Xenopus ANatomical entity (XAN): spinal cord

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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)

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

+ + + + + 5: Xenopus anatomical entity [XAO:0000000] <9>

+ + + + 4: anatomical structure [XAO:0003000] <11> (577|733) (577|400|163)

+ + + + 4: anatomical group [XAO:0003001] <2> (414|530) (418|309|134)

+ + + + 4: whole organism [XAO:0003004] <12> (461|598) (465|335|145)

+ + + 3: multicellular anatomical structure [XAO:0005002] <4> (436|565) (440|325|142)

+ + + 3: anatomical system [XAO:0003002] <19> (283|382) (289|204|93)

+ + 2: nervous system [XAO:0000177] <11> (134|201) (141|114|53)

+ + 2: compound organ [XAO:0003041] <8> (332|444) (336|275|125)

+ 1: central nervous system [XAO:0000215] <7> (129|191) (135|108|49)

+ 1: cavitated compound organ [XAO:0003165] <21> (287|395) (292|247|114)

0: spinal cord [XAO:0000020] <10> (18|26) (20|19|10)

- 1: astrocyte [XAO:0005131] <1> (0|0) (0|0|0)

- 1: central canal [XAO:0004543] (0|0) (0|0|0)

- 1: dorsal funiculus [XAO:0004580] (0|0) (0|0|0)

- 1: floor plate [XAO:0000306] (3|3) (3|1|1)

- 1: lateral funiculus [XAO:0004560] (0|0) (0|0|0)

- 1: oligodendrocyte [XAO:0005133] (0|0) (0|0|0)

- 1: roof plate [XAO:0000022] (0|1) (0|0|0)

- 1: solitary tract [XAO:0004586] (0|0) (0|0|0)

- 1: spinal neuron [XAO:0005018] (3|3) (3|1|0)

- 1: ventral funiculus [XAO:0004535] (0|0) (0|0|0)

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Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
Homeodomain-like	0	Direct
Nop domain	0	Direct
HLH, helix-loop-helix DNA-binding domain	0.000000000000001546	Direct
"Winged helix" DNA-binding domain	0.000009937	Direct
14-3-3 protein	0.00002278	Direct
Growth factor receptor domain	0.00002836	Direct
Orange domain-like	0.00003567	Direct
Kazal-type serine protease inhibitors	0.00005725	Direct
PYP-like sensor domain (PAS domain)	0.00006852	Direct
EGF/Laminin	0.0002398	Direct
Voltage-gated potassium channels	0.0002701	Direct
HMG-box	0.0002732	Direct
Glucocorticoid receptor-like (DNA-binding domain)	0.0004052	Direct
lambda repressor-like DNA-binding domains	0.0004445	Direct
RNA-binding domain, RBD	0.0006267	Direct
Intermediate filament protein, coiled coil region	0.007633	Inherited
Tubulin C-terminal domain-like	0.1691	Inherited
Tubulin nucleotide-binding domain-like	0.1968	Inherited

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
PAS domain of steroid receptor coactivator 1A, NCo-A1	0	Direct
Homeodomain	0	Direct
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain	0	Direct
Cyclin A/CDK2-associated p19, Skp2	0	Direct
Nop domain	0	Direct
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain	0	Direct
HLH, helix-loop-helix DNA-binding domain	0.00000000000001335	Direct
Growth factor receptor domain	0.0000004899	Direct
Forkhead DNA-binding domain	0.000004916	Direct
14-3-3 protein	0.00002618	Direct
L domain	0.00002618	Direct
Hairy Orange domain	0.00004314	Direct
I set domains	0.00008306	Direct
POU-specific domain	0.0001275	Direct
Paired domain	0.0002736	Direct
Canonical RBD	0.0002983	Direct
Ovomucoid domain III-like	0.0003049	Direct
Laminin G-like module	0.0003442	Direct
EGF-type module	0.0004665	Direct
HMG-box	0.0004844	Direct
ets domain	0.0005124	Direct
Classic zinc finger, C2H2	0.0006791	Direct
Extracellular domain of cell surface receptors	0.0009545	Direct
Intermediate filament protein, coiled coil region	0.0104	Inherited
Tubulin, GTPase domain	0.1836	Inherited
Tubulin, C-terminal domain	0.1836	Inherited

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

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Supra-domain (including individual superfamily)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Nop domain	0	Direct
Homeodomain-like	0	Direct
HLH, helix-loop-helix DNA-binding domain	0.000000000000001069	Direct
"Winged helix" DNA-binding domain	0.000007159	Direct
14-3-3 protein	0.00001653	Direct
Growth factor receptor domain	0.00002063	Direct
Orange domain-like	0.00002602	Direct
Kazal-type serine protease inhibitors	0.00004198	Direct
PYP-like sensor domain (PAS domain)	0.00005036	Direct
EGF/Laminin	0.0001787	Direct
Voltage-gated potassium channels	0.0002017	Direct
HMG-box	0.000204	Direct
Glucocorticoid receptor-like (DNA-binding domain)	0.0003038	Direct
lambda repressor-like DNA-binding domains	0.000334	Direct
RNA-binding domain, RBD	0.0004726	Direct
P-domain of calnexin/calreticulin	0.0009841	Direct
Nuclear receptor coactivator interlocking domain	0.0009841	Direct
Intermediate filament protein, coiled coil region	0.005961	Inherited
Tubulin C-terminal domain-like	0.1478	Inherited
Tubulin nucleotide-binding domain-like	0.1734	Inherited

(show details)

Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
57196,100895 57196 - EGF/Laminin 100895 - Kazal-type serine protease inhibitors	0	Direct
52540,53254 52540 - P-loop containing nucleoside triphosphate hydrolases 53254 - Phosphoglycerate mutase-like	0	Direct
49899,48726 49899 - Concanavalin A-like lectins/glucanases 48726 - Immunoglobulin	0	Direct
54631,54631 54631 - CBS-domain pair 54631 - CBS-domain pair	0	Direct
57184,100895 57184 - Growth factor receptor domain 100895 - Kazal-type serine protease inhibitors	0	Direct
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain	0.00001653	Direct
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like	0.00001653	Direct
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like	0.00002602	Direct
47459,55785 47459 - HLH, helix-loop-helix DNA-binding domain 55785 - PYP-like sensor domain (PAS domain)	0.0001755	Direct
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	0.0001839	Direct
57603,57603 57603 - FnI-like domain 57603 - FnI-like domain	0.0003499	Direct
49899,57196 49899 - Concanavalin A-like lectins/glucanases 57196 - EGF/Laminin	0.0003585	Direct
48726,49265 48726 - Immunoglobulin 49265 - Fibronectin type III	0.0003646	Direct
52799,52799 52799 - (Phosphotyrosine protein) phosphatases II 52799 - (Phosphotyrosine protein) phosphatases II	0.0004028	Direct
57716,48508 57716 - Glucocorticoid receptor-like (DNA-binding domain) 48508 - Nuclear receptor ligand-binding domain	0.0007445	Direct
57196,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases	0.0009096	Direct
49899,63887 49899 - Concanavalin A-like lectins/glucanases 63887 - P-domain of calnexin/calreticulin	0.0009841	Direct
48726,56436 48726 - Immunoglobulin 56436 - C-type lectin-like	0.0009841	Direct
52490,55307 52490 - Tubulin nucleotide-binding domain-like 55307 - Tubulin C-terminal domain-like	0.1478	Inherited

(show details)

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
49899,48726,49265 49899 - Concanavalin A-like lectins/glucanases 48726 - Immunoglobulin 49265 - Fibronectin type III	0	Direct
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like	0.0001292	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)	0.0004739	Direct
49899,57196,57196 49899 - Concanavalin A-like lectins/glucanases 57196 - EGF/Laminin 57196 - EGF/Laminin	0.0006657	Direct
57196,49899,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0.0006657	Direct
57603,57603,57603 57603 - FnI-like domain 57603 - FnI-like domain 57603 - FnI-like domain	0.0006657	Direct
48726,48726,49265 48726 - Immunoglobulin 48726 - Immunoglobulin 49265 - Fibronectin type III	0.000671	Direct
48726,56436,56436 48726 - Immunoglobulin 56436 - C-type lectin-like 56436 - C-type lectin-like	0.0009841	Direct
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin	0.007952	Inherited

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

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Xenopus ANatomical entity (XAN): spinal cord

Superfamily

Family

Supra-domain (including individual superfamily)