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CTD Chemicals (CC): Sodium Compounds 
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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) |
100920,100934
100920 - Heat shock protein 70kD (HSP70), peptide-binding domain
100934 - Heat shock protein 70kD (HSP70), C-terminal subdomain | 0 | DIRECT |
103637,103637
103637 - CCHHC domain
103637 - CCHHC domain | 0 | DIRECT |
54236,57889
54236 - Ubiquitin-like
57889 - Cysteine-rich domain | 0 | DIRECT |
57414,57440
57414 - Hairpin loop containing domain-like
57440 - Kringle-like | 0 | DIRECT |
49417,47719
49417 - p53-like transcription factors
47719 - p53 tetramerization domain | 0 | DIRECT |
53850,53850
53850 - Periplasmic binding protein-like II
53850 - Periplasmic binding protein-like II | 0 | DIRECT |
49899,63887
49899 - Concanavalin A-like lectins/glucanases
63887 - P-domain of calnexin/calreticulin | 0 | DIRECT |
48403,47986
48403 - Ankyrin repeat
47986 - DEATH domain | 0 | DIRECT |
82895,57424
82895 - TSP-1 type 1 repeat
57424 - LDL receptor-like module | 0 | DIRECT |
49265,56112
49265 - Fibronectin type III
56112 - Protein kinase-like (PK-like) | 0 | DIRECT |
57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.00009119 | DIRECT |
49417,81296
49417 - p53-like transcription factors
81296 - E set domains | 0.0001382 | DIRECT |
53067,100920
53067 - Actin-like ATPase domain
100920 - Heat shock protein 70kD (HSP70), peptide-binding domain | 0.0001382 | DIRECT |
57440,50494
57440 - Kringle-like
50494 - Trypsin-like serine proteases | 0.000377 | DIRECT |
57440,57440
57440 - Kringle-like
57440 - Kringle-like | 0.0004744 | DIRECT |
52799,52799
52799 - (Phosphotyrosine protein) phosphatases II
52799 - (Phosphotyrosine protein) phosphatases II | 0.0006548 | DIRECT |
50044,55550
50044 - SH3-domain
55550 - SH2 domain | 0.0009191 | DIRECT |
57184,52058
57184 - Growth factor receptor domain
52058 - L domain-like | 0.00271 | INHERITED FROM: sodium arsenite |
52058,57184
52058 - L domain-like
57184 - Growth factor receptor domain | 0.00271 | INHERITED FROM: sodium arsenite |
51905,55424
51905 - FAD/NAD(P)-binding domain
55424 - FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 0.1247 | INHERITED FROM: Sodium Selenite |
57850,57845
57850 - RING/U-box
57845 - B-box zinc-binding domain | 1 | INHERITED FROM: Sodium Hydroxide |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
100920,100934
100920 - Heat shock protein 70kD (HSP70), peptide-binding domain
100934 - Heat shock protein 70kD (HSP70), C-terminal subdomain | 0 | Direct |
103637,103637
103637 - CCHHC domain
103637 - CCHHC domain | 0 | Direct |
54236,57889
54236 - Ubiquitin-like
57889 - Cysteine-rich domain | 0 | Direct |
57414,57440
57414 - Hairpin loop containing domain-like
57440 - Kringle-like | 0 | Direct |
49417,47719
49417 - p53-like transcription factors
47719 - p53 tetramerization domain | 0 | Direct |
53850,53850
53850 - Periplasmic binding protein-like II
53850 - Periplasmic binding protein-like II | 0 | Direct |
49899,63887
49899 - Concanavalin A-like lectins/glucanases
63887 - P-domain of calnexin/calreticulin | 0 | Direct |
48403,47986
48403 - Ankyrin repeat
47986 - DEATH domain | 0 | Direct |
82895,57424
82895 - TSP-1 type 1 repeat
57424 - LDL receptor-like module | 0 | Direct |
49265,56112
49265 - Fibronectin type III
56112 - Protein kinase-like (PK-like) | 0 | Direct |
57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.00009119 | Direct |
49417,81296
49417 - p53-like transcription factors
81296 - E set domains | 0.0001382 | Direct |
53067,100920
53067 - Actin-like ATPase domain
100920 - Heat shock protein 70kD (HSP70), peptide-binding domain | 0.0001382 | Direct |
57440,50494
57440 - Kringle-like
50494 - Trypsin-like serine proteases | 0.000377 | Direct |
57440,57440
57440 - Kringle-like
57440 - Kringle-like | 0.0004744 | Direct |
52799,52799
52799 - (Phosphotyrosine protein) phosphatases II
52799 - (Phosphotyrosine protein) phosphatases II | 0.0006548 | Direct |
50044,55550
50044 - SH3-domain
55550 - SH2 domain | 0.0009191 | Direct |
57184,52058
57184 - Growth factor receptor domain
52058 - L domain-like | 0.00271 | Inherited |
52058,57184
52058 - L domain-like
57184 - Growth factor receptor domain | 0.00271 | Inherited |
51905,55424
51905 - FAD/NAD(P)-binding domain
55424 - FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 0.1247 | Inherited |
57850,57845
57850 - RING/U-box
57845 - B-box zinc-binding domain | 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) |
48726,49265,56112
48726 - Immunoglobulin
49265 - Fibronectin type III
56112 - Protein kinase-like (PK-like) | 0 | DIRECT |
47986,47986,52129
47986 - DEATH domain
47986 - DEATH domain
52129 - Caspase-like | 0 | DIRECT |
48552,48552,48552
48552 - Serum albumin-like
48552 - Serum albumin-like
48552 - Serum albumin-like | 0 | DIRECT |
49265,48726,48726
49265 - Fibronectin type III
48726 - Immunoglobulin
48726 - Immunoglobulin | 0 | DIRECT |
49785,57184,49265
49785 - Galactose-binding domain-like
57184 - Growth factor receptor domain
49265 - Fibronectin type III | 0 | DIRECT |
57414,57440,57440
57414 - Hairpin loop containing domain-like
57440 - Kringle-like
57440 - Kringle-like | 0 | DIRECT |
53067,100920,100934
53067 - Actin-like ATPase domain
100920 - Heat shock protein 70kD (HSP70), peptide-binding domain
100934 - Heat shock protein 70kD (HSP70), C-terminal subdomain | 0 | DIRECT |
103637,103637,103637
103637 - CCHHC domain
103637 - CCHHC domain
103637 - CCHHC domain | 0 | DIRECT |
49899,57196,49899
49899 - Concanavalin A-like lectins/glucanases
57196 - EGF/Laminin
49899 - Concanavalin A-like lectins/glucanases | 0 | DIRECT |
75399,75399,75399
75399 - Plakin repeat
75399 - Plakin repeat
75399 - Plakin repeat | 0 | DIRECT |
57440,57440,50494
57440 - Kringle-like
57440 - Kringle-like
50494 - Trypsin-like serine proteases | 0 | DIRECT |
57184,52058,57184
57184 - Growth factor receptor domain
52058 - L domain-like
57184 - Growth factor receptor domain | 0 | DIRECT |
53067,53067,100920
53067 - Actin-like ATPase domain
53067 - Actin-like ATPase domain
100920 - Heat shock protein 70kD (HSP70), peptide-binding domain | 0.0001382 | DIRECT |
52058,57184,52058
52058 - L domain-like
57184 - Growth factor receptor domain
52058 - L domain-like | 0.00271 | INHERITED FROM: sodium arsenite |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
48726,49265,56112
48726 - Immunoglobulin
49265 - Fibronectin type III
56112 - Protein kinase-like (PK-like) | 0 | Direct |
47986,47986,52129
47986 - DEATH domain
47986 - DEATH domain
52129 - Caspase-like | 0 | Direct |
48552,48552,48552
48552 - Serum albumin-like
48552 - Serum albumin-like
48552 - Serum albumin-like | 0 | Direct |
49265,48726,48726
49265 - Fibronectin type III
48726 - Immunoglobulin
48726 - Immunoglobulin | 0 | Direct |
49785,57184,49265
49785 - Galactose-binding domain-like
57184 - Growth factor receptor domain
49265 - Fibronectin type III | 0 | Direct |
57414,57440,57440
57414 - Hairpin loop containing domain-like
57440 - Kringle-like
57440 - Kringle-like | 0 | Direct |
53067,100920,100934
53067 - Actin-like ATPase domain
100920 - Heat shock protein 70kD (HSP70), peptide-binding domain
100934 - Heat shock protein 70kD (HSP70), C-terminal subdomain | 0 | Direct |
103637,103637,103637
103637 - CCHHC domain
103637 - CCHHC domain
103637 - CCHHC domain | 0 | Direct |
49899,57196,49899
49899 - Concanavalin A-like lectins/glucanases
57196 - EGF/Laminin
49899 - Concanavalin A-like lectins/glucanases | 0 | Direct |
75399,75399,75399
75399 - Plakin repeat
75399 - Plakin repeat
75399 - Plakin repeat | 0 | Direct |
57440,57440,50494
57440 - Kringle-like
57440 - Kringle-like
50494 - Trypsin-like serine proteases | 0 | Direct |
57184,52058,57184
57184 - Growth factor receptor domain
52058 - L domain-like
57184 - Growth factor receptor domain | 0 | Direct |
53067,53067,100920
53067 - Actin-like ATPase domain
53067 - Actin-like ATPase domain
100920 - Heat shock protein 70kD (HSP70), peptide-binding domain | 0.0001382 | Direct |
52058,57184,52058
52058 - L domain-like
57184 - Growth factor receptor domain
52058 - L domain-like | 0.00271 | 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
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Plot tree as:
| |
Download Newick format tree:
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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 > Sodium Compounds
