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CTD Chemicals (CC): Therapeutic Uses 
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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: CC Hierarchy (CTD chemicals from Comparative Toxicogenomics Database)
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) |
57889,49562
57889 - Cysteine-rich domain
49562 - C2 domain (Calcium/lipid-binding domain, CaLB) | 0 | DIRECT |
47576,48065
47576 - Calponin-homology domain, CH-domain
48065 - DBL homology domain (DH-domain) | 0 | DIRECT |
54452,48726
54452 - MHC antigen-recognition domain
48726 - Immunoglobulin | 0.00000006342 | DIRECT |
52540,48340
52540 - P-loop containing nucleoside triphosphate hydrolases
48340 - Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain | 0.00006987 | DIRECT |
48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.000274 | DIRECT |
48065,50729
48065 - DBL homology domain (DH-domain)
50729 - PH domain-like | 0.0123 | INHERITED FROM: Antirheumatic Agents |
55550,55550
55550 - SH2 domain
55550 - SH2 domain | 0.0145 | INHERITED FROM: Antirheumatic Agents |
57184,52058
57184 - Growth factor receptor domain
52058 - L domain-like | 0.0145 | INHERITED FROM: Antineoplastic Agents |
52058,57184
52058 - L domain-like
57184 - Growth factor receptor domain | 0.0145 | INHERITED FROM: Antineoplastic Agents |
57889,48350
57889 - Cysteine-rich domain
48350 - GTPase activation domain, GAP | 0.02728 | INHERITED FROM: Antirheumatic Agents |
57630,57196
57630 - GLA-domain
57196 - EGF/Laminin | 0.03183 | INHERITED FROM: Reproductive Control Agents |
90123,52540
90123 - ABC transporter transmembrane region
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.1292 | INHERITED FROM: Anticonvulsants || Central Nervous System Agents |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57889,49562
57889 - Cysteine-rich domain
49562 - C2 domain (Calcium/lipid-binding domain, CaLB) | 0 | Direct |
47576,48065
47576 - Calponin-homology domain, CH-domain
48065 - DBL homology domain (DH-domain) | 0 | Direct |
54452,48726
54452 - MHC antigen-recognition domain
48726 - Immunoglobulin | 0.00000006342 | Direct |
52540,48340
52540 - P-loop containing nucleoside triphosphate hydrolases
48340 - Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain | 0.00006987 | Direct |
48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.000274 | Direct |
48065,50729
48065 - DBL homology domain (DH-domain)
50729 - PH domain-like | 0.0123 | Inherited |
55550,55550
55550 - SH2 domain
55550 - SH2 domain | 0.0145 | Inherited |
57184,52058
57184 - Growth factor receptor domain
52058 - L domain-like | 0.0145 | Inherited |
52058,57184
52058 - L domain-like
57184 - Growth factor receptor domain | 0.0145 | Inherited |
57889,48350
57889 - Cysteine-rich domain
48350 - GTPase activation domain, GAP | 0.02728 | Inherited |
57630,57196
57630 - GLA-domain
57196 - EGF/Laminin | 0.03183 | Inherited |
90123,52540
90123 - ABC transporter transmembrane region
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.1292 | 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) |
57889,57889,49562
57889 - Cysteine-rich domain
57889 - Cysteine-rich domain
49562 - C2 domain (Calcium/lipid-binding domain, CaLB) | 0 | DIRECT |
50729,49562,48350
50729 - PH domain-like
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
48350 - GTPase activation domain, GAP | 0 | DIRECT |
47986,47986,52129
47986 - DEATH domain
47986 - DEATH domain
52129 - Caspase-like | 0 | DIRECT |
47576,48065,50729
47576 - Calponin-homology domain, CH-domain
48065 - DBL homology domain (DH-domain)
50729 - PH domain-like | 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 | 0.0145 | INHERITED FROM: Antineoplastic Agents |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57889,57889,49562
57889 - Cysteine-rich domain
57889 - Cysteine-rich domain
49562 - C2 domain (Calcium/lipid-binding domain, CaLB) | 0 | Direct |
50729,49562,48350
50729 - PH domain-like
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
48350 - GTPase activation domain, GAP | 0 | Direct |
47986,47986,52129
47986 - DEATH domain
47986 - DEATH domain
52129 - Caspase-like | 0 | Direct |
47576,48065,50729
47576 - Calponin-homology domain, CH-domain
48065 - DBL homology domain (DH-domain)
50729 - PH domain-like | 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 | 0.0145 | 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 CC 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 CC 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 > Therapeutic Uses
