Xenopus ANatomical entity (XAN): tail

(show info)

Phenotype Ontology
Like Gene Ontology (GO), phenotypy ontology classifies and organizes gene-mutant/null phenotypic information from the very general at the top to more specific terms in the directed acyclic graph (DAG) by viewing an individual term as a node and its relations to parental terms (allowing for multiple parents) as directed edges. To navigate this hierarchy, we display all parental phenotypic terms to the current phenotypic term of interest ordered by their shortest distances to the current term. Also, only direct children phenotypic terms of the current phenotypic term are listed. Phenotype ontologies we have incorporated are as follows:

Disease Ontology (DO) Ontology (DO)
DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI thesaurus, SNOMED and OMIM.
Human Phenotype (HP) Ontology (HP)
HP captures phenotypic abnormalities that are described in OMIM, along with the corresponding disease-causing genes. It includes three complementary biological concepts: Mode_of_Inheritance (MI), ONset_and_clinical_course (ON), and Phenotypic_Abnormality (PA).
Mouse Phenotype (MP) Ontology (MP)
MP describes phenotypes of the mouse after a specific gene is genetically disrupted. Using it, Mouse Genome Informatics (MGI) provides high-coverate gene-level phenotypes for the mouse.
Worm Phenotype (WP) Ontology (WP)
WP classifies and organizes phenotype descriptions for C. elegans and other nematodes. Using it, WormBase provides primary resource for phenotype annotations for C. elegans.
Yeast Phenotype (YP) Ontology (YP)
Based on YP which is the major contributor to the Ascomycete phenotype ontology, Saccharomyces Genome Database (SGD) provides single mutant phenotypes for every gene in the yeast genome.
Fly Phenotype (FP) Ontology (FP)
FP refers to FlyBase controlled vocabulary. Specifically, a structured controlled vocabulary is used for the annotation of alleles (for their mutagen etc) in FlyBase.
Fly Anatomy (FA) Ontology (FA)
FA is a structured controlled vocabulary of the anatomy of Drosophila melanogaster, used for the description of phenotypes and where a gene is expressed.
Zebrafish Anatomy (ZA) Ontology (ZA)
ZA displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
Xenopus Anatomy (XA) Ontology (XA)
XA represents the lineage of tissues and the timing of development for frogs (Xenopus laevis and Xenopus tropicalis). It is used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes.
Arabidopsis Plant Ontology (AP) Ontology (AP)
As a major contributor to Plant Ontology which describes plant anatomical and morphological structures (AN) and growth and developmental stages (DE), the Arabidopsis Information Resource (TAIR) provides arabidopsis plant ontology annotations for the model higher plant Arabidopsis thaliana.
Enzyme Commission (EC) Ontology (EC)
Each enzyme is allocated a four-digit EC number, the first three digits of which define the reaction catalysed and the fourth of which is a unique identifier (serial number). Each enzyme is also assigned a systematic name that uniquely defines the reaction catalysed.
DrugBank ATC (DB) Ontology (DB)
In the Anatomical Therapeutic Chemical (ATC) classification system, drugs are classified in groups at five different levels according to the organ or system (1st level, anatomical main group) on which they act and their therapeutic (2nd level, therapeutic subgroup), pharmacological (3rd level, pharmacological subgroup) and chemical properties (4th level, chemical subgroup; 5th level, chemical substance). Only drugs in DrugBank are considered.
UniProtKB KeyWords (KW) Ontology (KW)
Keywords in UniProtKB are controlled vocabulary, providing a summary of the entry content and are used to index UniProtKB/Swiss-Prot entries based on 10 categories (the category "Technical term" being excluded here). Each keyword is attributed manually to UniProtKB/Swiss-Prot entries and automatically to UniProtKB/TrEMBL entries (according to specific annotation rules).
UniProtKB UniPathway (UP) Ontology (UP)
UP is a fully manually curated resource for the representation and annotation of metabolic pathways, being used as controlled vocabulary for pathway annotation in UniProtKB.

Structural Domain Phenotype Ontology and its Annotations
Structural Classification of Proteins (SCOP) classifies evolutionary-related domains into Superfamily level and Family level. Using the phenotype ontologies above, we have generated the domain-centric phenotype annotations, and further identified those phenotype terms which are the most informative to annotate SCOP domains. Promisingly, domain-centric phenotypic annotations can serve as an alternative starting point to explore genotype-phenotype relationships. We provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

Structural Domain Disease Ontology (DO) Ontology (SDDO) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DO.txt, and the corresponding ontology:SDDO.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Human Phenotype (HP) Ontology (SDHP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2HP.txt, and the corresponding ontology:SDHP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Mouse Phenotype (MP) Ontology (SDMP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2MP.txt, and the corresponding ontology:SDMP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Worm Phenotype (WP) Ontology (SDWP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2WP.txt, and the corresponding ontology:SDWP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Yeast Phenotype (YP) Ontology (SDYP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2YP.txt, and the corresponding ontology:SDYP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Fly Phenotype (FP) Ontology (SDFP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FP.txt, and the corresponding ontology:SDFP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Fly Anatomy (FA) Ontology (SDFA) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FA.txt, and the corresponding ontology:SDFA.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Zebrafish Anatomy (ZA) Ontology (SDZA) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2ZA.txt, and the corresponding ontology:SDZA.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Xenopus Anatomy (XA) Ontology (SDXA) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2XA.txt, and the corresponding ontology:SDXA.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Arabidopsis Plant Ontology (AP) Ontology (SDAP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2AP.txt, and the corresponding ontology:SDAP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Enzyme Commission (EC) Ontology (SDEC) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2EC.txt, and the corresponding ontology:SDEC.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain DrugBank ATC (DB) Ontology (SDDB) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DB.txt, and the corresponding ontology:SDDB.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain UniProtKB KeyWords (KW) Ontology (SDKW) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2KW.txt, and the corresponding ontology:SDKW.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain UniProtKB UniPathway (UP) Ontology (SDUP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2UP.txt, and the corresponding ontology:SDUP.txt) and mysql tables (Domain2PO.sql.gz).

Supra-domain Phenotype Ontology and its Annotations
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are interested in domain combinations. Also, we provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

Supra-domain Domain Disease Ontology (DO) Ontology (SPDO) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DO.txt, and the corresponding ontology:SPDO.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Human Phenotype (HP) Ontology (SPHO) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2HP.txt, and the corresponding ontology:SPHO.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Mouse Phenotype (MP) Ontology (SPMP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2MP.txt, and the corresponding ontology:SPMP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Worm Phenotype (WP) Ontology (SPWP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2WP.txt, and the corresponding ontology:SPWP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Yeast Phenotype (YP) Ontology (SPYP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2YP.txt, and the corresponding ontology:SPYP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Fly Phenotype (FP) Ontology (SPFP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FP.txt, and the corresponding ontology:SPFP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Fly Anatomy (FA) Ontology (SPFA) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FA.txt, and the corresponding ontology:SPFA.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Zebrafish Anatomy (ZA) Ontology (SPZA) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2ZA.txt, and the corresponding ontology:SPZA.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Xenopus Anatomy (XA) Ontology (SPXA) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2XA.txt, and the corresponding ontology:SPXA.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Arabidopsis Plant Ontology (AP) Ontology (SPAP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2AP.txt, and the corresponding ontology:SPAP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Enzyme Commission (EC) Ontology (SPEC) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2EC.txt, and the corresponding ontology:SPEC.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain DrugBank ATC (DB) Ontology (SPDB) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DB.txt, and the corresponding ontology:SPDB.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain UniProtKB KeyWords (KW) Ontology (SPKW) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2KW.txt, and the corresponding ontology:SPKW.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain UniProtKB UniPathway (UP) Ontology (SPUP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2UP.txt, and the corresponding ontology:SPUP.txt) and mysql tables (SP2PO.sql.gz).

Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]

Root: XA Hierarchy (Xenopus anatomy and development from Xenbase frog anatomy ontology)

Shortest distance to current term (+ for parents, - for children) XA term [XA ID] <#Children> (#SF|#FA) #Supra-domain
(Single|Duplex|Triple)

+ + + 3: Xenopus anatomical entity [XAO:0000000] <9>

+ + + 3: anatomical structure [XAO:0003000] <11> (577|733) (577|400|163)

+ + + 3: whole organism [XAO:0003004] <12> (461|598) (465|335|145)

+ + 2: multicellular anatomical structure [XAO:0005002] <4> (436|565) (440|325|142)

+ + 2: anatomical region [XAO:0003186] <51> (370|484) (374|284|123)

+ 1: tail region [XAO:0000087] <2> (30|42) (30|16|8)

+ 1: organism subdivision [XAO:0003013] <11> (375|498) (381|292|126)

0: tail [XAO:0003026] <6> (23|34) (23|12|8)

- 1: tail somite [XAO:0003143] <5> (0|0) (0|0|1)

- 1: tail fin [XAO:0004062] <4> (7|6) (7|1|2)

- 1: tail vasculature [XAO:0004151] <4> (0|0) (0|0|0)

- 1: dorsal tail [XAO:0005264] (0|0) (0|0|0)

- 1: fin crest [XAO:0004229] (0|0) (0|0|0)

- 1: posterior tail [XAO:0005261] (0|0) (0|0|0)

Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]

Superfamily

(show details)

SCOP term	FDR (all)	Annotation (direct or inherited)
Aconitase iron-sulfur domain	0	Direct
LDH C-terminal domain-like	0	Direct
LeuD/IlvD-like	0	Direct
Isocitrate/Isopropylmalate dehydrogenase-like	0	Direct
Guanido kinase N-terminal domain	0	Direct
Subunits of heterodimeric actin filament capping protein Capz	0	Direct
Proteasome activator	0	Direct
PLP-binding barrel	0	Direct
Vasodilator-stimulated phosphoprotein, VASP, tetramerisation domain	0	Direct
Alanine racemase C-terminal domain-like	0	Direct
Notch domain	0	Direct
Intermediate filament protein, coiled coil region	0.0002313	Direct
Thioredoxin-like	0.0003762	Direct
Class II aaRS and biotin synthetases	0.0007202	Direct
SOCS box-like	0.0007349	Direct
GroEL equatorial domain-like	0.0009121	Direct
Cytokine	0.002016	Inherited
Orange domain-like	0.009067	Inherited
Growth factor receptor domain	0.3166	Inherited
"Winged helix" DNA-binding domain	0.3501	Inherited
Frizzled cysteine-rich domain	0.3611	Inherited
HLH, helix-loop-helix DNA-binding domain	0.6788	Inherited
Homeodomain-like	0.7514	Inherited

Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]

Family

(show details)

SCOP term	FDR (all)	Annotation (direct or inherited)
LeuD-like	0	Direct
Anticodon-binding domain	0	Direct
UDP-glucose pyrophosphorylase	0	Direct
LDH N-terminal domain-like	0	Direct
Proteasome activator	0	Direct
Guanido kinase catalytic domain	0	Direct
Group II chaperonin (CCT, TRIC), intermediate domain	0	Direct
Notch domain	0	Direct
Aconitase iron-sulfur domain	0	Direct
Guanido kinase N-terminal domain	0	Direct
Vasodilator-stimulated phosphoprotein, VASP, tetramerisation domain	0	Direct
Alanine racemase-like, N-terminal domain	0	Direct
Dimeric isocitrate & isopropylmalate dehydrogenases	0	Direct
Eukaryotic ODC-like	0	Direct
Lactate & malate dehydrogenases, C-terminal domain	0	Direct
A20-like zinc finger	0	Direct
Malic enzyme N-domain	0	Direct
Serine carboxypeptidase-like	0	Direct
Proteasome subunits	0.000004166	Direct
Group II chaperonin (CCT, TRIC), apical domain	0.0002369	Direct
Intermediate filament protein, coiled coil region	0.0003133	Direct
Canonical RBD	0.0003253	Direct
Glutathione peroxidase-like	0.0003819	Direct
Class I aldolase	0.0004972	Direct
Group II chaperonin (CCT, TRIC), ATPase domain	0.0004972	Direct
Actin/HSP70	0.0006269	Direct
SOCS box-like	0.0008349	Direct
Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	0.0008636	Direct
Fibroblast growth factors (FGF)	0.005148	Inherited
Hairy Orange domain	0.0088	Inherited
Frizzled cysteine-rich domain	0.3696	Inherited
HLH, helix-loop-helix DNA-binding domain	0.7213	Inherited
Forkhead DNA-binding domain	0.8738	Inherited
Homeodomain	0.9217	Inherited

Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term

Plot tree as:

Download Newick format tree:

(show help)

Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]

Supra-domain (including individual superfamily)

(show details)

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
LDH C-terminal domain-like	0	Direct
PLP-binding barrel	0	Direct
LeuD/IlvD-like	0	Direct
Subunits of heterodimeric actin filament capping protein Capz	0	Direct
Guanido kinase N-terminal domain	0	Direct
Isocitrate/Isopropylmalate dehydrogenase-like	0	Direct
Proteasome activator	0	Direct
Vasodilator-stimulated phosphoprotein, VASP, tetramerisation domain	0	Direct
Aconitase iron-sulfur domain	0	Direct
Alanine racemase C-terminal domain-like	0	Direct
Notch domain	0	Direct
Intermediate filament protein, coiled coil region	0.0001723	Direct
Thioredoxin-like	0.0002817	Direct
Class II aaRS and biotin synthetases	0.0005442	Direct
SOCS box-like	0.0005555	Direct
GroEL equatorial domain-like	0.0006914	Direct
Cytokine	0.001544	Inherited
Orange domain-like	0.007093	Inherited
Growth factor receptor domain	0.2873	Inherited
"Winged helix" DNA-binding domain	0.3196	Inherited
Frizzled cysteine-rich domain	0.3301	Inherited
HLH, helix-loop-helix DNA-binding domain	0.6434	Inherited
Homeodomain-like	0.7166	Inherited

(show details)

Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
53732,52016 53732 - Aconitase iron-sulfur domain 52016 - LeuD/IlvD-like	0	Direct
51419,50621 51419 - PLP-binding barrel 50621 - Alanine racemase C-terminal domain-like	0	Direct
57581,57184 57581 - TB module/8-cys domain 57184 - Growth factor receptor domain	0	Direct
64593,64593 64593 - Intermediate filament protein, coiled coil region 64593 - Intermediate filament protein, coiled coil region	0	Direct
57196,90193 57196 - EGF/Laminin 90193 - Notch domain	0	Direct
57184,57603 57184 - Growth factor receptor domain 57603 - FnI-like domain	0	Direct
57184,57581 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain	0	Direct
52540,46785 52540 - P-loop containing nucleoside triphosphate hydrolases 46785 - "Winged helix" DNA-binding domain	0	Direct
48034,55931 48034 - Guanido kinase N-terminal domain 55931 - Glutamine synthetase/guanido kinase	0	Direct
51735,56327 51735 - NAD(P)-binding Rossmann-fold domains 56327 - LDH C-terminal domain-like	0	Direct
48592,54849 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like	0.0006083	Direct
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like	0.007093	Inherited

(show details)

Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
57196,57581,57184 57196 - EGF/Laminin 57581 - TB module/8-cys domain 57184 - Growth factor receptor domain	0	Direct
57581,57184,57581 57581 - TB module/8-cys domain 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain	0	Direct
50249,50249,50249 50249 - Nucleic acid-binding proteins 50249 - Nucleic acid-binding proteins 50249 - Nucleic acid-binding proteins	0	Direct
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0	Direct
57184,57581,57196 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain 57196 - EGF/Laminin	0	Direct
48592,54849,52029 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0.0006083	Direct
48371,48371,48371 48371 - ARM repeat 48371 - ARM repeat 48371 - ARM repeat	0.00222	Inherited
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.003945	Inherited

Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term

Plot tree as:

Download Newick format tree:

(show help)

SEARCH

BROWSE

TOOLS

ABOUT

HELP

Xenopus ANatomical entity (XAN): tail

Superfamily

Family

Supra-domain (including individual superfamily)