Mammalian Phenotype (MP): abnormal somatic nervous system morphology

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)
Tubby C-terminal domain-like	0	Direct
Lamin A/C globular tail domain	0	Direct
Homeodomain-like	0.000003855	Direct
GDNF receptor-like	0.002035	Inherited
Growth factor receptor domain	0.003782	Inherited
EGF/Laminin	0.01488	Inherited
Nuclear receptor ligand-binding domain	0.02486	Inherited
Glucocorticoid receptor-like (DNA-binding domain)	0.03438	Inherited
Sema domain	0.0613	Inherited
lambda repressor-like DNA-binding domains	0.06611	Inherited
GAF domain-like	0.07138	Inherited
Cystine-knot cytokines	0.07694	Inherited
Intermediate filament protein, coiled coil region	0.07887	Inherited
Plexin repeat	0.08156	Inherited
Neurotransmitter-gated ion-channel transmembrane pore	0.09049	Inherited
Nicotinic receptor ligand binding domain-like	0.09049	Inherited
Cadherin-like	0.1381	Inherited
Orange domain-like	0.1658	Inherited
Clc chloride channel	0.1658	Inherited
Notch domain	0.1658	Inherited
HLH, helix-loop-helix DNA-binding domain	0.2286	Inherited
Integrin domains	0.2621	Inherited
Family A G protein-coupled receptor-like	0.2643	Inherited
Frizzled cysteine-rich domain	0.2707	Inherited
CBS-domain pair	0.2711	Inherited
HD-domain/PDEase-like	0.2842	Inherited
Spectrin repeat	0.2852	Inherited
HMG-box	0.3648	Inherited
E2F-DP heterodimerization region	0.3794	Inherited
Second domain of FERM	0.3979	Inherited
beta-beta-alpha zinc fingers	0.666	Inherited
Cyclin-like	0.7943	Inherited
SH3-domain	0.8126	Inherited
PDZ domain-like	0.8304	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)
Lamin A/C globular tail domain	0	Direct
Transcriptional factor tubby, C-terminal domain	0	Direct
Neurotrophin	0	Direct
Retinoblastoma tumor suppressor domains	0	Direct
Homeodomain	0.0000002303	Direct
L domain	0.0001722	Direct
GDNF receptor-like	0.001444	Inherited
Rel/Dorsal transcription factors, DNA-binding domain	0.002264	Inherited
Laminin-type module	0.009276	Inherited
Adenylyl and guanylyl cyclase catalytic domain	0.01579	Inherited
Nuclear receptor ligand-binding domain	0.02026	Inherited
Nuclear receptor	0.02026	Inherited
Paired domain	0.04058	Inherited
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0.04058	Inherited
POU-specific domain	0.04847	Inherited
Sema domain	0.05108	Inherited
Growth factor receptor domain	0.05108	Inherited
GAF domain	0.05678	Inherited
Plexin repeat	0.06978	Inherited
Intermediate filament protein, coiled coil region	0.07379	Inherited
Nicotinic receptor ligand binding domain-like	0.07703	Inherited
Extracellular domain of cell surface receptors	0.07703	Inherited
Neurotransmitter-gated ion-channel transmembrane pore	0.07703	Inherited
EGF-type module	0.07806	Inherited
Notch domain	0.1416	Inherited
Clc chloride channel	0.1416	Inherited
DIX domain	0.1416	Inherited
Hairy Orange domain	0.1416	Inherited
cAMP-binding domain	0.1449	Inherited
DEP domain	0.1467	Inherited
Cadherin	0.175	Inherited
Calmodulin-like	0.1759	Inherited
Rhodopsin-like	0.2125	Inherited
PDEase	0.2167	Inherited
HLH, helix-loop-helix DNA-binding domain	0.2171	Inherited
Spectrin repeat	0.2287	Inherited
E2F dimerization segment	0.2427	Inherited
CBS-domain pair	0.2427	Inherited
Frizzled cysteine-rich domain	0.2471	Inherited
Integrin domains	0.2498	Inherited
HMG-box	0.3409	Inherited
Cell cycle transcription factor e2f-dp	0.351	Inherited
EF-hand modules in multidomain proteins	0.4557	Inherited
PDZ domain	0.4855	Inherited
Classic zinc finger, C2H2	0.5147	Inherited
Motor proteins	0.5734	Inherited
SH3-domain	0.8094	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)
Tubby C-terminal domain-like	0	Direct
Lamin A/C globular tail domain	0	Direct
Homeodomain-like	0.000001644	Direct
GDNF receptor-like	0.001158	Inherited
Growth factor receptor domain	0.002219	Inherited
EGF/Laminin	0.009546	Inherited
Nucleotide cyclase	0.01214	Inherited
Nuclear receptor ligand-binding domain	0.01661	Inherited
Glucocorticoid receptor-like (DNA-binding domain)	0.02361	Inherited
Sema domain	0.04423	Inherited
lambda repressor-like DNA-binding domains	0.04807	Inherited
GAF domain-like	0.05228	Inherited
Cystine-knot cytokines	0.05663	Inherited
Intermediate filament protein, coiled coil region	0.05815	Inherited
Plexin repeat	0.06032	Inherited
Nicotinic receptor ligand binding domain-like	0.06761	Inherited
Neurotransmitter-gated ion-channel transmembrane pore	0.06761	Inherited
Cadherin-like	0.1083	Inherited
Notch domain	0.1325	Inherited
Orange domain-like	0.1325	Inherited
Clc chloride channel	0.1325	Inherited
L domain-like	0.1621	Inherited
HLH, helix-loop-helix DNA-binding domain	0.1898	Inherited
Integrin domains	0.2209	Inherited
Family A G protein-coupled receptor-like	0.223	Inherited
Frizzled cysteine-rich domain	0.2291	Inherited
CBS-domain pair	0.2294	Inherited
HD-domain/PDEase-like	0.2418	Inherited
Spectrin repeat	0.2428	Inherited
HMG-box	0.3191	Inherited
E2F-DP heterodimerization region	0.3332	Inherited
Second domain of FERM	0.3513	Inherited
beta-beta-alpha zinc fingers	0.6235	Inherited
"Winged helix" DNA-binding domain	0.7167	Inherited
Cyclin-like	0.7592	Inherited
SH3-domain	0.7785	Inherited
PDZ domain-like	0.7978	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)
64593,74853 64593 - Intermediate filament protein, coiled coil region 74853 - Lamin A/C globular tail domain	0	Direct
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like	0.0001255	Direct
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain	0.0001255	Direct
49417,81296 49417 - p53-like transcription factors 81296 - E set domains	0.00172	Inherited
56112,55073 56112 - Protein kinase-like (PK-like) 55073 - Nucleotide cyclase	0.001927	Inherited
57716,48508 57716 - Glucocorticoid receptor-like (DNA-binding domain) 48508 - Nuclear receptor ligand-binding domain	0.005405	Inherited
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.02153	Inherited
101912,103575 101912 - Sema domain 103575 - Plexin repeat	0.04423	Inherited
47413,46689 47413 - lambda repressor-like DNA-binding domains 46689 - Homeodomain-like	0.04681	Inherited
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.04681	Inherited
57184,49265 57184 - Growth factor receptor domain 49265 - Fibronectin type III	0.05228	Inherited
55781,55781 55781 - GAF domain-like 55781 - GAF domain-like	0.05228	Inherited
55781,109604 55781 - GAF domain-like 109604 - HD-domain/PDEase-like	0.05228	Inherited
63712,90112 63712 - Nicotinic receptor ligand binding domain-like 90112 - Neurotransmitter-gated ion-channel transmembrane pore	0.06761	Inherited
52058,48726 52058 - L domain-like 48726 - Immunoglobulin	0.07058	Inherited
57184,57196 57184 - Growth factor receptor domain 57196 - EGF/Laminin	0.0802	Inherited
81296,81296 81296 - E set domains 81296 - E set domains	0.0802	Inherited
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like	0.1325	Inherited
47473,57850 47473 - EF-hand 57850 - RING/U-box	0.1325	Inherited
49313,49313 49313 - Cadherin-like 49313 - Cadherin-like	0.2291	Inherited
46785,144074 46785 - "Winged helix" DNA-binding domain 144074 - E2F-DP heterodimerization region	0.3332	Inherited
46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat	0.3899	Inherited
50156,50156 50156 - PDZ domain-like 50156 - PDZ domain-like	0.5286	Inherited
47473,47473 47473 - EF-hand 47473 - EF-hand	0.5323	Inherited
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	0.5712	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)
52058,48726,48726 52058 - L domain-like 48726 - Immunoglobulin 48726 - Immunoglobulin	0	Direct
57184,52058,57184 57184 - Growth factor receptor domain 52058 - L domain-like 57184 - Growth factor receptor domain	0	Direct
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like	0.0001255	Direct
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin	0.0006755	Direct
57184,49899,49899 57184 - Growth factor receptor domain 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0.02416	Inherited
57184,57196,57196 57184 - Growth factor receptor domain 57196 - EGF/Laminin 57196 - EGF/Laminin	0.03652	Inherited
55781,55781,109604 55781 - GAF domain-like 55781 - GAF domain-like 109604 - HD-domain/PDEase-like	0.05228	Inherited
57196,57184,57196 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57196 - EGF/Laminin	0.07058	Inherited
81296,81296,81296 81296 - E set domains 81296 - E set domains 81296 - E set domains	0.0802	Inherited
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.0802	Inherited
49313,49313,49313 49313 - Cadherin-like 49313 - Cadherin-like 49313 - Cadherin-like	0.1221	Inherited
47473,47473,57850 47473 - EF-hand 47473 - EF-hand 57850 - RING/U-box	0.1325	Inherited
49899,57196,57196 49899 - Concanavalin A-like lectins/glucanases 57196 - EGF/Laminin 57196 - EGF/Laminin	0.1362	Inherited
46966,46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat 46966 - Spectrin repeat	0.2742	Inherited