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Xenopus ANatomical entity (XAN): muscular 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)
Superfamily domains annotated to this XA term (Not in SDXA)
Highlighted in gray are those with FDR_all>0.001
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Family(show details)
Family domains annotated to this XA term (Not in SDXA)
Highlighted in gray are those with FDR_all>0.001
SCOP term | FDR (all) | Annotation (direct or inherited) |
Group II chaperonin (CCT, TRIC), intermediate domain | 0 | DIRECT |
SRF-like | 0 | DIRECT |
GABARAP-like | 0 | DIRECT |
Branched-chain alpha-keto acid dehydrogenase PP module | 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 |
Hsp90 middle domain | 0 | DIRECT |
Mitochondrial cytochrome c oxidase subunit VIIa | 0 | DIRECT |
Malic enzyme N-domain | 0 | DIRECT |
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain | 0 | DIRECT |
GDI-like N domain | 0 | DIRECT |
Canonical RBD | 0.0000004608 | DIRECT |
HLH, helix-loop-helix DNA-binding domain | 0.0000006125 | DIRECT |
Proteasome subunits | 0.000001812 | DIRECT |
Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains | 0.000002952 | DIRECT |
Medium chain acyl-CoA dehydrogenase-like, C-terminal domain | 0.000002952 | DIRECT |
Hairy Orange domain | 0.00003817 | DIRECT |
Actin/HSP70 | 0.00004581 | DIRECT |
Group II chaperonin (CCT, TRIC), apical domain | 0.0001363 | DIRECT |
Group II chaperonin (CCT, TRIC), ATPase domain | 0.0003236 | DIRECT |
Parvalbumin | 0.001694 | INHERITED FROM: cranial muscle || somite |
Glutathione peroxidase-like | 0.002002 | INHERITED FROM: presomitic mesoderm |
Thiolase-related | 0.002739 | INHERITED FROM: skeletal muscle || muscle |
Translational machinery components | 0.002739 | INHERITED FROM: skeletal muscle || muscle |
Frizzled cysteine-rich domain | 0.007917 | INHERITED FROM: presomitic mesoderm || somite |
Heat shock protein 70kD (HSP70), peptide-binding domain | 0.008141 | INHERITED FROM: skeletal muscle |
Fibroblast growth factors (FGF) | 0.01444 | INHERITED FROM: presomitic mesoderm |
Hypoxia-inducible factor Hif2a, C-terminal domain | 0.01722 | INHERITED FROM: epaxial muscle || somite |
Tropomyosin | 0.01991 | INHERITED FROM: myocardium || myotome || dermomyotome || myocyte |
14-3-3 protein | 0.02315 | INHERITED FROM: somite |
L domain | 0.02315 | INHERITED FROM: somite |
T-box | 0.03786 | INHERITED FROM: myocardium |
Myosin rod fragments | 0.04485 | INHERITED FROM: musculature of face |
28-residue LRR | 0.07698 | INHERITED FROM: epaxial muscle |
Forkhead DNA-binding domain | 0.1565 | INHERITED FROM: myocardium || presomitic mesoderm |
Erythroid transcription factor GATA-1 | 0.1754 | INHERITED FROM: myocardium |
Homeodomain | 0.3571 | INHERITED FROM: caudal presomitic mesoderm || rostral presomitic mesoderm || presomitic mesoderm |
Motor proteins | 0.5761 | INHERITED FROM: musculature of face |
SCOP term | FDR (all) | Annotation (direct or inherited) |
Group II chaperonin (CCT, TRIC), intermediate domain | 0 | Direct |
SRF-like | 0 | Direct |
GABARAP-like | 0 | Direct |
Branched-chain alpha-keto acid dehydrogenase PP module | 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 |
Hsp90 middle domain | 0 | Direct |
Mitochondrial cytochrome c oxidase subunit VIIa | 0 | Direct |
Malic enzyme N-domain | 0 | Direct |
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain | 0 | Direct |
GDI-like N domain | 0 | Direct |
Canonical RBD | 0.0000004608 | Direct |
HLH, helix-loop-helix DNA-binding domain | 0.0000006125 | Direct |
Proteasome subunits | 0.000001812 | Direct |
Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains | 0.000002952 | Direct |
Medium chain acyl-CoA dehydrogenase-like, C-terminal domain | 0.000002952 | Direct |
Hairy Orange domain | 0.00003817 | Direct |
Actin/HSP70 | 0.00004581 | Direct |
Group II chaperonin (CCT, TRIC), apical domain | 0.0001363 | Direct |
Group II chaperonin (CCT, TRIC), ATPase domain | 0.0003236 | Direct |
Parvalbumin | 0.001694 | Inherited |
Glutathione peroxidase-like | 0.002002 | Inherited |
Thiolase-related | 0.002739 | Inherited |
Translational machinery components | 0.002739 | Inherited |
Frizzled cysteine-rich domain | 0.007917 | Inherited |
Heat shock protein 70kD (HSP70), peptide-binding domain | 0.008141 | Inherited |
Fibroblast growth factors (FGF) | 0.01444 | Inherited |
Hypoxia-inducible factor Hif2a, C-terminal domain | 0.01722 | Inherited |
Tropomyosin | 0.01991 | Inherited |
14-3-3 protein | 0.02315 | Inherited |
L domain | 0.02315 | Inherited |
T-box | 0.03786 | Inherited |
Myosin rod fragments | 0.04485 | Inherited |
28-residue LRR | 0.07698 | Inherited |
Forkhead DNA-binding domain | 0.1565 | Inherited |
Erythroid transcription factor GATA-1 | 0.1754 | Inherited |
Homeodomain | 0.3571 | Inherited |
Motor proteins | 0.5761 | Inherited |
Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term
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Trees by TreeVector
A presence/absence matrix is generated using protein domain
architecture data for all genomes in SUPERFAMILY. The PAUP
software is used to produce a single, large tree topology using
heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as
if individual trees had been produced. However, this data is extracted from the single
large tree. This produces a higher quality topology than if the trees had been produced
on their own, and allows the trees to be displayed instantly.
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Supra-domain (including individual superfamily)
(show details)
Supra-domains annotated to this XA term (Not in SPXA)
Highlighted in gray are those with FDR>0.001
(show details)
Supra-domains annotated to this XA term (Not in SPXA)
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 |
48592,54849 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like | 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 |
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like | 0.00002565 | DIRECT |
54928,54928 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD | 0.00004083 | DIRECT |
54849,52029 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like | 0.00009619 | DIRECT |
56645,47203 56645 - Acyl-CoA dehydrogenase NM domain-like 47203 - Acyl-CoA dehydrogenase C-terminal domain-like | 0.0001496 | DIRECT |
53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain | 0.001502 | INHERITED FROM: head somite || cranial muscle || jaw muscle || skeletal muscle || muscle || myocyte |
51735,56327 51735 - NAD(P)-binding Rossmann-fold domains 56327 - LDH C-terminal domain-like | 0.004642 | INHERITED FROM: skeletal muscle |
53067,100920 53067 - Actin-like ATPase domain 100920 - Heat shock protein 70kD (HSP70), peptide-binding domain | 0.006084 | INHERITED FROM: skeletal muscle |
100920,100934 100920 - Heat shock protein 70kD (HSP70), peptide-binding domain 100934 - Heat shock protein 70kD (HSP70), C-terminal subdomain | 0.006443 | INHERITED FROM: skeletal muscle |
53901,53901 53901 - Thiolase-like 53901 - Thiolase-like | 0.006633 | INHERITED FROM: skeletal muscle |
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain | 0.01915 | INHERITED FROM: somite |
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like | 0.01915 | INHERITED FROM: somite |
47459,55785 47459 - HLH, helix-loop-helix DNA-binding domain 55785 - PYP-like sensor domain (PAS domain) | 0.04114 | INHERITED FROM: somite |
55785,55785 55785 - PYP-like sensor domain (PAS domain) 55785 - PYP-like sensor domain (PAS domain) | 0.06803 | INHERITED FROM: somite |
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.1187 | INHERITED FROM: presomitic mesoderm |
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 |
48592,54849 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like | 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 |
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like | 0.00002565 | Direct |
54928,54928 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD | 0.00004083 | Direct |
54849,52029 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like | 0.00009619 | Direct |
56645,47203 56645 - Acyl-CoA dehydrogenase NM domain-like 47203 - Acyl-CoA dehydrogenase C-terminal domain-like | 0.0001496 | Direct |
53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain | 0.001502 | Inherited |
51735,56327 51735 - NAD(P)-binding Rossmann-fold domains 56327 - LDH C-terminal domain-like | 0.004642 | Inherited |
53067,100920 53067 - Actin-like ATPase domain 100920 - Heat shock protein 70kD (HSP70), peptide-binding domain | 0.006084 | Inherited |
100920,100934 100920 - Heat shock protein 70kD (HSP70), peptide-binding domain 100934 - Heat shock protein 70kD (HSP70), C-terminal subdomain | 0.006443 | Inherited |
53901,53901 53901 - Thiolase-like 53901 - Thiolase-like | 0.006633 | Inherited |
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain | 0.01915 | Inherited |
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like | 0.01915 | Inherited |
47459,55785 47459 - HLH, helix-loop-helix DNA-binding domain 55785 - PYP-like sensor domain (PAS domain) | 0.04114 | Inherited |
55785,55785 55785 - PYP-like sensor domain (PAS domain) 55785 - PYP-like sensor domain (PAS domain) | 0.06803 | Inherited |
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.1187 | Inherited |
(show details)
Supra-domains annotated to this XA term (Not in SPXA)
Highlighted in gray are those with FDR>0.001
Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
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 |
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.004642 | INHERITED FROM: presomitic mesoderm |
53067,53067,100920 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain 100920 - Heat shock protein 70kD (HSP70), peptide-binding domain | 0.006084 | INHERITED FROM: skeletal muscle |
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 | 0.006443 | INHERITED FROM: skeletal muscle |
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) | 0.03845 | INHERITED FROM: somite |
48371,48371,48371 48371 - ARM repeat 48371 - ARM repeat 48371 - ARM repeat | 0.07077 | INHERITED FROM: tail somite || trunk somite |
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain | 0.2003 | INHERITED FROM: presomitic mesoderm |
Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
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 |
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.004642 | Inherited |
53067,53067,100920 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain 100920 - Heat shock protein 70kD (HSP70), peptide-binding domain | 0.006084 | 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 | 0.006443 | 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) | 0.03845 | Inherited |
48371,48371,48371 48371 - ARM repeat 48371 - ARM repeat 48371 - ARM repeat | 0.07077 | Inherited |
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain | 0.2003 | 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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