Zebrafish Anatomy (ZA): nervous system

Biomedical Ontology
Like Gene Ontology (GO), biomedical ontology such as phenotype 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. Biomedical ontologies we have incorporated are as follows:

Disease Ontology (DO) Ontology
DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM.
Human Phenotype (HP) Ontology
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 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 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
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 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 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 displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
Xenopus Anatomy (XA) Ontology
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
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
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.
UniProtKB KeyWords (KW) Ontology
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).
CTD Diseases (CD) Ontology
CD is MEDIC disease vocabulary that is modified by CTD from the "Diseases" [C] branch of Medical Subject Headings (MeSH), combined with genetic disorders from the Online Mendelian Inheritance in OMIM database.
CTD Chemicals (CC) Ontology
CC is chemical vocabulary that is adapted by CTD from the "Chemicals and Drugs" category and Supplementary Concept Records of Medical Subject Headings (MeSH, a hierarchical vocabulary used to index articles for MEDLINE/PubMed).

Superfamily

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Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
SMAD MH1 domain	0	Direct
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0	Direct
HIT-like	0	Direct
ADC-like	0	Direct
Cap-Gly domain	0	Direct
Tubulin nucleotide-binding domain-like	0	Direct
Class II aaRS ABD-related	0	Direct
Class II aaRS and biotin synthetases	0	Direct
Ferredoxin reductase-like, C-terminal NADP-linked domain	0	Direct
L27 domain	0	Direct
PP2C-like	0	Direct
Cdc48 domain 2-like	0	Direct
Translational machinery components	0	Direct
Single hybrid motif	0	Direct
CCCH zinc finger	0	Direct
Soluble quinoprotein glucose dehydrogenase	0	Direct
BRK domain-like	0	Direct
JAB1/MPN domain	0	Direct
BPTI-like	0	Direct
Metallo-dependent hydrolases	0	Direct
Glutathione synthetase ATP-binding domain-like	0	Direct
Tubulin C-terminal domain-like	0	Direct
Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit	0	Direct
Composite domain of metallo-dependent hydrolases	0	Direct
Doublecortin (DC)	0	Direct
Nucleotide cyclase	0	Direct
SNARE fusion complex	0	Direct
Riboflavin synthase domain-like	0	Direct
HSP20-like chaperones	0	Direct
WD40 repeat-like	0.004736	Inherited
HMG-box	0.05654	Inherited
Homeodomain-like	0.1646	Inherited
SMAD/FHA domain	0.1771	Inherited
Serine protease inhibitors	0.2372	Inherited
Protease propeptides/inhibitors	0.2619	Inherited
Arginase/deacetylase	0.3164	Inherited
Sema domain	0.3324	Inherited
Cyclin-like	0.3324	Inherited
BAR/IMD domain-like	0.373	Inherited
Subtilisin-like	0.3751	Inherited
Cadherin-like	0.3907	Inherited
PDZ domain-like	0.453	Inherited
Plexin repeat	0.4836	Inherited
lambda repressor-like DNA-binding domains	0.484	Inherited
Multidrug efflux transporter AcrB transmembrane domain	0.529	Inherited
NAD(P)-binding Rossmann-fold domains	0.5567	Inherited
GTPase activation domain, GAP	0.6117	Inherited
Fibronectin type III	0.6362	Inherited
beta-beta-alpha zinc fingers	0.7103	Inherited
Growth factor receptor domain	0.7189	Inherited
Cytochrome P450	0.7491	Inherited
Nuclear receptor ligand-binding domain	0.7525	Inherited
HLH, helix-loop-helix DNA-binding domain	0.8242	Inherited
EGF/Laminin	0.9078	Inherited
Glucocorticoid receptor-like (DNA-binding domain)	1	Inherited
Immunoglobulin	1	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Family

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
UBA domain	0	Direct
Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit	0	Direct
Platelet-derived growth factor-like	0	Direct
Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A	0	Direct
Cdc48 domain 2-like	0	Direct
Hydantoinase (dihydropyrimidinase)	0	Direct
SNARE fusion complex	0	Direct
Biotinyl/lipoyl-carrier proteins and domains	0	Direct
FYVE, a phosphatidylinositol-3-phosphate binding domain	0	Direct
L27 domain	0	Direct
Adenylyl and guanylyl cyclase catalytic domain	0	Direct
Small Kunitz-type inhibitors & BPTI-like toxins	0	Direct
Cap-Gly domain	0	Direct
C5 cytosine-specific DNA methylase, DCM	0	Direct
Tubulin, GTPase domain	0	Direct
CCCH zinc finger	0	Direct
Tubulin, C-terminal domain	0	Direct
Connexin43	0	Direct
Anticodon-binding domain of Class II aaRS	0	Direct
Doublecortin (DC)	0	Direct
SMAD MH1 domain	0	Direct
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0	Direct
SMAD domain	0	Direct
Zf-UBP	0	Direct
Chromo domain	0	Direct
Hydantoinase (dihydropyrimidinase), catalytic domain	0	Direct
Tetramerization domain of potassium channels	0	Direct
Long-chain cytokines	0	Direct
Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	0	Direct
PP2C-like	0	Direct
Cdc48 N-terminal domain-like	0	Direct
Ovomucoid domain III-like	0	Direct
BRK domain-like	0	Direct
WD40-repeat	0.01705	Inherited
HMG-box	0.03965	Inherited
L domain	0.06978	Inherited
Tetratricopeptide repeat (TPR)	0.09475	Inherited
Multidrug efflux transporter AcrB transmembrane domain	0.1317	Inherited
Homeodomain	0.141	Inherited
Aquaporin-like	0.2749	Inherited
Histone deacetylase, HDAC	0.2749	Inherited
Growth factor receptor domain	0.2758	Inherited
Sema domain	0.2817	Inherited
POU-specific domain	0.328	Inherited
Cadherin	0.4027	Inherited
Motor proteins	0.4087	Inherited
PDZ domain	0.4237	Inherited
Plexin repeat	0.4303	Inherited
Fibronectin type III	0.5605	Inherited
Paired domain	0.6799	Inherited
Nuclear receptor ligand-binding domain	0.703	Inherited
Cytochrome P450	0.7124	Inherited
I set domains	0.7433	Inherited
Nuclear receptor	0.757	Inherited
HLH, helix-loop-helix DNA-binding domain	0.7716	Inherited
EGF-type module	0.8068	Inherited
Classic zinc finger, C2H2	0.9185	Inherited
Transforming growth factor (TGF)-beta	0.999	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Supra-domain (Single|Duplex|Triple)

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Supra-domain (Single)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Class II aaRS ABD-related	0	Direct
BRK domain-like	0	Direct
Glutathione synthetase ATP-binding domain-like	0	Direct
SNARE fusion complex	0	Direct
Soluble quinoprotein glucose dehydrogenase	0	Direct
JAB1/MPN domain	0	Direct
Riboflavin synthase domain-like	0	Direct
BPTI-like	0	Direct
L27 domain	0	Direct
Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit	0	Direct
Metallo-dependent hydrolases	0	Direct
Composite domain of metallo-dependent hydrolases	0	Direct
Tubulin nucleotide-binding domain-like	0	Direct
Class II aaRS and biotin synthetases	0	Direct
HSP20-like chaperones	0	Direct
HIT-like	0	Direct
Ferredoxin reductase-like, C-terminal NADP-linked domain	0	Direct
Doublecortin (DC)	0	Direct
Tubulin C-terminal domain-like	0	Direct
CCCH zinc finger	0	Direct
PP2C-like	0	Direct
SMAD MH1 domain	0	Direct
ADC-like	0	Direct
Nucleotide cyclase	0	Direct
Translational machinery components	0	Direct
Cap-Gly domain	0	Direct
Single hybrid motif	0	Direct
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0	Direct
Cdc48 domain 2-like	0	Direct
WD40 repeat-like	0.003101	Inherited
HMG-box	0.04279	Inherited
Homeodomain-like	0.1382	Inherited
SMAD/FHA domain	0.15	Inherited
Neurotransmitter-gated ion-channel transmembrane pore	0.1563	Inherited
Serine protease inhibitors	0.2056	Inherited
Protease propeptides/inhibitors	0.2302	Inherited
Arginase/deacetylase	0.2834	Inherited
Cyclin-like	0.2986	Inherited
Sema domain	0.2986	Inherited
BAR/IMD domain-like	0.3382	Inherited
Subtilisin-like	0.3404	Inherited
Cadherin-like	0.3562	Inherited
PDZ domain-like	0.4191	Inherited
p53-like transcription factors	0.4486	Inherited
Plexin repeat	0.4507	Inherited
lambda repressor-like DNA-binding domains	0.451	Inherited
Multidrug efflux transporter AcrB transmembrane domain	0.497	Inherited
NAD(P)-binding Rossmann-fold domains	0.5259	Inherited
GTPase activation domain, GAP	0.5823	Inherited
Ankyrin repeat	0.5846	Inherited
Fibronectin type III	0.6083	Inherited
beta-beta-alpha zinc fingers	0.6852	Inherited
Growth factor receptor domain	0.6948	Inherited
Cytochrome P450	0.7275	Inherited
Nuclear receptor ligand-binding domain	0.7318	Inherited
HLH, helix-loop-helix DNA-binding domain	0.8093	Inherited
EGF/Laminin	0.8997	Inherited
Cystine-knot cytokines	0.9036	Inherited
Glucocorticoid receptor-like (DNA-binding domain)	1	Inherited
Immunoglobulin	1	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

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Supra-domain (Duplex) in N- to C-terminal order

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
101288,50156 101288 - L27 domain 50156 - PDZ domain-like	0	Direct
89837,89837 89837 - Doublecortin (DC) 89837 - Doublecortin (DC)	0	Direct
51556,51338 51556 - Metallo-dependent hydrolases 51338 - Composite domain of metallo-dependent hydrolases	0	Direct
52490,55307 52490 - Tubulin nucleotide-binding domain-like 55307 - Tubulin C-terminal domain-like	0	Direct
52058,49265 52058 - L domain-like 49265 - Fibronectin type III	0	Direct
48097,56112 48097 - Regulator of G-protein signaling, RGS 56112 - Protein kinase-like (PK-like)	0	Direct
54001,143791 54001 - Cysteine proteinases 143791 - DUSP-like	0	Direct
82199,57667 82199 - SET domain 57667 - beta-beta-alpha zinc fingers	0	Direct
57362,57362 57362 - BPTI-like 57362 - BPTI-like	0	Direct
63380,52343 63380 - Riboflavin synthase domain-like 52343 - Ferredoxin reductase-like, C-terminal NADP-linked domain	0	Direct
54585,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	Direct
103575,81296 103575 - Plexin repeat 81296 - E set domains	0	Direct
52374,47323 52374 - Nucleotidylyl transferase 47323 - Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0	Direct
50978,50998 50978 - WD40 repeat-like 50998 - Quinoprotein alcohol dehydrogenase-like	0	Direct
54160,54160 54160 - Chromo domain-like 54160 - Chromo domain-like	0	Direct
50692,54585 50692 - ADC-like 54585 - Cdc48 domain 2-like	0	Direct
54160,52540 54160 - Chromo domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	Direct
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like	0.07246	Inherited
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain	0.07246	Inherited
54897,52743 54897 - Protease propeptides/inhibitors 52743 - Subtilisin-like	0.1454	Inherited
49562,48350 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 48350 - GTPase activation domain, GAP	0.2834	Inherited
101912,103575 101912 - Sema domain 103575 - Plexin repeat	0.2986	Inherited
81296,81296 81296 - E set domains 81296 - E set domains	0.3404	Inherited
49313,49313 49313 - Cadherin-like 49313 - Cadherin-like	0.4922	Inherited
48726,49265 48726 - Immunoglobulin 49265 - Fibronectin type III	0.5081	Inherited
50156,50156 50156 - PDZ domain-like 50156 - PDZ domain-like	0.6844	Inherited
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.7605	Inherited
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	0.7697	Inherited
90257,90257 90257 - Myosin rod fragments 90257 - Myosin rod fragments	0.8688	Inherited
48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin	0.9312	Inherited
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.9855	Inherited
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain)	0.9956	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

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Supra-domain (Triple) in N- to C-terminal order

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
54585,52540,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0	Direct
57184,57184,57196 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57196 - EGF/Laminin	0	Direct
54160,52540,52540 54160 - Chromo domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0	Direct
54160,54160,52540 54160 - Chromo domain-like 54160 - Chromo domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	Direct
52058,49265,49265 52058 - L domain-like 49265 - Fibronectin type III 49265 - Fibronectin type III	0	Direct
57184,52058,49265 57184 - Growth factor receptor domain 52058 - L domain-like 49265 - Fibronectin type III	0	Direct
50692,54585,52540 50692 - ADC-like 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	Direct
82199,57667,57667 82199 - SET domain 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	0	Direct
57196,49899,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0	Direct
103575,81296,81296 103575 - Plexin repeat 81296 - E set domains 81296 - E set domains	0	Direct
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like	0.07246	Inherited
48726,48726,49265 48726 - Immunoglobulin 48726 - Immunoglobulin 49265 - Fibronectin type III	0.2148	Inherited
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.2391	Inherited
81296,81296,81296 81296 - E set domains 81296 - E set domains 81296 - E set domains	0.3404	Inherited
90257,90257,90257 90257 - Myosin rod fragments 90257 - Myosin rod fragments 90257 - Myosin rod fragments	0.5429	Inherited
49313,49313,49313 49313 - Cadherin-like 49313 - Cadherin-like 49313 - Cadherin-like	0.5709	Inherited
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin	0.7185	Inherited