Phenotypic Abnormality (PA): Abnormal homeostasis

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

Jump to [ Top · Hierarchy ]

Superfamily

(show details)

SCOP term	FDR (all)	Annotation (direct or inherited)
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0	Direct
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	Direct
Plakin repeat	0	Direct
Smc hinge domain	0	Direct
Fibrinogen coiled-coil and central regions	0	Direct
Apolipoprotein A-I	0	Direct
MHC antigen-recognition domain	0.00638	Inherited
Transcription factor STAT-4 N-domain	0.007751	Inherited
STAT	0.007751	Inherited
ClpP/crotonase	0.01429	Inherited
Ras GEF	0.01893	Inherited
Thiolase-like	0.01893	Inherited
HD-domain/PDEase-like	0.02815	Inherited
PreATP-grasp domain	0.02815	Inherited
GAF domain-like	0.04394	Inherited
Terpenoid synthases	0.04394	Inherited
Rudiment single hybrid motif	0.04394	Inherited
Insulin-like	0.04394	Inherited
Glutathione synthetase ATP-binding domain-like	0.04812	Inherited
Ribonuclease H-like	0.06162	Inherited
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0.08363	Inherited
Translation proteins	0.1068	Inherited
Class II aaRS and biotin synthetases	0.1218	Inherited
4-helical cytokines	0.1228	Inherited
Acyl-CoA dehydrogenase C-terminal domain-like	0.1266	Inherited
Acyl-CoA dehydrogenase NM domain-like	0.1266	Inherited
Thiamin diphosphate-binding fold (THDP-binding)	0.1594	Inherited
Mitochondrial carrier	0.191	Inherited
SH2 domain	0.1925	Inherited
SCOP hierarchy in SUPERFAMILY	0.2012	Inherited
Nucleotidylyl transferase	0.2128	Inherited
Adenine nucleotide alpha hydrolases-like	0.2166	Inherited
DEATH domain	0.2336	Inherited
Single hybrid motif	0.2692	Inherited
RNI-like	0.2931	Inherited
4Fe-4S ferredoxins	0.2953	Inherited
Fibrinogen C-terminal domain-like	0.2963	Inherited
Complement control module/SCR domain	0.5064	Inherited
Voltage-gated potassium channels	0.5711	Inherited
E set domains	0.5927	Inherited
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	0.7143	Inherited
Trypsin-like serine proteases	0.721	Inherited
Neurotransmitter-gated ion-channel transmembrane pore	0.8158	Inherited
Nicotinic receptor ligand binding domain-like	0.8158	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Family

Jump to [ Top · Hierarchy ]

Family

(show details)

SCOP term	FDR (all)	Annotation (direct or inherited)
Proteasome subunits	0	Direct
Amylase, catalytic domain	0	Direct
alpha-Amylases, C-terminal beta-sheet domain	0	Direct
Apolipoprotein A-I	0	Direct
Medium chain acyl-CoA dehydrogenase-like, C-terminal domain	0	Direct
Smc hinge domain	0	Direct
Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains	0	Direct
Long-chain cytokines	0	Direct
Plakin repeat	0	Direct
HCDH C-domain-like	0	Direct
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0	Direct
Fibrinogen coiled-coil and central regions	0	Direct
IF2B-like	0	Direct
MHC antigen-recognition domain	0.004863	Inherited
BC N-terminal domain-like	0.0057	Inherited
Transcription factor STAT-4 N-domain	0.0057	Inherited
STAT DNA-binding domain	0.0057	Inherited
STAT	0.0057	Inherited
BC ATP-binding domain-like	0.0057	Inherited
Ras GEF	0.01448	Inherited
Pyrin domain, PYD	0.01448	Inherited
Insulin-like	0.03535	Inherited
GAF domain	0.03535	Inherited
BC C-terminal domain-like	0.03535	Inherited
Hypoxia-inducible factor Hif2a, C-terminal domain	0.03535	Inherited
Crotonase-like	0.04462	Inherited
PDEase	0.04598	Inherited
Class I aminoacyl-tRNA synthetases (RS), catalytic domain	0.07358	Inherited
Caspase recruitment domain, CARD	0.09204	Inherited
28-residue LRR	0.09923	Inherited
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0.1263	Inherited
Cytoplasmic domain of inward rectifier potassium channel	0.1381	Inherited
G proteins	0.1617	Inherited
Mitochondrial carrier	0.1712	Inherited
SH2 domain	0.1762	Inherited
Ras-binding domain, RBD	0.1918	Inherited
Biotinyl/lipoyl-carrier proteins and domains	0.2437	Inherited
Branched-chain alpha-keto acid dehydrogenase Pyr module	0.2657	Inherited
Branched-chain alpha-keto acid dehydrogenase PP module	0.2657	Inherited
Fibrinogen C-terminal domain-like	0.2766	Inherited
Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	0.3193	Inherited
Complement control module/SCR domain	0.4821	Inherited
Phosphotyrosine-binding domain (PTB)	0.505	Inherited
Eukaryotic proteases	0.6383	Inherited
Neurotransmitter-gated ion-channel transmembrane pore	0.8113	Inherited
Nicotinic receptor ligand binding domain-like	0.8113	Inherited
Voltage-gated potassium channels	0.8374	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Supra-domain (Single|Duplex|Triple)

Jump to [ Top · Hierarchy ]

Supra-domain (Single)

(show details)

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Plakin repeat	0	Direct
Apolipoprotein A-I	0	Direct
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0	Direct
Fibrinogen coiled-coil and central regions	0	Direct
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	Direct
Smc hinge domain	0	Direct
MHC antigen-recognition domain	0.003962	Inherited
Transcription factor STAT-4 N-domain	0.004896	Inherited
STAT	0.004896	Inherited
ClpP/crotonase	0.00946	Inherited
Ras GEF	0.01277	Inherited
Thiolase-like	0.01277	Inherited
HD-domain/PDEase-like	0.01966	Inherited
PreATP-grasp domain	0.01966	Inherited
Rudiment single hybrid motif	0.03188	Inherited
Terpenoid synthases	0.03188	Inherited
Insulin-like	0.03188	Inherited
GAF domain-like	0.03188	Inherited
Glutathione synthetase ATP-binding domain-like	0.03526	Inherited
Ribonuclease H-like	0.04636	Inherited
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0.06465	Inherited
Translation proteins	0.08415	Inherited
Class II aaRS and biotin synthetases	0.09725	Inherited
4-helical cytokines	0.09813	Inherited
Acyl-CoA dehydrogenase C-terminal domain-like	0.1016	Inherited
Acyl-CoA dehydrogenase NM domain-like	0.1016	Inherited
Thiamin diphosphate-binding fold (THDP-binding)	0.1306	Inherited
Mitochondrial carrier	0.1591	Inherited
SH2 domain	0.1604	Inherited
Nucleotidylyl transferase	0.1791	Inherited
Adenine nucleotide alpha hydrolases-like	0.1825	Inherited
DEATH domain	0.1981	Inherited
Single hybrid motif	0.2312	Inherited
RNI-like	0.2535	Inherited
4Fe-4S ferredoxins	0.2556	Inherited
Fibrinogen C-terminal domain-like	0.2566	Inherited
Complement control module/SCR domain	0.4621	Inherited
Voltage-gated potassium channels	0.5281	Inherited
E set domains	0.5499	Inherited
Homeodomain-like	0.6684	Inherited
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	0.6757	Inherited
Trypsin-like serine proteases	0.6826	Inherited
Nicotinic receptor ligand binding domain-like	0.7813	Inherited
Neurotransmitter-gated ion-channel transmembrane pore	0.7813	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

Jump to [ Top · Hierarchy ]

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

(show details)

Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
51230,47005 51230 - Single hybrid motif 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	0	Direct
47005,52777 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 52777 - CoA-dependent acyltransferases	0	Direct
103473,100895 103473 - MFS general substrate transporter 100895 - Kazal-type serine protease inhibitors	0	Direct
75399,75399 75399 - Plakin repeat 75399 - Plakin repeat	0	Direct
51905,55424 51905 - FAD/NAD(P)-binding domain 55424 - FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0	Direct
52096,52096 52096 - ClpP/crotonase 52096 - ClpP/crotonase	0	Direct
52374,47323 52374 - Nucleotidylyl transferase 47323 - Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0.001784	Inherited
54452,48726 54452 - MHC antigen-recognition domain 48726 - Immunoglobulin	0.003962	Inherited
48092,47655 48092 - Transcription factor STAT-4 N-domain 47655 - STAT	0.004896	Inherited
47655,49417 47655 - STAT 49417 - p53-like transcription factors	0.004896	Inherited
49417,55550 49417 - p53-like transcription factors 55550 - SH2 domain	0.004896	Inherited
53901,53901 53901 - Thiolase-like 53901 - Thiolase-like	0.01277	Inherited
47986,52540 47986 - DEATH domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0.01277	Inherited
47459,55785 47459 - HLH, helix-loop-helix DNA-binding domain 55785 - PYP-like sensor domain (PAS domain)	0.03188	Inherited
56059,51246 56059 - Glutathione synthetase ATP-binding domain-like 51246 - Rudiment single hybrid motif	0.03188	Inherited
55781,109604 55781 - GAF domain-like 109604 - HD-domain/PDEase-like	0.03188	Inherited
55781,55781 55781 - GAF domain-like 55781 - GAF domain-like	0.03188	Inherited
52440,56059 52440 - PreATP-grasp domain 56059 - Glutathione synthetase ATP-binding domain-like	0.0404	Inherited
56645,47203 56645 - Acyl-CoA dehydrogenase NM domain-like 47203 - Acyl-CoA dehydrogenase C-terminal domain-like	0.1016	Inherited
81324,81296 81324 - Voltage-gated potassium channels 81296 - E set domains	0.1306	Inherited
57535,57535 57535 - Complement control module/SCR domain 57535 - Complement control module/SCR domain	0.3166	Inherited
63712,90112 63712 - Nicotinic receptor ligand binding domain-like 90112 - Neurotransmitter-gated ion-channel transmembrane pore	0.7813	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

Jump to [ Top · Hierarchy ]

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

(show details)

Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
51230,47005,52777 51230 - Single hybrid motif 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 52777 - CoA-dependent acyltransferases	0	Direct
48092,47655,49417 48092 - Transcription factor STAT-4 N-domain 47655 - STAT 49417 - p53-like transcription factors	0.004896	Inherited
47655,49417,55550 47655 - STAT 49417 - p53-like transcription factors 55550 - SH2 domain	0.004896	Inherited
55781,55781,109604 55781 - GAF domain-like 55781 - GAF domain-like 109604 - HD-domain/PDEase-like	0.03188	Inherited
52440,56059,51246 52440 - PreATP-grasp domain 56059 - Glutathione synthetase ATP-binding domain-like 51246 - Rudiment single hybrid motif	0.03188	Inherited
57196,57184,57196 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57196 - EGF/Laminin	0.1825	Inherited
57184,57196,57196 57184 - Growth factor receptor domain 57196 - EGF/Laminin 57196 - EGF/Laminin	0.3855	Inherited
57535,57535,57535 57535 - Complement control module/SCR domain 57535 - Complement control module/SCR domain 57535 - Complement control module/SCR domain	0.4756	Inherited