Mammalian Phenotype (MP): behavior/neurological phenotype

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)
Metallothionein	0	Direct
Nitric oxide (NO) synthase oxygenase domain	0	Direct
SRF-like	0	Direct
IP3 receptor type 1 binding core, domain 2	0	Direct
C-terminal domain of PLC-beta	0	Direct
p53 tetramerization domain	0	Direct
Aromatic aminoacid monoxygenases, catalytic and oligomerization domains	0	Direct
Family A G protein-coupled receptor-like	0.000000008725	Direct
Neurotransmitter-gated ion-channel transmembrane pore	0.00000976	Direct
Nicotinic receptor ligand binding domain-like	0.00000976	Direct
Nuclear receptor ligand-binding domain	0.0000405	Direct
Periplasmic binding protein-like I	0.00006552	Direct
Voltage-gated potassium channels	0.00009561	Direct
Periplasmic binding protein-like II	0.0005306	Direct
PYP-like sensor domain (PAS domain)	0.003129	Inherited
p53-like transcription factors	0.004547	Inherited
Hormone receptor domain	0.006919	Inherited
Homeodomain-like	0.007886	Inherited
HLH, helix-loop-helix DNA-binding domain	0.02886	Inherited
ACT-like	0.03333	Inherited
SNF-like	0.03722	Inherited
STAT	0.04868	Inherited
Transcription factor STAT-4 N-domain	0.04868	Inherited
Flavoproteins	0.04868	Inherited
Riboflavin synthase domain-like	0.06049	Inherited
Ferredoxin reductase-like, C-terminal NADP-linked domain	0.06049	Inherited
Transducin (alpha subunit), insertion domain	0.06139	Inherited
Glycosyl hydrolase domain	0.1599	Inherited
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	0.1635	Inherited
PDZ domain-like	0.2211	Inherited
PreATP-grasp domain	0.2305	Inherited
Glutathione synthetase ATP-binding domain-like	0.2712	Inherited
(Trans)glycosidases	0.3226	Inherited
Protein kinase-like (PK-like)	0.3551	Inherited
Second domain of FERM	0.3858	Inherited
Spectrin repeat	0.4596	Inherited
Chromo domain-like	0.5896	Inherited
Cadherin-like	0.6769	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)
p53 DNA-binding domain-like	0	Direct
IP3 receptor type 1 binding core, domain 2	0	Direct
Nitric oxide (NO) synthase oxygenase domain	0	Direct
MutT-like	0	Direct
Steroid-binding domain	0	Direct
Synapsin C-terminal domain	0	Direct
C-terminal domain of PLC-beta	0	Direct
Neurotrophin	0	Direct
p53 tetramerization domain	0	Direct
Metallothionein	0	Direct
Aromatic aminoacid monoxygenases, catalytic and oligomerization domains	0	Direct
SRF-like	0	Direct
Cytochrome p450 reductase N-terminal domain-like	0	Direct
Synapsin domain	0	Direct
Phenylalanine metabolism regulatory domain	0	Direct
D-aminoacid oxidase-like	0	Direct
Rhodopsin-like	0.000000366	Direct
Nuclear receptor	0.000006746	Direct
Nicotinic receptor ligand binding domain-like	0.000006808	Direct
Neurotransmitter-gated ion-channel transmembrane pore	0.000006808	Direct
Nuclear receptor ligand-binding domain	0.00002926	Direct
Phosphate binding protein-like	0.00003413	Direct
L-arabinose binding protein-like	0.0004915	Direct
Tetramerization domain of potassium channels	0.002713	Inherited
Clathrin adaptor core protein	0.00459	Inherited
Hormone receptor domain	0.005093	Inherited
YWTD domain	0.008229	Inherited
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0.008229	Inherited
Homeodomain	0.008641	Inherited
Voltage-gated potassium channels	0.01732	Inherited
Rel/Dorsal transcription factors, DNA-binding domain	0.02425	Inherited
Enabled/VASP homology 1 domain (EVH1 domain)	0.02425	Inherited
NADPH-cytochrome p450 reductase-like	0.02505	Inherited
NADPH-cytochrome p450 reductase FAD-binding domain-like	0.02505	Inherited
HLH, helix-loop-helix DNA-binding domain	0.02582	Inherited
Cytoplasmic domain of inward rectifier potassium channel	0.02734	Inherited
SNF-like	0.02912	Inherited
Hypoxia-inducible factor Hif2a, C-terminal domain	0.02912	Inherited
Laminin-type module	0.03007	Inherited
STAT DNA-binding domain	0.03784	Inherited
Transcription factor STAT-4 N-domain	0.03784	Inherited
L domain	0.03784	Inherited
STAT	0.03784	Inherited
Laminin G-like module	0.04854	Inherited
Transducin (alpha subunit), insertion domain	0.04985	Inherited
beta-glycanases	0.05413	Inherited
Pyridoxal-dependent decarboxylase	0.07306	Inherited
ZZ domain	0.08069	Inherited
Acetylcholinesterase-like	0.1321	Inherited
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	0.1398	Inherited
Leucine zipper domain	0.1542	Inherited
PDZ domain	0.1574	Inherited
BAR domain	0.2149	Inherited
Spectrin repeat	0.2773	Inherited
Long-chain cytokines	0.3252	Inherited
Myb/SANT domain	0.3611	Inherited
Phosphotyrosine-binding domain (PTB)	0.3847	Inherited
Chromo domain	0.4266	Inherited
Protein kinases, catalytic subunit	0.5068	Inherited
T-box	0.535	Inherited
Cadherin	0.6969	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)
IP3 receptor type 1 binding core, domain 2	0	Direct
Nitric oxide (NO) synthase oxygenase domain	0	Direct
SRF-like	0	Direct
C-terminal domain of PLC-beta	0	Direct
Metallothionein	0	Direct
p53 tetramerization domain	0	Direct
Aromatic aminoacid monoxygenases, catalytic and oligomerization domains	0	Direct
Family A G protein-coupled receptor-like	0.000000003304	Direct
Nicotinic receptor ligand binding domain-like	0.000004284	Direct
Neurotransmitter-gated ion-channel transmembrane pore	0.000004284	Direct
Nuclear receptor ligand-binding domain	0.00001884	Direct
Periplasmic binding protein-like I	0.00003108	Direct
Voltage-gated potassium channels	0.00004603	Direct
Periplasmic binding protein-like II	0.0002812	Direct
PYP-like sensor domain (PAS domain)	0.001821	Inherited
p53-like transcription factors	0.0027	Inherited
Hormone receptor domain	0.004232	Inherited
Homeodomain-like	0.004846	Inherited
YWTD domain	0.006964	Inherited
HLH, helix-loop-helix DNA-binding domain	0.01954	Inherited
ACT-like	0.02283	Inherited
SNF-like	0.02568	Inherited
STAT	0.0343	Inherited
Transcription factor STAT-4 N-domain	0.0343	Inherited
Flavoproteins	0.0343	Inherited
Riboflavin synthase domain-like	0.04359	Inherited
Ferredoxin reductase-like, C-terminal NADP-linked domain	0.04359	Inherited
Transducin (alpha subunit), insertion domain	0.04431	Inherited
Glycosyl hydrolase domain	0.1275	Inherited
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	0.1306	Inherited
Leucine zipper domain	0.1349	Inherited
PDZ domain-like	0.1828	Inherited
PreATP-grasp domain	0.1915	Inherited
Glutathione synthetase ATP-binding domain-like	0.2296	Inherited
(Trans)glycosidases	0.2784	Inherited
Protein kinase-like (PK-like)	0.3096	Inherited
Second domain of FERM	0.3394	Inherited
SH3-domain	0.3656	Inherited
Spectrin repeat	0.4118	Inherited
Chromo domain-like	0.5435	Inherited
Cadherin-like	0.6349	Inherited
GTPase activation domain, GAP	0.9938	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)
55021,56534 55021 - ACT-like 56534 - Aromatic aminoacid monoxygenases, catalytic and oligomerization domains	0	Direct
57535,49854 57535 - Complement control module/SCR domain 49854 - Spermadhesin, CUB domain	0	Direct
57184,57581 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain	0	Direct
81324,53850 81324 - Voltage-gated potassium channels 53850 - Periplasmic binding protein-like II	0	Direct
82109,82109 82109 - MIR domain 82109 - MIR domain	0	Direct
57196,57424 57196 - EGF/Laminin 57424 - LDL receptor-like module	0	Direct
56496,49899 56496 - Fibrinogen C-terminal domain-like 49899 - Concanavalin A-like lectins/glucanases	0	Direct
57196,56496 57196 - EGF/Laminin 56496 - Fibrinogen C-terminal domain-like	0	Direct
54236,57889 54236 - Ubiquitin-like 57889 - Cysteine-rich domain	0	Direct
82109,100909 82109 - MIR domain 100909 - IP3 receptor type 1 binding core, domain 2	0	Direct
49417,47719 49417 - p53-like transcription factors 47719 - p53 tetramerization domain	0	Direct
54637,54637 54637 - Thioesterase/thiol ester dehydrase-isomerase 54637 - Thioesterase/thiol ester dehydrase-isomerase	0	Direct
50044,50156 50044 - SH3-domain 50156 - PDZ domain-like	0	Direct
103473,103473 103473 - MFS general substrate transporter 103473 - MFS general substrate transporter	0	Direct
57184,82895 57184 - Growth factor receptor domain 82895 - TSP-1 type 1 repeat	0	Direct
100909,49899 100909 - IP3 receptor type 1 binding core, domain 2 49899 - Concanavalin A-like lectins/glucanases	0	Direct
63712,90112 63712 - Nicotinic receptor ligand binding domain-like 90112 - Neurotransmitter-gated ion-channel transmembrane pore	0.000004284	Direct
57716,48508 57716 - Glucocorticoid receptor-like (DNA-binding domain) 48508 - Nuclear receptor ligand-binding domain	0.0001475	Direct
63825,57196 63825 - YWTD domain 57196 - EGF/Laminin	0.0008167	Direct
111418,81321 111418 - Hormone receptor domain 81321 - Family A G protein-coupled receptor-like	0.001326	Inherited
53822,53850 53822 - Periplasmic binding protein-like I 53850 - Periplasmic binding protein-like II	0.01018	Inherited
49899,49899 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0.01446	Inherited
47459,55785 47459 - HLH, helix-loop-helix DNA-binding domain 55785 - PYP-like sensor domain (PAS domain)	0.01514	Inherited
49417,81296 49417 - p53-like transcription factors 81296 - E set domains	0.02154	Inherited
47473,57850 47473 - EF-hand 57850 - RING/U-box	0.02283	Inherited
52799,52799 52799 - (Phosphotyrosine protein) phosphatases II 52799 - (Phosphotyrosine protein) phosphatases II	0.02427	Inherited
81324,81296 81324 - Voltage-gated potassium channels 81296 - E set domains	0.02427	Inherited
47655,49417 47655 - STAT 49417 - p53-like transcription factors	0.0343	Inherited
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like	0.0343	Inherited
49417,55550 49417 - p53-like transcription factors 55550 - SH2 domain	0.0343	Inherited
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain	0.0343	Inherited
48092,47655 48092 - Transcription factor STAT-4 N-domain 47655 - STAT	0.0343	Inherited
50044,48065 50044 - SH3-domain 48065 - DBL homology domain (DH-domain)	0.0343	Inherited
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0.07217	Inherited
54160,54160 54160 - Chromo domain-like 54160 - Chromo domain-like	0.1216	Inherited
51445,51011 51445 - (Trans)glycosidases 51011 - Glycosyl hydrolase domain	0.1275	Inherited
52440,56059 52440 - PreATP-grasp domain 56059 - Glutathione synthetase ATP-binding domain-like	0.1275	Inherited
50729,49562 50729 - PH domain-like 49562 - C2 domain (Calcium/lipid-binding domain, CaLB)	0.1276	Inherited
48065,50729 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like	0.4944	Inherited
49313,49313 49313 - Cadherin-like 49313 - Cadherin-like	0.7427	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)
63825,57196,57424 63825 - YWTD domain 57196 - EGF/Laminin 57424 - LDL receptor-like module	0	Direct
57184,57184,57581 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain	0	Direct
49854,57535,49854 49854 - Spermadhesin, CUB domain 57535 - Complement control module/SCR domain 49854 - Spermadhesin, CUB domain	0	Direct
57196,57424,57424 57196 - EGF/Laminin 57424 - LDL receptor-like module 57424 - LDL receptor-like module	0	Direct
57535,49854,57535 57535 - Complement control module/SCR domain 49854 - Spermadhesin, CUB domain 57535 - Complement control module/SCR domain	0	Direct
57196,56496,49899 57196 - EGF/Laminin 56496 - Fibrinogen C-terminal domain-like 49899 - Concanavalin A-like lectins/glucanases	0	Direct
82109,100909,49899 82109 - MIR domain 100909 - IP3 receptor type 1 binding core, domain 2 49899 - Concanavalin A-like lectins/glucanases	0	Direct
82109,82109,100909 82109 - MIR domain 82109 - MIR domain 100909 - IP3 receptor type 1 binding core, domain 2	0	Direct
49899,57196,56496 49899 - Concanavalin A-like lectins/glucanases 57196 - EGF/Laminin 56496 - Fibrinogen C-terminal domain-like	0	Direct
56496,49899,49899 56496 - Fibrinogen C-terminal domain-like 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0	Direct
49785,49899,49899 49785 - Galactose-binding domain-like 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0	Direct
103473,103473,141571 103473 - MFS general substrate transporter 103473 - MFS general substrate transporter 141571 - Pentapeptide repeat-like	0	Direct
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin	0.0004137	Direct
57424,57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module 57424 - LDL receptor-like module	0.003586	Inherited
50044,50044,50044 50044 - SH3-domain 50044 - SH3-domain 50044 - SH3-domain	0.01018	Inherited
57196,63825,57196 57196 - EGF/Laminin 63825 - YWTD domain 57196 - EGF/Laminin	0.01018	Inherited
47473,47473,57850 47473 - EF-hand 47473 - EF-hand 57850 - RING/U-box	0.02283	Inherited
50044,48065,50729 50044 - SH3-domain 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like	0.0343	Inherited
48092,47655,49417 48092 - Transcription factor STAT-4 N-domain 47655 - STAT 49417 - p53-like transcription factors	0.0343	Inherited
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like	0.0343	Inherited
47655,49417,55550 47655 - STAT 49417 - p53-like transcription factors 55550 - SH2 domain	0.0343	Inherited
49854,57535,57535 49854 - Spermadhesin, CUB domain 57535 - Complement control module/SCR domain 57535 - Complement control module/SCR domain	0.0672	Inherited
46966,46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat 46966 - Spectrin repeat	0.2384	Inherited
49313,49313,49313 49313 - Cadherin-like 49313 - Cadherin-like 49313 - Cadherin-like	0.8681	Inherited