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Disease Ontology (DO): neurodegenerative disease 
(show info)
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).
Jump to [ Top · Hierarchy · Annotations ]
Root: DO Hierarchy (disease ontology from University of Maryland)
Jump to [ Top · Hierarchy ]
Supra-domain (Single)( show details)
Highlighted in gray are those with FDR>0.001
LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm
Jump to [ Top · Hierarchy ]
Supra-domain (Duplex) in N- to C-terminal order( show details)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
81324,53850
81324 - Voltage-gated potassium channels
53850 - Periplasmic binding protein-like II | 0 | DIRECT |
50729,50156
50729 - PH domain-like
50156 - PDZ domain-like | 0 | DIRECT |
53850,53850
53850 - Periplasmic binding protein-like II
53850 - Periplasmic binding protein-like II | 0 | DIRECT |
57414,57440
57414 - Hairpin loop containing domain-like
57440 - Kringle-like | 0 | DIRECT |
53822,53850
53822 - Periplasmic binding protein-like I
53850 - Periplasmic binding protein-like II | 0.0002983 | DIRECT |
57924,57924
57924 - Inhibitor of apoptosis (IAP) repeat
57924 - Inhibitor of apoptosis (IAP) repeat | 0.0002983 | DIRECT |
57424,57424
57424 - LDL receptor-like module
57424 - LDL receptor-like module | 0.004486 | INHERITED FROM: Alzheimer's disease || tauopathy |
57586,57586
57586 - TNF receptor-like
57586 - TNF receptor-like | 0.004936 | INHERITED FROM: multiple sclerosis |
57184,63825
57184 - Growth factor receptor domain
63825 - YWTD domain | 0.005787 | INHERITED FROM: Alzheimer's disease || tauopathy |
57424,57184
57424 - LDL receptor-like module
57184 - Growth factor receptor domain | 0.005787 | INHERITED FROM: Alzheimer's disease || tauopathy |
49723,48484
49723 - Lipase/lipooxygenase domain (PLAT/LH2 domain)
48484 - Lipoxigenase | 0.01273 | INHERITED FROM: Alzheimer's disease || tauopathy |
54452,48726
54452 - MHC antigen-recognition domain
48726 - Immunoglobulin | 0.03105 | INHERITED FROM: demyelinating disease || multiple sclerosis |
48371,48371
48371 - ARM repeat
48371 - ARM repeat | 0.08127 | INHERITED FROM: hereditary ataxia || ataxia telangiectasia || autosomal recessive cerebellar ataxia |
57440,57440
57440 - Kringle-like
57440 - Kringle-like | 0.1846 | INHERITED FROM: lateral sclerosis || amyotrophic lateral sclerosis |
48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.2074 | INHERITED FROM: demyelinating disease || multiple sclerosis |
49265,49265
49265 - Fibronectin type III
49265 - Fibronectin type III | 0.5824 | INHERITED FROM: demyelinating disease || multiple sclerosis |
63712,90112
63712 - Nicotinic receptor ligand binding domain-like
90112 - Neurotransmitter-gated ion-channel transmembrane pore | 1 | INHERITED FROM: Lewy body dementia |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
81324,53850
81324 - Voltage-gated potassium channels
53850 - Periplasmic binding protein-like II | 0 | Direct |
50729,50156
50729 - PH domain-like
50156 - PDZ domain-like | 0 | Direct |
53850,53850
53850 - Periplasmic binding protein-like II
53850 - Periplasmic binding protein-like II | 0 | Direct |
57414,57440
57414 - Hairpin loop containing domain-like
57440 - Kringle-like | 0 | Direct |
53822,53850
53822 - Periplasmic binding protein-like I
53850 - Periplasmic binding protein-like II | 0.0002983 | Direct |
57924,57924
57924 - Inhibitor of apoptosis (IAP) repeat
57924 - Inhibitor of apoptosis (IAP) repeat | 0.0002983 | Direct |
57424,57424
57424 - LDL receptor-like module
57424 - LDL receptor-like module | 0.004486 | Inherited |
57586,57586
57586 - TNF receptor-like
57586 - TNF receptor-like | 0.004936 | Inherited |
57184,63825
57184 - Growth factor receptor domain
63825 - YWTD domain | 0.005787 | Inherited |
57424,57184
57424 - LDL receptor-like module
57184 - Growth factor receptor domain | 0.005787 | Inherited |
49723,48484
49723 - Lipase/lipooxygenase domain (PLAT/LH2 domain)
48484 - Lipoxigenase | 0.01273 | Inherited |
54452,48726
54452 - MHC antigen-recognition domain
48726 - Immunoglobulin | 0.03105 | Inherited |
48371,48371
48371 - ARM repeat
48371 - ARM repeat | 0.08127 | Inherited |
57440,57440
57440 - Kringle-like
57440 - Kringle-like | 0.1846 | Inherited |
48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.2074 | Inherited |
49265,49265
49265 - Fibronectin type III
49265 - Fibronectin type III | 0.5824 | Inherited |
63712,90112
63712 - Nicotinic receptor ligand binding domain-like
90112 - Neurotransmitter-gated ion-channel transmembrane pore | 1 | Inherited |
LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm
Jump to [ Top · Hierarchy ]
Supra-domain (Triple) in N- to C-terminal order( show details)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57414,57440,57440
57414 - Hairpin loop containing domain-like
57440 - Kringle-like
57440 - Kringle-like | 0 | DIRECT |
57924,57924,57924
57924 - Inhibitor of apoptosis (IAP) repeat
57924 - Inhibitor of apoptosis (IAP) repeat
57924 - Inhibitor of apoptosis (IAP) repeat | 0 | DIRECT |
50729,50156,50156
50729 - PH domain-like
50156 - PDZ domain-like
50156 - PDZ domain-like | 0 | DIRECT |
57424,57184,63825
57424 - LDL receptor-like module
57184 - Growth factor receptor domain
63825 - YWTD domain | 0.001716 | INHERITED FROM: Alzheimer's disease || tauopathy |
57424,57424,57184
57424 - LDL receptor-like module
57424 - LDL receptor-like module
57184 - Growth factor receptor domain | 0.001716 | INHERITED FROM: Alzheimer's disease || tauopathy |
57424,57424,57424
57424 - LDL receptor-like module
57424 - LDL receptor-like module
57424 - LDL receptor-like module | 0.002807 | INHERITED FROM: Alzheimer's disease || tauopathy |
57440,57440,57440
57440 - Kringle-like
57440 - Kringle-like
57440 - Kringle-like | 0.2858 | INHERITED FROM: lateral sclerosis || amyotrophic lateral sclerosis |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57414,57440,57440
57414 - Hairpin loop containing domain-like
57440 - Kringle-like
57440 - Kringle-like | 0 | Direct |
57924,57924,57924
57924 - Inhibitor of apoptosis (IAP) repeat
57924 - Inhibitor of apoptosis (IAP) repeat
57924 - Inhibitor of apoptosis (IAP) repeat | 0 | Direct |
50729,50156,50156
50729 - PH domain-like
50156 - PDZ domain-like
50156 - PDZ domain-like | 0 | Direct |
57424,57184,63825
57424 - LDL receptor-like module
57184 - Growth factor receptor domain
63825 - YWTD domain | 0.001716 | Inherited |
57424,57424,57184
57424 - LDL receptor-like module
57424 - LDL receptor-like module
57184 - Growth factor receptor domain | 0.001716 | Inherited |
57424,57424,57424
57424 - LDL receptor-like module
57424 - LDL receptor-like module
57424 - LDL receptor-like module | 0.002807 | Inherited |
57440,57440,57440
57440 - Kringle-like
57440 - Kringle-like
57440 - Kringle-like | 0.2858 | Inherited |
LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm
Plot distribution on species Tree Of Life (sTOL) for Superfamily and/or Family domains annotated by this DO term
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Plot tree as:
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Download Newick format tree:
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( show help)
Trees by TreeVector
A presence/absence matrix is generated using protein domain
architecture data for all genomes in SUPERFAMILY. The PAUP
software is used to produce a single, large tree topology using
heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as
if individual trees had been produced. However, this data is extracted from the single
large tree. This produces a higher quality topology than if the trees had been produced
on their own, and allows the trees to be displayed instantly.
Plot distribution on species Tree Of Life (sTOL) for single supra-domains annotated by this DO term
|
Plot tree as:
| |
Download Newick format tree:
| |
Browsing in TREE OF LIFE:
|
( show help)
Trees by TreeVector
A presence/absence matrix is generated using protein domains and supradomains
for all genomes in SUPERFAMILY. The RAxML
software is used to produce a single, large tree topology using
heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as
if individual trees had been produced. However, this data is extracted from the single
large tree. This produces a higher quality topology than if the trees had been produced
on their own, and allows the trees to be displayed instantly.
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> BO Hierarchy > neurodegenerative disease
