Mammalian Phenotype (MP): liver/biliary system phenotype

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

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Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
Thioesterase/thiol ester dehydrase-isomerase	0	Direct
Nitric oxide (NO) synthase oxygenase domain	0	Direct
Hairpin loop containing domain-like	0	Direct
Nuclear receptor ligand-binding domain	0.000002946	Direct
(Trans)glycosidases	0.00002773	Direct
Glucocorticoid receptor-like (DNA-binding domain)	0.000511	Direct
Acyl-CoA dehydrogenase NM domain-like	0.0006138	Direct
Acyl-CoA dehydrogenase C-terminal domain-like	0.0006138	Direct
p53-like transcription factors	0.0008506	Direct
STAT	0.0008913	Direct
Transcription factor STAT-4 N-domain	0.0008913	Direct
Flavoproteins	0.0008913	Direct
Families 57/38 glycoside transferase middle domain	0.001008	Inherited
4-helical cytokines	0.001523	Inherited
HMA, heavy metal-associated domain	0.004685	Inherited
DHS-like NAD/FAD-binding domain	0.005076	Inherited
Alpha-macroglobulin receptor domain	0.008722	Inherited
Terpenoid cyclases/Protein prenyltransferases	0.009201	Inherited
Kringle-like	0.01462	Inherited
Multidrug efflux transporter AcrB transmembrane domain	0.01637	Inherited
Bet v1-like	0.01795	Inherited
SH2 domain	0.02434	Inherited
TNF receptor-like	0.02512	Inherited
DEATH domain	0.0333	Inherited
ABC transporter transmembrane region	0.04044	Inherited
Riboflavin synthase domain-like	0.05632	Inherited
Ferredoxin reductase-like, C-terminal NADP-linked domain	0.05632	Inherited
Leucine zipper domain	0.0649	Inherited
Cyclin-like	0.085	Inherited
YWTD domain	0.1186	Inherited
C-type lectin-like	0.1241	Inherited
WW domain	0.1289	Inherited
lambda repressor-like DNA-binding domains	0.1296	Inherited
A DNA-binding domain in eukaryotic transcription factors	0.169	Inherited
Trypsin-like serine proteases	0.3806	Inherited
Family A G protein-coupled receptor-like	0.8036	Inherited
Homeodomain-like	0.8137	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Family

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
Nitric oxide (NO) synthase oxygenase domain	0	Direct
Retinoblastoma tumor suppressor domains	0	Direct
Cytochrome p450 reductase N-terminal domain-like	0	Direct
Nuclear receptor ligand-binding domain	0.000002459	Direct
Nuclear receptor	0.00000478	Direct
Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains	0.0005994	Direct
STAT DNA-binding domain	0.0005994	Direct
Transcription factor STAT-4 N-domain	0.0005994	Direct
Sir2 family of transcriptional regulators	0.0005994	Direct
STAT	0.0005994	Direct
Medium chain acyl-CoA dehydrogenase-like, C-terminal domain	0.0005994	Direct
NADPH-cytochrome p450 reductase-like	0.0006665	Direct
alpha-mannosidase	0.0006665	Direct
alpha-mannosidase, domain 2	0.0006665	Direct
NADPH-cytochrome p450 reductase FAD-binding domain-like	0.0006665	Direct
Rel/Dorsal transcription factors, DNA-binding domain	0.001008	Inherited
HMA, heavy metal-associated domain	0.003279	Inherited
Fatty acid binding protein-like	0.003405	Inherited
Phoshoinositide 3-kinase (PI3K), catalytic domain	0.006273	Inherited
Complement components	0.006415	Inherited
Alpha-macroglobulin receptor domain	0.006415	Inherited
DEATH domain, DD	0.00673	Inherited
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0.009758	Inherited
Erythroid transcription factor GATA-1	0.01248	Inherited
ABC transporter ATPase domain-like	0.01411	Inherited
TNF receptor-like	0.02	Inherited
SH2 domain	0.02309	Inherited
p120GAP domain-like	0.03208	Inherited
Kringle modules	0.03533	Inherited
Forkhead DNA-binding domain	0.03699	Inherited
ABC transporter transmembrane region	0.04527	Inherited
Leucine zipper domain	0.05826	Inherited
YWTD domain	0.1029	Inherited
WW domain	0.1159	Inherited
A DNA-binding domain in eukaryotic transcription factors	0.1503	Inherited
Eukaryotic proteases	0.401	Inherited
Chaperone J-domain	0.4116	Inherited
Rhodopsin-like	0.6401	Inherited
Homeodomain	0.9615	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Supra-domain (Single|Duplex|Triple)

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Supra-domain (Single)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Hairpin loop containing domain-like	0	Direct
Nitric oxide (NO) synthase oxygenase domain	0	Direct
Thioesterase/thiol ester dehydrase-isomerase	0	Direct
Nuclear receptor ligand-binding domain	0.000001244	Direct
(Trans)glycosidases	0.00001272	Direct
Glucocorticoid receptor-like (DNA-binding domain)	0.0002707	Direct
Acyl-CoA dehydrogenase C-terminal domain-like	0.0003263	Direct
Acyl-CoA dehydrogenase NM domain-like	0.0003263	Direct
p53-like transcription factors	0.0004606	Direct
Transcription factor STAT-4 N-domain	0.0004831	Direct
Flavoproteins	0.0004831	Direct
STAT	0.0004831	Direct
Families 57/38 glycoside transferase middle domain	0.0005505	Direct
Protein kinase-like (PK-like)	0.0005688	Direct
4-helical cytokines	0.0008537	Direct
HMA, heavy metal-associated domain	0.002792	Inherited
DHS-like NAD/FAD-binding domain	0.00304	Inherited
Alpha-macroglobulin receptor domain	0.005392	Inherited
Terpenoid cyclases/Protein prenyltransferases	0.005709	Inherited
Kringle-like	0.009375	Inherited
Multidrug efflux transporter AcrB transmembrane domain	0.01059	Inherited
Bet v1-like	0.01169	Inherited
SH2 domain	0.01623	Inherited
TNF receptor-like	0.0168	Inherited
DEATH domain	0.02281	Inherited
ABC transporter transmembrane region	0.02812	Inherited
Riboflavin synthase domain-like	0.04026	Inherited
Ferredoxin reductase-like, C-terminal NADP-linked domain	0.04026	Inherited
Leucine zipper domain	0.04711	Inherited
Cyclin-like	0.06312	Inherited
EGF/Laminin	0.06533	Inherited
Insulin-like	0.07407	Inherited
YWTD domain	0.09132	Inherited
C-type lectin-like	0.09605	Inherited
WW domain	0.1002	Inherited
lambda repressor-like DNA-binding domains	0.1008	Inherited
A DNA-binding domain in eukaryotic transcription factors	0.1352	Inherited
Trypsin-like serine proteases	0.3344	Inherited
Chaperone J-domain	0.3794	Inherited
Family A G protein-coupled receptor-like	0.769	Inherited
Homeodomain-like	0.7798	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

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Supra-domain (Duplex) in N- to C-terminal order

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
57196,57424 57196 - EGF/Laminin 57424 - LDL receptor-like module	0	Direct
57414,57440 57414 - Hairpin loop containing domain-like 57440 - Kringle-like	0	Direct
54637,54637 54637 - Thioesterase/thiol ester dehydrase-isomerase 54637 - Thioesterase/thiol ester dehydrase-isomerase	0	Direct
52980,47781 52980 - Restriction endonuclease-like 47781 - RuvA domain 2-like	0	Direct
57716,48508 57716 - Glucocorticoid receptor-like (DNA-binding domain) 48508 - Nuclear receptor ligand-binding domain	0.00001272	Direct
56645,47203 56645 - Acyl-CoA dehydrogenase NM domain-like 47203 - Acyl-CoA dehydrogenase C-terminal domain-like	0.0003263	Direct
47655,49417 47655 - STAT 49417 - p53-like transcription factors	0.0004831	Direct
48092,47655 48092 - Transcription factor STAT-4 N-domain 47655 - STAT	0.0004831	Direct
49417,55550 49417 - p53-like transcription factors 55550 - SH2 domain	0.0004831	Direct
88713,88688 88713 - Glycoside hydrolase/deacetylase 88688 - Families 57/38 glycoside transferase middle domain	0.0005505	Direct
49417,81296 49417 - p53-like transcription factors 81296 - E set domains	0.0008	Direct
57440,50494 57440 - Kringle-like 50494 - Trypsin-like serine proteases	0.001367	Inherited
57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module	0.004221	Inherited
63825,57196 63825 - YWTD domain 57196 - EGF/Laminin	0.01805	Inherited
103473,100895 103473 - MFS general substrate transporter 100895 - Kazal-type serine protease inhibitors	0.01954	Inherited
90123,52540 90123 - ABC transporter transmembrane region 52540 - P-loop containing nucleoside triphosphate hydrolases	0.02812	Inherited
49265,49265 49265 - Fibronectin type III 49265 - Fibronectin type III	0.07167	Inherited
51045,51045 51045 - WW domain 51045 - WW domain	0.07198	Inherited
47454,57959 47454 - A DNA-binding domain in eukaryotic transcription factors 57959 - Leucine zipper domain	0.2531	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

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Supra-domain (Triple) in N- to C-terminal order

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
49503,49503,49503 49503 - Cupredoxins 49503 - Cupredoxins 49503 - Cupredoxins	0	Direct
57414,57440,57440 57414 - Hairpin loop containing domain-like 57440 - Kringle-like 57440 - Kringle-like	0	Direct
57196,57424,57424 57196 - EGF/Laminin 57424 - LDL receptor-like module 57424 - LDL receptor-like module	0	Direct
63825,57196,57424 63825 - YWTD domain 57196 - EGF/Laminin 57424 - LDL receptor-like module	0	Direct
48092,47655,49417 48092 - Transcription factor STAT-4 N-domain 47655 - STAT 49417 - p53-like transcription factors	0.0004831	Direct
47655,49417,55550 47655 - STAT 49417 - p53-like transcription factors 55550 - SH2 domain	0.0004831	Direct
57424,57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module 57424 - LDL receptor-like module	0.002687	Inherited
57586,57586,57586 57586 - TNF receptor-like 57586 - TNF receptor-like 57586 - TNF receptor-like	0.009141	Inherited
57196,63825,57196 57196 - EGF/Laminin 63825 - YWTD domain 57196 - EGF/Laminin	0.01954	Inherited
63825,57196,63825 63825 - YWTD domain 57196 - EGF/Laminin 63825 - YWTD domain	0.01954	Inherited