|
Xenopus ANatomical entity (XAN): viscus
(show info)
Phenotype Ontology
Like Gene Ontology (GO), phenotypy 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. Phenotype ontologies we have incorporated are as follows:
- Disease Ontology (DO) Ontology (DO) DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI thesaurus, SNOMED and OMIM.
- Human Phenotype (HP) Ontology (HP) 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) 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) 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 (YP) 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) 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) 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) ZA displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
- Xenopus Anatomy (XA) Ontology (XA) 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 (AP) 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 (EC) 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.
- DrugBank ATC (DB) Ontology (DB) In the Anatomical Therapeutic Chemical (ATC) classification system, drugs are classified in groups at five different levels according to the organ or system (1st level, anatomical main group) on which they act and their therapeutic (2nd level, therapeutic subgroup), pharmacological (3rd level, pharmacological subgroup) and chemical properties (4th level, chemical subgroup; 5th level, chemical substance). Only drugs in DrugBank are considered.
- UniProtKB KeyWords (KW) Ontology (KW) 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).
- UniProtKB UniPathway (UP) Ontology (UP) UP is a fully manually curated resource for the representation and annotation of metabolic pathways, being used as controlled vocabulary for pathway annotation in UniProtKB.
Structural Domain Phenotype Ontology and its Annotations
Structural Classification of Proteins (SCOP) classifies evolutionary-related domains into Superfamily level and Family level. Using the phenotype ontologies above, we have generated the domain-centric phenotype annotations, and further identified those phenotype terms which are the most informative to annotate SCOP domains. Promisingly, domain-centric phenotypic annotations can serve as an alternative starting point to explore genotype-phenotype relationships. We provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.
- Structural Domain Disease Ontology (DO) Ontology (SDDO) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DO.txt, and the corresponding ontology:SDDO.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Human Phenotype (HP) Ontology (SDHP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2HP.txt, and the corresponding ontology:SDHP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Mouse Phenotype (MP) Ontology (SDMP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2MP.txt, and the corresponding ontology:SDMP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Worm Phenotype (WP) Ontology (SDWP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2WP.txt, and the corresponding ontology:SDWP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Yeast Phenotype (YP) Ontology (SDYP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2YP.txt, and the corresponding ontology:SDYP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Fly Phenotype (FP) Ontology (SDFP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FP.txt, and the corresponding ontology:SDFP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Fly Anatomy (FA) Ontology (SDFA) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FA.txt, and the corresponding ontology:SDFA.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Zebrafish Anatomy (ZA) Ontology (SDZA) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2ZA.txt, and the corresponding ontology:SDZA.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Xenopus Anatomy (XA) Ontology (SDXA) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2XA.txt, and the corresponding ontology:SDXA.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Arabidopsis Plant Ontology (AP) Ontology (SDAP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2AP.txt, and the corresponding ontology:SDAP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Enzyme Commission (EC) Ontology (SDEC) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2EC.txt, and the corresponding ontology:SDEC.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain DrugBank ATC (DB) Ontology (SDDB) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DB.txt, and the corresponding ontology:SDDB.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain UniProtKB KeyWords (KW) Ontology (SDKW) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2KW.txt, and the corresponding ontology:SDKW.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain UniProtKB UniPathway (UP) Ontology (SDUP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2UP.txt, and the corresponding ontology:SDUP.txt) and mysql tables (Domain2PO.sql.gz).
Supra-domain Phenotype Ontology and its Annotations
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are interested in domain combinations. Also, we provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.
- Supra-domain Domain Disease Ontology (DO) Ontology (SPDO) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DO.txt, and the corresponding ontology:SPDO.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Human Phenotype (HP) Ontology (SPHO) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2HP.txt, and the corresponding ontology:SPHO.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Mouse Phenotype (MP) Ontology (SPMP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2MP.txt, and the corresponding ontology:SPMP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Worm Phenotype (WP) Ontology (SPWP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2WP.txt, and the corresponding ontology:SPWP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Yeast Phenotype (YP) Ontology (SPYP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2YP.txt, and the corresponding ontology:SPYP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Fly Phenotype (FP) Ontology (SPFP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FP.txt, and the corresponding ontology:SPFP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Fly Anatomy (FA) Ontology (SPFA) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FA.txt, and the corresponding ontology:SPFA.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Zebrafish Anatomy (ZA) Ontology (SPZA) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2ZA.txt, and the corresponding ontology:SPZA.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Xenopus Anatomy (XA) Ontology (SPXA) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2XA.txt, and the corresponding ontology:SPXA.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Arabidopsis Plant Ontology (AP) Ontology (SPAP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2AP.txt, and the corresponding ontology:SPAP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Enzyme Commission (EC) Ontology (SPEC) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2EC.txt, and the corresponding ontology:SPEC.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain DrugBank ATC (DB) Ontology (SPDB) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DB.txt, and the corresponding ontology:SPDB.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain UniProtKB KeyWords (KW) Ontology (SPKW) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2KW.txt, and the corresponding ontology:SPKW.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain UniProtKB UniPathway (UP) Ontology (SPUP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2UP.txt, and the corresponding ontology:SPUP.txt) and mysql tables (SP2PO.sql.gz).
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Root: XA Hierarchy (Xenopus anatomy and development from Xenbase frog anatomy ontology)
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Superfamily(show details)
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Family(show details)
Family domains annotated to this XA term (SDXA level: Moderately Informative)
Highlighted in gray are those with FDR_all>0.001
SCOP term | FDR (all) | Annotation (direct or inherited) |
Thiolase-related | 0 | DIRECT |
Hedgehog (development protein), N-terminal signaling domain | 0 | DIRECT |
Ferritin | 0 | DIRECT |
Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain | 0 | DIRECT |
IP3 receptor type 1 binding core, domain 2 | 0 | DIRECT |
Pumilio repeat | 0 | DIRECT |
Neurolysin-like | 0 | DIRECT |
eIF1-like | 0 | DIRECT |
Fibronectin type II module | 0 | DIRECT |
Glyoxalase II (hydroxyacylglutathione hydrolase) | 0 | DIRECT |
Arginase-like amidino hydrolases | 0 | DIRECT |
Protein-L-isoaspartyl O-methyltransferase | 0 | DIRECT |
RuBisCo LSMT catalytic domain | 0 | DIRECT |
HCDH C-domain-like | 0 | DIRECT |
Glucose 6-phosphate dehydrogenase-like | 0 | DIRECT |
Mannose 6-phosphate receptor domain | 0 | DIRECT |
Crotonase-like | 0 | DIRECT |
HAT/Suf repeat | 0 | DIRECT |
gamma-adaptin C-terminal appendage domain-like | 0 | DIRECT |
Guanido kinase catalytic domain | 0 | DIRECT |
Group II chaperonin (CCT, TRIC), intermediate domain | 0 | DIRECT |
F1F0 ATP synthase subunit C | 0 | DIRECT |
UDPGT-like | 0 | DIRECT |
DNA ligase | 0 | DIRECT |
Fibronectin type I module | 0 | DIRECT |
Alpha-adaptin ear subdomain-like | 0 | DIRECT |
GABARAP-like | 0 | DIRECT |
Aminomethyltransferase beta-barrel domain | 0 | DIRECT |
PDI-like | 0 | DIRECT |
D-aminoacid oxidase-like | 0 | DIRECT |
Guanido kinase N-terminal domain | 0 | DIRECT |
MSP-like | 0 | DIRECT |
Vasodilator-stimulated phosphoprotein, VASP, tetramerisation domain | 0 | DIRECT |
Delta-sleep-inducing peptide immunoreactive peptide | 0 | DIRECT |
Variant RING domain | 0 | DIRECT |
Sterol carrier protein, SCP | 0 | DIRECT |
Alanine racemase-like, N-terminal domain | 0 | DIRECT |
Hypoxia-inducible factor HIF ihhibitor (FIH1) | 0 | DIRECT |
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 0 | DIRECT |
Dimeric isocitrate & isopropylmalate dehydrogenases | 0 | DIRECT |
Branched-chain alpha-keto acid dehydrogenase PP module | 0 | DIRECT |
Lipovitellin-phosvitin complex, superhelical domain | 0 | DIRECT |
Moesin tail domain | 0 | DIRECT |
CAT-like | 0 | DIRECT |
Apolipoprotein A-I | 0 | DIRECT |
Eukaryotic ODC-like | 0 | DIRECT |
NAP-like | 0 | DIRECT |
PAH2 domain | 0 | DIRECT |
alpha-catenin/vinculin | 0 | DIRECT |
Amidase signature (AS) enzymes | 0 | DIRECT |
MAPEG domain | 0 | DIRECT |
Fibrinogen coiled-coil and central regions | 0 | DIRECT |
Lipovitellin-phosvitin complex; beta-sheet shell regions | 0 | DIRECT |
Threonyl-tRNA synthetase (ThrRS), second 'additional' domain | 0 | DIRECT |
C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | DIRECT |
Chromo barrel domain | 0 | DIRECT |
BSD domain | 0 | DIRECT |
Malic enzyme N-domain | 0 | DIRECT |
Phosphoribosylpyrophosphate synthetase-like | 0 | DIRECT |
N-acetylmuramoyl-L-alanine amidase-like | 0 | DIRECT |
Steroid-binding domain | 0 | DIRECT |
S-adenosylhomocystein hydrolase | 0 | DIRECT |
Noncollagenous (NC1) domain of collagen IV | 0 | DIRECT |
Transferrin | 0 | DIRECT |
Anticodon-binding domain of Class II aaRS | 0 | DIRECT |
Surp module (SWAP domain) | 0 | DIRECT |
Succinyl-CoA synthetase domains | 0 | DIRECT |
AraD-like aldolase/epimerase | 0 | DIRECT |
Clathrin adaptor appendage, alpha and beta chain-specific domain | 0 | DIRECT |
ALDH-like | 0.001524 | INHERITED FROM: intestine |
Canonical RBD | 0.002096 | INHERITED FROM: intestine |
GABA-aminotransferase-like | 0.002183 | INHERITED FROM: intestine |
Leukotriene A4 hydrolase N-terminal domain | 0.01253 | INHERITED FROM: pancreas |
Class I aldolase | 0.03816 | INHERITED FROM: heart |
Eukaryotic proteases | 0.04088 | INHERITED FROM: pancreas |
Actin/HSP70 | 0.08928 | INHERITED FROM: pancreas || heart |
SMAD domain | 0.09838 | INHERITED FROM: heart || endocardium |
Leukotriene A4 hydrolase catalytic domain | 0.09838 | INHERITED FROM: pancreas |
Complement components | 0.1373 | INHERITED FROM: liver |
SMAD MH1 domain | 0.1373 | INHERITED FROM: heart || endocardium |
Erythroid transcription factor GATA-1 | 0.1946 | INHERITED FROM: heart || myocardium |
MHC antigen-recognition domain | 0.2607 | INHERITED FROM: pancreas |
WD40-repeat | 0.2757 | INHERITED FROM: intestine |
HMG-box | 0.3352 | INHERITED FROM: endocardial tube || endocardium |
LIM domain | 0.349 | INHERITED FROM: heart |
Lectin leg-like | 0.3537 | INHERITED FROM: pancreas |
Translational machinery components | 0.6611 | INHERITED FROM: pancreas |
Calmodulin-like | 0.812 | INHERITED FROM: cardiac atrium || right atrium || left atrium || cardiac ventricle |
T-box | 0.8822 | INHERITED FROM: heart || myocardium |
Forkhead DNA-binding domain | 0.9748 | INHERITED FROM: myocardium || stomach |
Frizzled cysteine-rich domain | 0.9899 | INHERITED FROM: gall bladder || small intestine || stomach |
Homeodomain | 1 | INHERITED FROM: heart || small intestine || stomach || large intestine |
Transforming growth factor (TGF)-beta | 1 | INHERITED FROM: heart |
HLH, helix-loop-helix DNA-binding domain | 1 | INHERITED FROM: heart || stomach |
Growth factor receptor domain | 1 | INHERITED FROM: heart |
Tropomyosin | 1 | INHERITED FROM: cardiac atrium || outflow tract || left atrium || myocardium |
SCOP term | FDR (all) | Annotation (direct or inherited) |
Thiolase-related | 0 | Direct |
Hedgehog (development protein), N-terminal signaling domain | 0 | Direct |
Ferritin | 0 | Direct |
Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain | 0 | Direct |
IP3 receptor type 1 binding core, domain 2 | 0 | Direct |
Pumilio repeat | 0 | Direct |
Neurolysin-like | 0 | Direct |
eIF1-like | 0 | Direct |
Fibronectin type II module | 0 | Direct |
Glyoxalase II (hydroxyacylglutathione hydrolase) | 0 | Direct |
Arginase-like amidino hydrolases | 0 | Direct |
Protein-L-isoaspartyl O-methyltransferase | 0 | Direct |
RuBisCo LSMT catalytic domain | 0 | Direct |
HCDH C-domain-like | 0 | Direct |
Glucose 6-phosphate dehydrogenase-like | 0 | Direct |
Mannose 6-phosphate receptor domain | 0 | Direct |
Crotonase-like | 0 | Direct |
HAT/Suf repeat | 0 | Direct |
gamma-adaptin C-terminal appendage domain-like | 0 | Direct |
Guanido kinase catalytic domain | 0 | Direct |
Group II chaperonin (CCT, TRIC), intermediate domain | 0 | Direct |
F1F0 ATP synthase subunit C | 0 | Direct |
UDPGT-like | 0 | Direct |
DNA ligase | 0 | Direct |
Fibronectin type I module | 0 | Direct |
Alpha-adaptin ear subdomain-like | 0 | Direct |
GABARAP-like | 0 | Direct |
Aminomethyltransferase beta-barrel domain | 0 | Direct |
PDI-like | 0 | Direct |
D-aminoacid oxidase-like | 0 | Direct |
Guanido kinase N-terminal domain | 0 | Direct |
MSP-like | 0 | Direct |
Vasodilator-stimulated phosphoprotein, VASP, tetramerisation domain | 0 | Direct |
Delta-sleep-inducing peptide immunoreactive peptide | 0 | Direct |
Variant RING domain | 0 | Direct |
Sterol carrier protein, SCP | 0 | Direct |
Alanine racemase-like, N-terminal domain | 0 | Direct |
Hypoxia-inducible factor HIF ihhibitor (FIH1) | 0 | Direct |
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 0 | Direct |
Dimeric isocitrate & isopropylmalate dehydrogenases | 0 | Direct |
Branched-chain alpha-keto acid dehydrogenase PP module | 0 | Direct |
Lipovitellin-phosvitin complex, superhelical domain | 0 | Direct |
Moesin tail domain | 0 | Direct |
CAT-like | 0 | Direct |
Apolipoprotein A-I | 0 | Direct |
Eukaryotic ODC-like | 0 | Direct |
NAP-like | 0 | Direct |
PAH2 domain | 0 | Direct |
alpha-catenin/vinculin | 0 | Direct |
Amidase signature (AS) enzymes | 0 | Direct |
MAPEG domain | 0 | Direct |
Fibrinogen coiled-coil and central regions | 0 | Direct |
Lipovitellin-phosvitin complex; beta-sheet shell regions | 0 | Direct |
Threonyl-tRNA synthetase (ThrRS), second 'additional' domain | 0 | Direct |
C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | Direct |
Chromo barrel domain | 0 | Direct |
BSD domain | 0 | Direct |
Malic enzyme N-domain | 0 | Direct |
Phosphoribosylpyrophosphate synthetase-like | 0 | Direct |
N-acetylmuramoyl-L-alanine amidase-like | 0 | Direct |
Steroid-binding domain | 0 | Direct |
S-adenosylhomocystein hydrolase | 0 | Direct |
Noncollagenous (NC1) domain of collagen IV | 0 | Direct |
Transferrin | 0 | Direct |
Anticodon-binding domain of Class II aaRS | 0 | Direct |
Surp module (SWAP domain) | 0 | Direct |
Succinyl-CoA synthetase domains | 0 | Direct |
AraD-like aldolase/epimerase | 0 | Direct |
Clathrin adaptor appendage, alpha and beta chain-specific domain | 0 | Direct |
ALDH-like | 0.001524 | Inherited |
Canonical RBD | 0.002096 | Inherited |
GABA-aminotransferase-like | 0.002183 | Inherited |
Leukotriene A4 hydrolase N-terminal domain | 0.01253 | Inherited |
Class I aldolase | 0.03816 | Inherited |
Eukaryotic proteases | 0.04088 | Inherited |
Actin/HSP70 | 0.08928 | Inherited |
SMAD domain | 0.09838 | Inherited |
Leukotriene A4 hydrolase catalytic domain | 0.09838 | Inherited |
Complement components | 0.1373 | Inherited |
SMAD MH1 domain | 0.1373 | Inherited |
Erythroid transcription factor GATA-1 | 0.1946 | Inherited |
MHC antigen-recognition domain | 0.2607 | Inherited |
WD40-repeat | 0.2757 | Inherited |
HMG-box | 0.3352 | Inherited |
LIM domain | 0.349 | Inherited |
Lectin leg-like | 0.3537 | Inherited |
Translational machinery components | 0.6611 | Inherited |
Calmodulin-like | 0.812 | Inherited |
T-box | 0.8822 | Inherited |
Forkhead DNA-binding domain | 0.9748 | Inherited |
Frizzled cysteine-rich domain | 0.9899 | Inherited |
Homeodomain | 1 | Inherited |
Transforming growth factor (TGF)-beta | 1 | Inherited |
HLH, helix-loop-helix DNA-binding domain | 1 | Inherited |
Growth factor receptor domain | 1 | Inherited |
Tropomyosin | 1 | Inherited |
Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term
 |
Plot tree as:
| |
Download Newick format tree:
|
(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.
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Supra-domain (including individual superfamily)
(show details)
(show details)
Supra-domains annotated to this XA term (SPXA level: Moderately Informative)
Highlighted in gray are those with FDR>0.001
Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57184,49899 57184 - Growth factor receptor domain 49899 - Concanavalin A-like lectins/glucanases | 0 | DIRECT |
54534,47473 54534 - FKBP-like 47473 - EF-hand | 0 | DIRECT |
54403,54403 54403 - Cystatin/monellin 54403 - Cystatin/monellin | 0 | DIRECT |
51419,50621 51419 - PLP-binding barrel 50621 - Alanine racemase C-terminal domain-like | 0 | DIRECT |
55550,50729 55550 - SH2 domain 50729 - PH domain-like | 0 | DIRECT |
49899,52540 49899 - Concanavalin A-like lectins/glucanases 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
52518,52922 52518 - Thiamin diphosphate-binding fold (THDP-binding) 52922 - TK C-terminal domain-like | 0 | DIRECT |
51230,47005 51230 - Single hybrid motif 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 0 | DIRECT |
57196,50494 57196 - EGF/Laminin 50494 - Trypsin-like serine proteases | 0 | DIRECT |
48592,54849 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like | 0 | DIRECT |
103025,101790 103025 - Folate-binding domain 101790 - Aminomethyltransferase beta-barrel domain | 0 | DIRECT |
52540,47917 52540 - P-loop containing nucleoside triphosphate hydrolases 47917 - C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | DIRECT |
56059,52210 56059 - Glutathione synthetase ATP-binding domain-like 52210 - Succinyl-CoA synthetase domains | 0 | DIRECT |
56968,48431 56968 - Lipovitellin-phosvitin complex; beta-sheet shell regions 48431 - Lipovitellin-phosvitin complex, superhelical domain | 0 | DIRECT |
47005,52777 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 52777 - CoA-dependent acyltransferases | 0 | DIRECT |
81995,81811 81995 - beta-sandwich domain of Sec23/24 81811 - Helical domain of Sec23/24 | 0 | DIRECT |
53901,53901 53901 - Thiolase-like 53901 - Thiolase-like | 0 | DIRECT |
82895,57424 82895 - TSP-1 type 1 repeat 57424 - LDL receptor-like module | 0 | DIRECT |
53300,81995 53300 - vWA-like 81995 - beta-sandwich domain of Sec23/24 | 0 | DIRECT |
47095,47095 47095 - HMG-box 47095 - HMG-box | 0 | DIRECT |
48034,55931 48034 - Guanido kinase N-terminal domain 55931 - Glutamine synthetase/guanido kinase | 0 | DIRECT |
57424,57184 57424 - LDL receptor-like module 57184 - Growth factor receptor domain | 0 | DIRECT |
54534,54534 54534 - FKBP-like 54534 - FKBP-like | 0 | DIRECT |
81271,55186 81271 - TGS-like 55186 - ThrRS/AlaRS common domain | 0 | DIRECT |
48371,46785 48371 - ARM repeat 46785 - "Winged helix" DNA-binding domain | 0 | DIRECT |
53850,53850 53850 - Periplasmic binding protein-like II 53850 - Periplasmic binding protein-like II | 0 | DIRECT |
57603,57440 57603 - FnI-like domain 57440 - Kringle-like | 0 | DIRECT |
54160,57850 54160 - Chromo domain-like 57850 - RING/U-box | 0 | DIRECT |
50729,55550 50729 - PH domain-like 55550 - SH2 domain | 0 | DIRECT |
55486,48371 55486 - Metalloproteases ("zincins"), catalytic domain 48371 - ARM repeat | 0 | DIRECT |
57630,57196 57630 - GLA-domain 57196 - EGF/Laminin | 0 | DIRECT |
57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat | 0 | DIRECT |
54236,50729 54236 - Ubiquitin-like 50729 - PH domain-like | 0 | DIRECT |
54928,54928 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD | 0.0002503 | DIRECT |
63737,55486 63737 - Leukotriene A4 hydrolase N-terminal domain 55486 - Metalloproteases ("zincins"), catalytic domain | 0.06178 | INHERITED FROM: pancreas |
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like | 0.08843 | INHERITED FROM: heart |
53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain | 0.1152 | INHERITED FROM: heart || pancreas |
103657,50729 103657 - BAR/IMD domain-like 50729 - PH domain-like | 0.1966 | INHERITED FROM: pancreas |
54791,54791 54791 - Eukaryotic type KH-domain (KH-domain type I) 54791 - Eukaryotic type KH-domain (KH-domain type I) | 0.2283 | INHERITED FROM: pancreas |
52518,52518 52518 - Thiamin diphosphate-binding fold (THDP-binding) 52518 - Thiamin diphosphate-binding fold (THDP-binding) | 0.2442 | INHERITED FROM: pancreas |
50494,50494 50494 - Trypsin-like serine proteases 50494 - Trypsin-like serine proteases | 0.2442 | INHERITED FROM: pancreas |
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain | 0.3351 | INHERITED FROM: heart |
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.3859 | INHERITED FROM: heart |
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.4429 | INHERITED FROM: heart |
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.8417 | INHERITED FROM: heart |
Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57184,49899 57184 - Growth factor receptor domain 49899 - Concanavalin A-like lectins/glucanases | 0 | Direct |
54534,47473 54534 - FKBP-like 47473 - EF-hand | 0 | Direct |
54403,54403 54403 - Cystatin/monellin 54403 - Cystatin/monellin | 0 | Direct |
51419,50621 51419 - PLP-binding barrel 50621 - Alanine racemase C-terminal domain-like | 0 | Direct |
55550,50729 55550 - SH2 domain 50729 - PH domain-like | 0 | Direct |
49899,52540 49899 - Concanavalin A-like lectins/glucanases 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
52518,52922 52518 - Thiamin diphosphate-binding fold (THDP-binding) 52922 - TK C-terminal domain-like | 0 | Direct |
51230,47005 51230 - Single hybrid motif 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 0 | Direct |
57196,50494 57196 - EGF/Laminin 50494 - Trypsin-like serine proteases | 0 | Direct |
48592,54849 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like | 0 | Direct |
103025,101790 103025 - Folate-binding domain 101790 - Aminomethyltransferase beta-barrel domain | 0 | Direct |
52540,47917 52540 - P-loop containing nucleoside triphosphate hydrolases 47917 - C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | Direct |
56059,52210 56059 - Glutathione synthetase ATP-binding domain-like 52210 - Succinyl-CoA synthetase domains | 0 | Direct |
56968,48431 56968 - Lipovitellin-phosvitin complex; beta-sheet shell regions 48431 - Lipovitellin-phosvitin complex, superhelical domain | 0 | Direct |
47005,52777 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 52777 - CoA-dependent acyltransferases | 0 | Direct |
81995,81811 81995 - beta-sandwich domain of Sec23/24 81811 - Helical domain of Sec23/24 | 0 | Direct |
53901,53901 53901 - Thiolase-like 53901 - Thiolase-like | 0 | Direct |
82895,57424 82895 - TSP-1 type 1 repeat 57424 - LDL receptor-like module | 0 | Direct |
53300,81995 53300 - vWA-like 81995 - beta-sandwich domain of Sec23/24 | 0 | Direct |
47095,47095 47095 - HMG-box 47095 - HMG-box | 0 | Direct |
48034,55931 48034 - Guanido kinase N-terminal domain 55931 - Glutamine synthetase/guanido kinase | 0 | Direct |
57424,57184 57424 - LDL receptor-like module 57184 - Growth factor receptor domain | 0 | Direct |
54534,54534 54534 - FKBP-like 54534 - FKBP-like | 0 | Direct |
81271,55186 81271 - TGS-like 55186 - ThrRS/AlaRS common domain | 0 | Direct |
48371,46785 48371 - ARM repeat 46785 - "Winged helix" DNA-binding domain | 0 | Direct |
53850,53850 53850 - Periplasmic binding protein-like II 53850 - Periplasmic binding protein-like II | 0 | Direct |
57603,57440 57603 - FnI-like domain 57440 - Kringle-like | 0 | Direct |
54160,57850 54160 - Chromo domain-like 57850 - RING/U-box | 0 | Direct |
50729,55550 50729 - PH domain-like 55550 - SH2 domain | 0 | Direct |
55486,48371 55486 - Metalloproteases ("zincins"), catalytic domain 48371 - ARM repeat | 0 | Direct |
57630,57196 57630 - GLA-domain 57196 - EGF/Laminin | 0 | Direct |
57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat | 0 | Direct |
54236,50729 54236 - Ubiquitin-like 50729 - PH domain-like | 0 | Direct |
54928,54928 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD | 0.0002503 | Direct |
63737,55486 63737 - Leukotriene A4 hydrolase N-terminal domain 55486 - Metalloproteases ("zincins"), catalytic domain | 0.06178 | Inherited |
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like | 0.08843 | Inherited |
53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain | 0.1152 | Inherited |
103657,50729 103657 - BAR/IMD domain-like 50729 - PH domain-like | 0.1966 | Inherited |
54791,54791 54791 - Eukaryotic type KH-domain (KH-domain type I) 54791 - Eukaryotic type KH-domain (KH-domain type I) | 0.2283 | Inherited |
52518,52518 52518 - Thiamin diphosphate-binding fold (THDP-binding) 52518 - Thiamin diphosphate-binding fold (THDP-binding) | 0.2442 | Inherited |
50494,50494 50494 - Trypsin-like serine proteases 50494 - Trypsin-like serine proteases | 0.2442 | Inherited |
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain | 0.3351 | Inherited |
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.3859 | Inherited |
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.4429 | Inherited |
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.8417 | Inherited |
(show details)
Supra-domains annotated to this XA term (SPXA level: Moderately Informative)
Highlighted in gray are those with FDR>0.001
Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
50729,55550,56112 50729 - PH domain-like 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) | 0 | DIRECT |
54791,54791,54791 54791 - Eukaryotic type KH-domain (KH-domain type I) 54791 - Eukaryotic type KH-domain (KH-domain type I) 54791 - Eukaryotic type KH-domain (KH-domain type I) | 0 | DIRECT |
63737,55486,48371 63737 - Leukotriene A4 hydrolase N-terminal domain 55486 - Metalloproteases ("zincins"), catalytic domain 48371 - ARM repeat | 0 | DIRECT |
57424,57424,57184 57424 - LDL receptor-like module 57424 - LDL receptor-like module 57184 - Growth factor receptor domain | 0 | DIRECT |
53300,81995,81811 53300 - vWA-like 81995 - beta-sandwich domain of Sec23/24 81811 - Helical domain of Sec23/24 | 0 | DIRECT |
48592,54849,52029 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like | 0 | DIRECT |
57196,49854,57535 57196 - EGF/Laminin 49854 - Spermadhesin, CUB domain 57535 - Complement control module/SCR domain | 0 | DIRECT |
56436,56436,56436 56436 - C-type lectin-like 56436 - C-type lectin-like 56436 - C-type lectin-like | 0 | DIRECT |
57630,57196,57196 57630 - GLA-domain 57196 - EGF/Laminin 57196 - EGF/Laminin | 0 | DIRECT |
81995,81811,82754 81995 - beta-sandwich domain of Sec23/24 81811 - Helical domain of Sec23/24 82754 - C-terminal, gelsolin-like domain of Sec23/24 | 0 | DIRECT |
52058,52058,52058 52058 - L domain-like 52058 - L domain-like 52058 - L domain-like | 0 | DIRECT |
50249,50249,50249 50249 - Nucleic acid-binding proteins 50249 - Nucleic acid-binding proteins 50249 - Nucleic acid-binding proteins | 0 | DIRECT |
54160,57850,57845 54160 - Chromo domain-like 57850 - RING/U-box 57845 - B-box zinc-binding domain | 0 | DIRECT |
52833,52833,52833 52833 - Thioredoxin-like 52833 - Thioredoxin-like 52833 - Thioredoxin-like | 0 | DIRECT |
51230,47005,52777 51230 - Single hybrid motif 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 52777 - CoA-dependent acyltransferases | 0 | DIRECT |
57424,57184,63825 57424 - LDL receptor-like module 57184 - Growth factor receptor domain 63825 - YWTD domain | 0 | DIRECT |
55550,56112,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) 56112 - Protein kinase-like (PK-like) | 0 | DIRECT |
57716,57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.2282 | INHERITED FROM: heart |
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.2442 | INHERITED FROM: heart |
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain | 0.5402 | INHERITED FROM: heart |
57184,57196,57196 57184 - Growth factor receptor domain 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.9658 | INHERITED FROM: heart |
Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
50729,55550,56112 50729 - PH domain-like 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) | 0 | Direct |
54791,54791,54791 54791 - Eukaryotic type KH-domain (KH-domain type I) 54791 - Eukaryotic type KH-domain (KH-domain type I) 54791 - Eukaryotic type KH-domain (KH-domain type I) | 0 | Direct |
63737,55486,48371 63737 - Leukotriene A4 hydrolase N-terminal domain 55486 - Metalloproteases ("zincins"), catalytic domain 48371 - ARM repeat | 0 | Direct |
57424,57424,57184 57424 - LDL receptor-like module 57424 - LDL receptor-like module 57184 - Growth factor receptor domain | 0 | Direct |
53300,81995,81811 53300 - vWA-like 81995 - beta-sandwich domain of Sec23/24 81811 - Helical domain of Sec23/24 | 0 | Direct |
48592,54849,52029 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like | 0 | Direct |
57196,49854,57535 57196 - EGF/Laminin 49854 - Spermadhesin, CUB domain 57535 - Complement control module/SCR domain | 0 | Direct |
56436,56436,56436 56436 - C-type lectin-like 56436 - C-type lectin-like 56436 - C-type lectin-like | 0 | Direct |
57630,57196,57196 57630 - GLA-domain 57196 - EGF/Laminin 57196 - EGF/Laminin | 0 | Direct |
81995,81811,82754 81995 - beta-sandwich domain of Sec23/24 81811 - Helical domain of Sec23/24 82754 - C-terminal, gelsolin-like domain of Sec23/24 | 0 | Direct |
52058,52058,52058 52058 - L domain-like 52058 - L domain-like 52058 - L domain-like | 0 | Direct |
50249,50249,50249 50249 - Nucleic acid-binding proteins 50249 - Nucleic acid-binding proteins 50249 - Nucleic acid-binding proteins | 0 | Direct |
54160,57850,57845 54160 - Chromo domain-like 57850 - RING/U-box 57845 - B-box zinc-binding domain | 0 | Direct |
52833,52833,52833 52833 - Thioredoxin-like 52833 - Thioredoxin-like 52833 - Thioredoxin-like | 0 | Direct |
51230,47005,52777 51230 - Single hybrid motif 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 52777 - CoA-dependent acyltransferases | 0 | Direct |
57424,57184,63825 57424 - LDL receptor-like module 57184 - Growth factor receptor domain 63825 - YWTD domain | 0 | Direct |
55550,56112,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) 56112 - Protein kinase-like (PK-like) | 0 | Direct |
57716,57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.2282 | Inherited |
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.2442 | Inherited |
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain | 0.5402 | Inherited |
57184,57196,57196 57184 - Growth factor receptor domain 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.9658 | Inherited |
Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term
 |
Plot tree as:
| |
Download Newick format tree:
|
(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.
|