrolases
53254 - Phosphoglycerate mutase-like | 0 | Direct |
46966,47473
46966 - Spectrin repeat
47473 - EF-hand | 0 | Direct |
48592,54849
48592 - GroEL equatorial domain-like
54849 - GroEL-intermediate domain like | 0 | Direct |
69012,55874
69012 - alpha-ketoacid dehydrogenase kinase, N-terminal domain
55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 0 | Direct |
48371,46785
48371 - ARM repeat
46785 - "Winged helix" DNA-binding domain | 0 | Direct |
54631,54631
54631 - CBS-domain pair
54631 - CBS-domain pair | 0 | Direct |
57938,49493
57938 - DnaJ/Hsp40 cysteine-rich domain
49493 - HSP40/DnaJ peptide-binding domain | 0 | Direct |
46565,57938
46565 - Chaperone J-domain
57938 - DnaJ/Hsp40 cysteine-rich domain | 0 | Direct |
54928,54928
54928 - RNA-binding domain, RBD
54928 - RNA-binding domain, RBD | 0.0001063 | Direct |
47459,158457
47459 - HLH, helix-loop-helix DNA-binding domain
158457 - Orange domain-like | 0.0004127 | Direct |
54849,52029
54849 - GroEL-intermediate domain like
52029 - GroEL apical domain-like | 0.001114 | Inherited |
56645,47203
56645 - Acyl-CoA dehydrogenase NM domain-like
47203 - Acyl-CoA dehydrogenase C-terminal domain-like | 0.003021 | Inherited |
46966,46966
46966 - Spectrin repeat
46966 - Spectrin repeat | 0.006729 | Inherited |
57716,57716
57716 - Glucocorticoid receptor-like (DNA-binding domain)
57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.008383 | Inherited |
53067,53067
53067 - Actin-like ATPase domain
53067 - Actin-like ATPase domain | 0.01064 | Inherited |
47095,47095
47095 - HMG-box
47095 - HMG-box | 0.01961 | Inherited |
51735,56327
51735 - NAD(P)-binding Rossmann-fold domains
56327 - LDH C-terminal domain-like | 0.01961 | Inherited |
100920,100934
100920 - Heat shock protein 70kD (HSP70), peptide-binding domain
100934 - Heat shock protein 70kD (HSP70), C-terminal subdomain | 0.03206 | Inherited |
53901,53901
53901 - Thiolase-like
53901 - Thiolase-like | 0.03911 | Inherited |
53067,100920
53067 - Actin-like ATPase domain
100920 - Heat shock protein 70kD (HSP70), peptide-binding domain | 0.04263 | Inherited |
48726,56436
48726 - Immunoglobulin
56436 - C-type lectin-like | 0.04839 | Inherited |
52058,57184
52058 - L domain-like
57184 - Growth factor receptor domain | 0.06861 | Inherited |
57184,52058
57184 - Growth factor receptor domain
52058 - L domain-like | 0.06861 | Inherited |
57184,57184
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain | 0.07691 | Inherited |
47459,55785
47459 - HLH, helix-loop-helix DNA-binding domain
55785 - PYP-like sensor domain (PAS domain) | 0.1875 | Inherited |
55785,55785
55785 - PYP-like sensor domain (PAS domain)
55785 - PYP-like sensor domain (PAS domain) | 0.221 | Inherited |
57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 1 | 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) |
57938,49493,49493
57938 - DnaJ/Hsp40 cysteine-rich domain
49493 - HSP40/DnaJ peptide-binding domain
49493 - HSP40/DnaJ peptide-binding domain | 0 | DIRECT |
90257,90257,90257
90257 - Myosin rod fragments
90257 - Myosin rod fragments
90257 - Myosin rod fragments | 0 | DIRECT |
57184,52058,57184
57184 - Growth factor receptor domain
52058 - L domain-like
57184 - Growth factor receptor domain | 0 | DIRECT |
48592,54849,52029
48592 - GroEL equatorial domain-like
54849 - GroEL-intermediate domain like
52029 - GroEL apical domain-like | 0 | DIRECT |
51338,51556,51338
51338 - Composite domain of metallo-dependent hydrolases
51556 - Metallo-dependent hydrolases
51338 - Composite domain of metallo-dependent hydrolases | 0 | DIRECT |
46565,57938,49493
46565 - Chaperone J-domain
57938 - DnaJ/Hsp40 cysteine-rich domain
49493 - HSP40/DnaJ peptide-binding domain | 0 | DIRECT |
46966,46966,47473
46966 - Spectrin repeat
46966 - Spectrin repeat
47473 - EF-hand | 0 | DIRECT |
46966,46966,46966
46966 - Spectrin repeat
46966 - Spectrin repeat
46966 - Spectrin repeat | 0.001766 | INHERITED FROM: bone element || skeletal system || auditory ossicle || skeleton |
57716,57716,57716
57716 - Glucocorticoid receptor-like (DNA-binding domain)
57716 - Glucocorticoid receptor-like (DNA-binding domain)
57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.01501 | INHERITED FROM: skeletal system |
57196,57184,57184
57196 - EGF/Laminin
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain | 0.01961 | INHERITED FROM: presomitic mesoderm |
53067,100920,100934
53067 - Actin-like ATPase domain
100920 - Heat shock protein 70kD (HSP70), peptide-binding domain
100934 - Heat shock protein 70kD (HSP70), C-terminal subdomain | 0.03206 | INHERITED FROM: skeletal muscle |
53067,53067,100920
53067 - Actin-like ATPase domain
53067 - Actin-like ATPase domain
100920 - Heat shock protein 70kD (HSP70), peptide-binding domain | 0.04263 | INHERITED FROM: skeletal muscle |
48726,56436,56436
48726 - Immunoglobulin
56436 - C-type lectin-like
56436 - C-type lectin-like | 0.04839 | INHERITED FROM: cranium |
48371,48371,48371
48371 - ARM repeat
48371 - ARM repeat
48371 - ARM repeat | 0.05944 | INHERITED FROM: trunk somite || tail somite |
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) | 0.142 | INHERITED FROM: somite |
57196,57196,57184
57196 - EGF/Laminin
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.221 | INHERITED FROM: presomitic mesoderm |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57938,49493,49493
57938 - DnaJ/Hsp40 cysteine-rich domain
49493 - HSP40/DnaJ peptide-binding domain
49493 - HSP40/DnaJ peptide-binding domain | 0 | Direct |
90257,90257,90257
90257 - Myosin rod fragments
90257 - Myosin rod fragments
90257 - Myosin rod fragments | 0 | Direct |
57184,52058,57184
57184 - Growth factor receptor domain
52058 - L domain-like
57184 - Growth factor receptor domain | 0 | Direct |
48592,54849,52029
48592 - GroEL equatorial domain-like
54849 - GroEL-intermediate domain like
52029 - GroEL apical domain-like | 0 | Direct |
51338,51556,51338
51338 - Composite domain of metallo-dependent hydrolases
51556 - Metallo-dependent hydrolases
51338 - Composite domain of metallo-dependent hydrolases | 0 | Direct |
46565,57938,49493
46565 - Chaperone J-domain
57938 - DnaJ/Hsp40 cysteine-rich domain
49493 - HSP40/DnaJ peptide-binding domain | 0 | Direct |
46966,46966,47473
46966 - Spectrin repeat
46966 - Spectrin repeat
47473 - EF-hand | 0 | Direct |
46966,46966,46966
46966 - Spectrin repeat
46966 - Spectrin repeat
46966 - Spectrin repeat | 0.001766 | Inherited |
57716,57716,57716
57716 - Glucocorticoid receptor-like (DNA-binding domain)
57716 - Glucocorticoid receptor-like (DNA-binding domain)
57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.01501 | Inherited |
57196,57184,57184
57196 - EGF/Laminin
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain | 0.01961 | Inherited |
53067,100920,100934
53067 - Actin-like ATPase domain
100920 - Heat shock protein 70kD (HSP70), peptide-binding domain
100934 - Heat shock protein 70kD (HSP70), C-terminal subdomain | 0.03206 | Inherited |
53067,53067,100920
53067 - Actin-like ATPase domain
53067 - Actin-like ATPase domain
100920 - Heat shock protein 70kD (HSP70), peptide-binding domain | 0.04263 | Inherited |
48726,56436,56436
48726 - Immunoglobulin
56436 - C-type lectin-like
56436 - C-type lectin-like | 0.04839 | Inherited |
48371,48371,48371
48371 - ARM repeat
48371 - ARM repeat
48371 - ARM repeat | 0.05944 | Inherited |
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) | 0.142 | Inherited |
57196,57196,57184
57196 - EGF/Laminin
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.221 | 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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