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CTD Chemicals (CC): Cholanes 
(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: CC Hierarchy (CTD chemicals from Comparative Toxicogenomics Database)
| Shortest distance to current term (+ for parents, - for children) |
CC term [CC ID] <#Children> |
#Domains (Superfamily|Family) |
#Supra-domain (Single|Duplex|Triple) |
| + + + + 4: | Chemicals [MESH:D] <13> |
| + + + 3: | Polycyclic Compounds [MESH:D011083] <191> | (419|579) |
(431|390|204) |
| + + 2: | Fused-Ring Compounds [MESH:D000072473] <2> | (146|200) |
(156|135|57) |
| + 1: | Steroids [MESH:D013256] <415> | (116|152) |
(126|85|35) |
| 0: | Cholanes [MESH:D002757] <20> | (28|33) |
(32|24|10) |
| - 1: | Cholic Acids [MESH:D002793] <107> | (28|33) |
(31|24|10) |
| - 1: | Cholenes [MESH:D002770] <17> | (0|0) |
(0|0|0) |
| - 1: | 2,3,6,7-tetrahydroxycholanoic acid [MESH:C035926] | (0|0) |
(0|0|0) |
| - 1: | 23-(isopropyltelluro)-24-norcholan-3-ol [MESH:C024561] | (0|0) |
(0|0|0) |
| - 1: | 23-(trimethylstannyl)-24-norcholan-3-ol [MESH:C039373] | (0|0) |
(0|0|0) |
| - 1: | 24-norcholan-2,3,24-tryl-2,3,23-sulfuric acid [MESH:C562251] | (0|0) |
(0|0|0) |
| - 1: | 3,6,7,12-tetrahydroxycholanoic acid [MESH:C035925] | (0|0) |
(0|0|0) |
| - 1: | 3,7,12-triformoxycholan-24-al [MESH:C073868] | (0|0) |
(0|0|0) |
| - 1: | 3,7,12-trihydroxy-24-norcholan-23-sulfonate [MESH:C102743] | (0|0) |
(0|0|0) |
| - 1: | 3-tosyloxycholan-24-ol [MESH:C544815] | (0|0) |
(0|0|0) |
| - 1: | 7-hydroxy-3,12-dioxocholan-24-oic acid [MESH:C013035] | (0|0) |
(0|0|0) |
| - 1: | 7-methylchenooxazoline [MESH:C037264] | (0|0) |
(0|0|0) |
| - 1: | BAR502 [MESH:C000656652] | (0|0) |
(0|0|0) |
| - 1: | N-(3-hydroxypropyl) 3,12-dihydroxycholan-24-amide [MESH:C524700] | (0|0) |
(0|0|0) |
| - 1: | chenooxazoline [MESH:C037265] | (0|0) |
(0|0|0) |
| - 1: | cholan-2,3,24-tryl-2,3,24-trisulfate [MESH:C561233] | (0|0) |
(0|0|0) |
| - 1: | cholan-24-ol [MESH:C544816] | (0|0) |
(0|0|0) |
| - 1: | cholan-24-yl tosylate [MESH:C544817] | (0|0) |
(0|0|0) |
| - 1: | hyodeoxyoxazoline [MESH:C042066] | (0|0) |
(0|0|0) |
| - 1: | lithooxazoline [MESH:C037266] | (0|0) |
(0|0|0) |
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) |
57716,48508
57716 - Glucocorticoid receptor-like (DNA-binding domain)
48508 - Nuclear receptor ligand-binding domain | 0.00000002397 | DIRECT |
47986,52129
47986 - DEATH domain
52129 - Caspase-like | 0.00000004229 | DIRECT |
51905,55424
51905 - FAD/NAD(P)-binding domain
55424 - FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 0.00001162 | DIRECT |
47454,57959
47454 - A DNA-binding domain in eukaryotic transcription factors
57959 - Leucine zipper domain | 0.0000157 | DIRECT |
53901,53901
53901 - Thiolase-like
53901 - Thiolase-like | 0.00002065 | DIRECT |
90123,52540
90123 - ABC transporter transmembrane region
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.00002615 | DIRECT |
56112,56112
56112 - Protein kinase-like (PK-like)
56112 - Protein kinase-like (PK-like) | 0.00005623 | DIRECT |
56645,47203
56645 - Acyl-CoA dehydrogenase NM domain-like
47203 - Acyl-CoA dehydrogenase C-terminal domain-like | 0.00007616 | DIRECT |
47203,47203
47203 - Acyl-CoA dehydrogenase C-terminal domain-like
47203 - Acyl-CoA dehydrogenase C-terminal domain-like | 0.0001456 | DIRECT |
52777,52777
52777 - CoA-dependent acyltransferases
52777 - CoA-dependent acyltransferases | 0.0003861 | DIRECT |
57440,57440
57440 - Kringle-like
57440 - Kringle-like | 0.0009509 | DIRECT |
50729,56112
50729 - PH domain-like
56112 - Protein kinase-like (PK-like) | 0.00169 | INHERITED FROM: Cholic Acids |
57196,69687
57196 - EGF/Laminin
69687 - Integrin beta tail domain | 0.00169 | INHERITED FROM: Cholic Acids |
47986,47986
47986 - DEATH domain
47986 - DEATH domain | 0.00169 | INHERITED FROM: Cholic Acids || Chenodeoxycholic Acid || Deoxycholic Acid |
55785,55785
55785 - PYP-like sensor domain (PAS domain)
55785 - PYP-like sensor domain (PAS domain) | 0.00169 | INHERITED FROM: Chenodeoxycholic Acid || Deoxycholic Acid |
57889,57889
57889 - Cysteine-rich domain
57889 - Cysteine-rich domain | 0.001714 | INHERITED FROM: Cholic Acids || Deoxycholic Acid |
103473,100895
103473 - MFS general substrate transporter
100895 - Kazal-type serine protease inhibitors | 0.003501 | INHERITED FROM: Lithocholic Acid |
57535,57535
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.00365 | INHERITED FROM: Cholic Acids |
49417,81296
49417 - p53-like transcription factors
81296 - E set domains | 0.006233 | INHERITED FROM: Deoxycholic Acid |
47459,55785
47459 - HLH, helix-loop-helix DNA-binding domain
55785 - PYP-like sensor domain (PAS domain) | 0.006454 | INHERITED FROM: Chenodeoxycholic Acid || Deoxycholic Acid |
52540,90123
52540 - P-loop containing nucleoside triphosphate hydrolases
90123 - ABC transporter transmembrane region | 0.009994 | INHERITED FROM: Deoxycholic Acid |
47954,47954
47954 - Cyclin-like
47954 - Cyclin-like | 0.0123 | INHERITED FROM: Ursodeoxycholic Acid || HS 1183 || HS-1199 || HS 1200 || HS 1030 |
69179,69179
69179 - Integrin domains
69179 - Integrin domains | 0.04588 | INHERITED FROM: Lithocholic Acid |
69318,69179
69318 - Integrin alpha N-terminal domain
69179 - Integrin domains | 0.04588 | INHERITED FROM: Lithocholic Acid |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57716,48508
57716 - Glucocorticoid receptor-like (DNA-binding domain)
48508 - Nuclear receptor ligand-binding domain | 0.00000002397 | Direct |
47986,52129
47986 - DEATH domain
52129 - Caspase-like | 0.00000004229 | Direct |
51905,55424
51905 - FAD/NAD(P)-binding domain
55424 - FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 0.00001162 | Direct |
47454,57959
47454 - A DNA-binding domain in eukaryotic transcription factors
57959 - Leucine zipper domain | 0.0000157 | Direct |
53901,53901
53901 - Thiolase-like
53901 - Thiolase-like | 0.00002065 | Direct |
90123,52540
90123 - ABC transporter transmembrane region
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.00002615 | Direct |
56112,56112
56112 - Protein kinase-like (PK-like)
56112 - Protein kinase-like (PK-like) | 0.00005623 | Direct |
56645,47203
56645 - Acyl-CoA dehydrogenase NM domain-like
47203 - Acyl-CoA dehydrogenase C-terminal domain-like | 0.00007616 | Direct |
47203,47203
47203 - Acyl-CoA dehydrogenase C-terminal domain-like
47203 - Acyl-CoA dehydrogenase C-terminal domain-like | 0.0001456 | Direct |
52777,52777
52777 - CoA-dependent acyltransferases
52777 - CoA-dependent acyltransferases | 0.0003861 | Direct |
57440,57440
57440 - Kringle-like
57440 - Kringle-like | 0.0009509 | Direct |
50729,56112
50729 - PH domain-like
56112 - Protein kinase-like (PK-like) | 0.00169 | Inherited |
57196,69687
57196 - EGF/Laminin
69687 - Integrin beta tail domain | 0.00169 | Inherited |
47986,47986
47986 - DEATH domain
47986 - DEATH domain | 0.00169 | Inherited |
55785,55785
55785 - PYP-like sensor domain (PAS domain)
55785 - PYP-like sensor domain (PAS domain) | 0.00169 | Inherited |
57889,57889
57889 - Cysteine-rich domain
57889 - Cysteine-rich domain | 0.001714 | Inherited |
103473,100895
103473 - MFS general substrate transporter
100895 - Kazal-type serine protease inhibitors | 0.003501 | Inherited |
57535,57535
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.00365 | Inherited |
49417,81296
49417 - p53-like transcription factors
81296 - E set domains | 0.006233 | Inherited |
47459,55785
47459 - HLH, helix-loop-helix DNA-binding domain
55785 - PYP-like sensor domain (PAS domain) | 0.006454 | Inherited |
52540,90123
52540 - P-loop containing nucleoside triphosphate hydrolases
90123 - ABC transporter transmembrane region | 0.009994 | Inherited |
47954,47954
47954 - Cyclin-like
47954 - Cyclin-like | 0.0123 | Inherited |
69179,69179
69179 - Integrin domains
69179 - Integrin domains | 0.04588 | Inherited |
69318,69179
69318 - Integrin alpha N-terminal domain
69179 - Integrin domains | 0.04588 | 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) |
47986,47986,52129
47986 - DEATH domain
47986 - DEATH domain
52129 - Caspase-like | 0 | DIRECT |
57440,57440,57440
57440 - Kringle-like
57440 - Kringle-like
57440 - Kringle-like | 0.00006225 | DIRECT |
56645,47203,47203
56645 - Acyl-CoA dehydrogenase NM domain-like
47203 - Acyl-CoA dehydrogenase C-terminal domain-like
47203 - Acyl-CoA dehydrogenase C-terminal domain-like | 0.0001456 | DIRECT |
57535,57535,57535
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.001654 | INHERITED FROM: Cholic Acids |
47459,55785,55785
47459 - HLH, helix-loop-helix DNA-binding domain
55785 - PYP-like sensor domain (PAS domain)
55785 - PYP-like sensor domain (PAS domain) | 0.00169 | INHERITED FROM: Cholic Acids || Chenodeoxycholic Acid || Deoxycholic Acid |
57196,57196,69687
57196 - EGF/Laminin
57196 - EGF/Laminin
69687 - Integrin beta tail domain | 0.00169 | INHERITED FROM: Cholic Acids |
52540,90123,52540
52540 - P-loop containing nucleoside triphosphate hydrolases
90123 - ABC transporter transmembrane region
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.009994 | INHERITED FROM: Deoxycholic Acid |
90123,52540,90123
90123 - ABC transporter transmembrane region
52540 - P-loop containing nucleoside triphosphate hydrolases
90123 - ABC transporter transmembrane region | 0.009994 | INHERITED FROM: Deoxycholic Acid |
69179,69179,69179
69179 - Integrin domains
69179 - Integrin domains
69179 - Integrin domains | 0.04588 | INHERITED FROM: Lithocholic Acid |
69318,69179,69179
69318 - Integrin alpha N-terminal domain
69179 - Integrin domains
69179 - Integrin domains | 0.04588 | INHERITED FROM: Lithocholic Acid |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
47986,47986,52129
47986 - DEATH domain
47986 - DEATH domain
52129 - Caspase-like | 0 | Direct |
57440,57440,57440
57440 - Kringle-like
57440 - Kringle-like
57440 - Kringle-like | 0.00006225 | Direct |
56645,47203,47203
56645 - Acyl-CoA dehydrogenase NM domain-like
47203 - Acyl-CoA dehydrogenase C-terminal domain-like
47203 - Acyl-CoA dehydrogenase C-terminal domain-like | 0.0001456 | Direct |
57535,57535,57535
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.001654 | Inherited |
47459,55785,55785
47459 - HLH, helix-loop-helix DNA-binding domain
55785 - PYP-like sensor domain (PAS domain)
55785 - PYP-like sensor domain (PAS domain) | 0.00169 | Inherited |
57196,57196,69687
57196 - EGF/Laminin
57196 - EGF/Laminin
69687 - Integrin beta tail domain | 0.00169 | Inherited |
52540,90123,52540
52540 - P-loop containing nucleoside triphosphate hydrolases
90123 - ABC transporter transmembrane region
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.009994 | Inherited |
90123,52540,90123
90123 - ABC transporter transmembrane region
52540 - P-loop containing nucleoside triphosphate hydrolases
90123 - ABC transporter transmembrane region | 0.009994 | Inherited |
69179,69179,69179
69179 - Integrin domains
69179 - Integrin domains
69179 - Integrin domains | 0.04588 | Inherited |
69318,69179,69179
69318 - Integrin alpha N-terminal domain
69179 - Integrin domains
69179 - Integrin domains | 0.04588 | 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:
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( 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 > Cholanes
