CTD Chemicals (CC): Nicotinic Acids

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)
Protein kinase-like (PK-like)	0.00000000493	Direct
Bcl-2 inhibitors of programmed cell death	0.000006676	Direct
4-helical cytokines	0.00001557	Direct
Cyclin-like	0.00001946	Direct
ABC transporter transmembrane region	0.00002879	Direct
Inhibitor of apoptosis (IAP) repeat	0.00003843	Direct
Nuclear receptor ligand-binding domain	0.00003878	Direct
DHS-like NAD/FAD-binding domain	0.0002779	Direct
Caspase-like	0.0003883	Direct
SCOP hierarchy in SUPERFAMILY	0.000687	Direct
STAT	0.001174	Inherited
Transcription factor STAT-4 N-domain	0.001174	Inherited
p53-like transcription factors	0.00129	Inherited
SH2 domain	0.006747	Inherited
DEATH domain	0.03001	Inherited
Voltage-gated potassium channels	0.4284	Inherited
MFS general substrate transporter	0.4541	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Family

Jump to [ Top · Hierarchy ]

Family

(show details)

SCOP term	FDR (all)	Annotation (direct or inherited)
Protein kinases, catalytic subunit	0.0000004033	Direct
ABC transporter ATPase domain-like	0.000006459	Direct
Bcl-2 inhibitors of programmed cell death	0.000006758	Direct
Sir2 family of transcriptional regulators	0.000006852	Direct
Cyclin	0.00002185	Direct
Nuclear receptor	0.00002559	Direct
ABC transporter transmembrane region	0.0000296	Direct
Inhibitor of apoptosis (IAP) repeat	0.00003632	Direct
Nuclear receptor ligand-binding domain	0.0000466	Direct
Caspase catalytic domain	0.0002337	Direct
Phoshoinositide 3-kinase (PI3K), catalytic domain	0.0009928	Direct
STAT	0.001126	Inherited
Transcription factor STAT-4 N-domain	0.001126	Inherited
STAT DNA-binding domain	0.001126	Inherited
Long-chain cytokines	0.002325	Inherited
SH2 domain	0.007913	Inherited
Voltage-gated potassium channels	0.1839	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)
Protein kinase-like (PK-like)	0.000000002054	Direct
Bcl-2 inhibitors of programmed cell death	0.000003241	Direct
4-helical cytokines	0.000007769	Direct
Cyclin-like	0.000009797	Direct
ABC transporter transmembrane region	0.00001468	Direct
Inhibitor of apoptosis (IAP) repeat	0.00001982	Direct
Nuclear receptor ligand-binding domain	0.00002	Direct
DHS-like NAD/FAD-binding domain	0.0001558	Direct
Caspase-like	0.0002211	Direct
Transcription factor STAT-4 N-domain	0.0007068	Direct
STAT	0.0007068	Direct
p53-like transcription factors	0.0007809	Direct
SH2 domain	0.004447	Inherited
DEATH domain	0.02156	Inherited
Voltage-gated potassium channels	0.3654	Inherited
MFS general substrate transporter	0.3893	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)
57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat	0.000003614	Direct
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like	0.0000103	Direct
90123,52540 90123 - ABC transporter transmembrane region 52540 - P-loop containing nucleoside triphosphate hydrolases	0.00001468	Direct
57716,48508 57716 - Glucocorticoid receptor-like (DNA-binding domain) 48508 - Nuclear receptor ligand-binding domain	0.0001394	Direct
57440,57440 57440 - Kringle-like 57440 - Kringle-like	0.0003229	Direct
47655,49417 47655 - STAT 49417 - p53-like transcription factors	0.0007068	Direct
81324,81324 81324 - Voltage-gated potassium channels 81324 - Voltage-gated potassium channels	0.0007068	Direct
49417,55550 49417 - p53-like transcription factors 55550 - SH2 domain	0.0007068	Direct
48092,47655 48092 - Transcription factor STAT-4 N-domain 47655 - STAT	0.0007068	Direct
47986,52129 47986 - DEATH domain 52129 - Caspase-like	0.004486	Inherited
50044,55550 50044 - SH3-domain 55550 - SH2 domain	0.00476	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)
57924,57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat	0.00005807	Direct
57440,57440,57440 57440 - Kringle-like 57440 - Kringle-like 57440 - Kringle-like	0.0007068	Direct
48092,47655,49417 48092 - Transcription factor STAT-4 N-domain 47655 - STAT 49417 - p53-like transcription factors	0.0007068	Direct
47655,49417,55550 47655 - STAT 49417 - p53-like transcription factors 55550 - SH2 domain	0.0007068	Direct
50044,55550,56112 50044 - SH3-domain 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.009808	Inherited