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Zebrafish Anatomy (ZA): organism subdivision
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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: ZA Hierarchy (zebrafish anatomy from ZFIN zebrafish 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 ZA term (SDZA level: Least Informative)
Highlighted in gray are those with FDR_all>0.001
SCOP term | FDR (all) | Annotation (direct or inherited) |
p53 tetramerization domain | 0 | DIRECT |
Elongation factors | 0 | DIRECT |
PWWP domain | 0 | DIRECT |
Platelet-derived growth factor-like | 0 | DIRECT |
CRAL/TRIO domain | 0 | DIRECT |
Cdc48 domain 2-like | 0 | DIRECT |
Hydantoinase (dihydropyrimidinase) | 0 | DIRECT |
Retrovirus zinc finger-like domains | 0 | DIRECT |
Sec7 domain | 0 | DIRECT |
Aquaporin-like | 0 | DIRECT |
Nitrogenase iron protein-like | 0 | DIRECT |
Class I glutamine amidotransferases (GAT) | 0 | DIRECT |
Biotinyl/lipoyl-carrier proteins and domains | 0 | DIRECT |
FYVE, a phosphatidylinositol-3-phosphate binding domain | 0 | DIRECT |
CalX-beta domain | 0 | DIRECT |
LDL receptor-like module | 0 | DIRECT |
V set domains (antibody variable domain-like) | 0 | DIRECT |
Clathrin coat assembly domain | 0 | DIRECT |
Adenylyl and guanylyl cyclase catalytic domain | 0 | DIRECT |
Small Kunitz-type inhibitors & BPTI-like toxins | 0 | DIRECT |
Lipovitellin-phosvitin complex; beta-sheet shell regions | 0 | DIRECT |
Plakophilin 1 helical region | 0 | DIRECT |
Cap-Gly domain | 0 | DIRECT |
C5 cytosine-specific DNA methylase, DCM | 0 | DIRECT |
Cell cycle control phosphatase, catalytic domain | 0 | DIRECT |
Histone deacetylase, HDAC | 0 | DIRECT |
Tubulin, GTPase domain | 0 | DIRECT |
RUNT domain | 0 | DIRECT |
Noncollagenous (NC1) domain of collagen IV | 0 | DIRECT |
CCCH zinc finger | 0 | DIRECT |
Phenylalanine metabolism regulatory domain | 0 | DIRECT |
Aromatic aminoacid monoxygenases, catalytic and oligomerization domains | 0 | DIRECT |
Tubulin, C-terminal domain | 0 | DIRECT |
LCCL domain | 0 | DIRECT |
Connexin43 | 0 | DIRECT |
Anticodon-binding domain of Class II aaRS | 0 | DIRECT |
Proprotein convertase P-domain | 0 | DIRECT |
p53 DNA-binding domain-like | 0 | DIRECT |
Extracellular domain of cell surface receptors | 0 | DIRECT |
CRAL/TRIO N-terminal domain | 0 | DIRECT |
SMAD MH1 domain | 0 | DIRECT |
SMAD domain | 0 | DIRECT |
Heat shock protein 70kD (HSP70), peptide-binding domain | 0 | DIRECT |
Nuclear receptor coactivator interlocking domain | 0 | DIRECT |
Zf-UBP | 0 | DIRECT |
Chromo domain | 0 | DIRECT |
Smc hinge domain | 0 | DIRECT |
Hydantoinase (dihydropyrimidinase), catalytic domain | 0 | DIRECT |
Moesin tail domain | 0 | DIRECT |
DUSP, domain in ubiquitin-specific proteases | 0 | DIRECT |
Myotubularin-like phosphatases | 0 | DIRECT |
Prohormone convertase 1 pro-domain | 0 | DIRECT |
Ubiquitin-related | 0 | DIRECT |
Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain | 0 | DIRECT |
Notch domain | 0 | DIRECT |
Cdc48 N-terminal domain-like | 0 | DIRECT |
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0 | DIRECT |
Ovomucoid domain III-like | 0 | DIRECT |
Single strand DNA-binding domain, SSB | 0 | DIRECT |
Lipovitellin-phosvitin complex, superhelical domain | 0 | DIRECT |
BRK domain-like | 0 | DIRECT |
HMG-box | 0.000965 | DIRECT |
Ubiquitin carboxyl-terminal hydrolase, UCH | 0.001283 | INHERITED FROM: post-vent region || neurocranium || ventral mandibular arch || mandibular arch skeleton || splanchnocranium || olfactory region || caudal fin upper lobe || pharyngeal arch 1 || cranial cartilage || ethmoid cartilage || caudal fin lower lobe || pharyngeal arch cartilage || chondrocranium || somite |
T-box | 0.02243 | INHERITED FROM: surface structure |
Protein kinases, catalytic subunit | 0.07969 | INHERITED FROM: dermal superficial region || dermis || scale || dorsal longitudinal anastomotic vessel |
Tetratricopeptide repeat (TPR) | 0.2104 | INHERITED FROM: retinal rod cell |
WD40-repeat | 0.2422 | INHERITED FROM: photoreceptor outer segment layer || retinal cone cell |
Short-chain cytokines | 0.253 | INHERITED FROM: integument |
Multidrug efflux transporter AcrB transmembrane domain | 0.253 | INHERITED FROM: hyosymplectic cartilage || suspensorium || retinal ganglion cell layer || pharyngeal arch 2 || dorsal hyoid arch || ventral hyoid arch || pharyngeal arch 2 skeleton |
Fibroblast growth factors (FGF) | 0.2715 | INHERITED FROM: dermatocranium || olfactory region || paired fin || pectoral fin || fin bud |
VWC domain | 0.2715 | INHERITED FROM: median fin fold || ventral fin fold |
Motor proteins | 0.6914 | INHERITED FROM: photoreceptor outer segment layer |
SCOP term | FDR (all) | Annotation (direct or inherited) |
p53 tetramerization domain | 0 | Direct |
Elongation factors | 0 | Direct |
PWWP domain | 0 | Direct |
Platelet-derived growth factor-like | 0 | Direct |
CRAL/TRIO domain | 0 | Direct |
Cdc48 domain 2-like | 0 | Direct |
Hydantoinase (dihydropyrimidinase) | 0 | Direct |
Retrovirus zinc finger-like domains | 0 | Direct |
Sec7 domain | 0 | Direct |
Aquaporin-like | 0 | Direct |
Nitrogenase iron protein-like | 0 | Direct |
Class I glutamine amidotransferases (GAT) | 0 | Direct |
Biotinyl/lipoyl-carrier proteins and domains | 0 | Direct |
FYVE, a phosphatidylinositol-3-phosphate binding domain | 0 | Direct |
CalX-beta domain | 0 | Direct |
LDL receptor-like module | 0 | Direct |
V set domains (antibody variable domain-like) | 0 | Direct |
Clathrin coat assembly domain | 0 | Direct |
Adenylyl and guanylyl cyclase catalytic domain | 0 | Direct |
Small Kunitz-type inhibitors & BPTI-like toxins | 0 | Direct |
Lipovitellin-phosvitin complex; beta-sheet shell regions | 0 | Direct |
Plakophilin 1 helical region | 0 | Direct |
Cap-Gly domain | 0 | Direct |
C5 cytosine-specific DNA methylase, DCM | 0 | Direct |
Cell cycle control phosphatase, catalytic domain | 0 | Direct |
Histone deacetylase, HDAC | 0 | Direct |
Tubulin, GTPase domain | 0 | Direct |
RUNT domain | 0 | Direct |
Noncollagenous (NC1) domain of collagen IV | 0 | Direct |
CCCH zinc finger | 0 | Direct |
Phenylalanine metabolism regulatory domain | 0 | Direct |
Aromatic aminoacid monoxygenases, catalytic and oligomerization domains | 0 | Direct |
Tubulin, C-terminal domain | 0 | Direct |
LCCL domain | 0 | Direct |
Connexin43 | 0 | Direct |
Anticodon-binding domain of Class II aaRS | 0 | Direct |
Proprotein convertase P-domain | 0 | Direct |
p53 DNA-binding domain-like | 0 | Direct |
Extracellular domain of cell surface receptors | 0 | Direct |
CRAL/TRIO N-terminal domain | 0 | Direct |
SMAD MH1 domain | 0 | Direct |
SMAD domain | 0 | Direct |
Heat shock protein 70kD (HSP70), peptide-binding domain | 0 | Direct |
Nuclear receptor coactivator interlocking domain | 0 | Direct |
Zf-UBP | 0 | Direct |
Chromo domain | 0 | Direct |
Smc hinge domain | 0 | Direct |
Hydantoinase (dihydropyrimidinase), catalytic domain | 0 | Direct |
Moesin tail domain | 0 | Direct |
DUSP, domain in ubiquitin-specific proteases | 0 | Direct |
Myotubularin-like phosphatases | 0 | Direct |
Prohormone convertase 1 pro-domain | 0 | Direct |
Ubiquitin-related | 0 | Direct |
Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain | 0 | Direct |
Notch domain | 0 | Direct |
Cdc48 N-terminal domain-like | 0 | Direct |
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0 | Direct |
Ovomucoid domain III-like | 0 | Direct |
Single strand DNA-binding domain, SSB | 0 | Direct |
Lipovitellin-phosvitin complex, superhelical domain | 0 | Direct |
BRK domain-like | 0 | Direct |
HMG-box | 0.000965 | Direct |
Ubiquitin carboxyl-terminal hydrolase, UCH | 0.001283 | Inherited |
T-box | 0.02243 | Inherited |
Protein kinases, catalytic subunit | 0.07969 | Inherited |
Tetratricopeptide repeat (TPR) | 0.2104 | Inherited |
WD40-repeat | 0.2422 | Inherited |
Short-chain cytokines | 0.253 | Inherited |
Multidrug efflux transporter AcrB transmembrane domain | 0.253 | Inherited |
Fibroblast growth factors (FGF) | 0.2715 | Inherited |
VWC domain | 0.2715 | Inherited |
Motor proteins | 0.6914 | Inherited |
Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term
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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)
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Supra-domains annotated to this ZA term (SPZA level: Least 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) |
57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module | 0 | DIRECT |
55550,55550 55550 - SH2 domain 55550 - SH2 domain | 0 | DIRECT |
48425,50729 48425 - Sec7 domain 50729 - PH domain-like | 0 | DIRECT |
52058,49265 52058 - L domain-like 49265 - Fibronectin type III | 0 | DIRECT |
54160,54160 54160 - Chromo domain-like 54160 - Chromo domain-like | 0 | DIRECT |
56968,48431 56968 - Lipovitellin-phosvitin complex; beta-sheet shell regions 48431 - Lipovitellin-phosvitin complex, superhelical domain | 0 | DIRECT |
81324,81324 81324 - Voltage-gated potassium channels 81324 - Voltage-gated potassium channels | 0 | DIRECT |
49785,57184 49785 - Galactose-binding domain-like 57184 - Growth factor receptor domain | 0 | DIRECT |
50729,47473 50729 - PH domain-like 47473 - EF-hand | 0 | DIRECT |
90193,90193 90193 - Notch domain 90193 - Notch domain | 0 | DIRECT |
47473,51695 47473 - EF-hand 51695 - PLC-like phosphodiesterases | 0 | DIRECT |
57362,57362 57362 - BPTI-like 57362 - BPTI-like | 0 | DIRECT |
46785,46785 46785 - "Winged helix" DNA-binding domain 46785 - "Winged helix" DNA-binding domain | 0 | DIRECT |
57196,63825 57196 - EGF/Laminin 63825 - YWTD domain | 0 | DIRECT |
141072,141072 141072 - CalX-like 141072 - CalX-like | 0 | DIRECT |
53300,53300 53300 - vWA-like 53300 - vWA-like | 0 | DIRECT |
46938,52087 46938 - CRAL/TRIO N-terminal domain 52087 - CRAL/TRIO domain | 0 | DIRECT |
55021,56534 55021 - ACT-like 56534 - Aromatic aminoacid monoxygenases, catalytic and oligomerization domains | 0 | DIRECT |
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0 | DIRECT |
57196,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases | 0 | DIRECT |
57903,47370 57903 - FYVE/PHD zinc finger 47370 - Bromodomain | 0 | DIRECT |
53067,100920 53067 - Actin-like ATPase domain 100920 - Heat shock protein 70kD (HSP70), peptide-binding domain | 0 | DIRECT |
57184,57603 57184 - Growth factor receptor domain 57603 - FnI-like domain | 0 | DIRECT |
54001,143791 54001 - Cysteine proteinases 143791 - DUSP-like | 0 | DIRECT |
50978,50998 50978 - WD40 repeat-like 50998 - Quinoprotein alcohol dehydrogenase-like | 0 | DIRECT |
50156,50044 50156 - PDZ domain-like 50044 - SH3-domain | 0 | DIRECT |
54791,54791 54791 - Eukaryotic type KH-domain (KH-domain type I) 54791 - Eukaryotic type KH-domain (KH-domain type I) | 0 | DIRECT |
52743,49785 52743 - Subtilisin-like 49785 - Galactose-binding domain-like | 0 | DIRECT |
50447,50465 50447 - Translation proteins 50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0 | DIRECT |
54585,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
52540,50447 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins | 0 | DIRECT |
51556,51338 51556 - Metallo-dependent hydrolases 51338 - Composite domain of metallo-dependent hydrolases | 0 | DIRECT |
90257,57997 90257 - Myosin rod fragments 57997 - Tropomyosin | 0 | DIRECT |
63825,57196 63825 - YWTD domain 57196 - EGF/Laminin | 0 | DIRECT |
57196,90193 57196 - EGF/Laminin 90193 - Notch domain | 0 | DIRECT |
49854,57196 49854 - Spermadhesin, CUB domain 57196 - EGF/Laminin | 0 | DIRECT |
50692,54585 50692 - ADC-like 54585 - Cdc48 domain 2-like | 0 | DIRECT |
49417,47719 49417 - p53-like transcription factors 47719 - p53 tetramerization domain | 0 | DIRECT |
57850,57850 57850 - RING/U-box 57850 - RING/U-box | 0 | DIRECT |
52490,55307 52490 - Tubulin nucleotide-binding domain-like 55307 - Tubulin C-terminal domain-like | 0 | DIRECT |
57903,57903 57903 - FYVE/PHD zinc finger 57903 - FYVE/PHD zinc finger | 0 | DIRECT |
50729,56112 50729 - PH domain-like 56112 - Protein kinase-like (PK-like) | 0 | DIRECT |
48452,81901 48452 - TPR-like 81901 - HCP-like | 0 | DIRECT |
54160,52540 54160 - Chromo domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
57440,57440 57440 - Kringle-like 57440 - Kringle-like | 0.3359 | INHERITED FROM: pharyngeal arch 1 |
57196,49854 57196 - EGF/Laminin 49854 - Spermadhesin, CUB domain | 0.3359 | INHERITED FROM: fin |
49313,49313 49313 - Cadherin-like 49313 - Cadherin-like | 0.641 | INHERITED FROM: retinal ganglion cell layer |
50156,50156 50156 - PDZ domain-like 50156 - PDZ domain-like | 0.705 | INHERITED FROM: eye photoreceptor cell || retinal outer nuclear layer |
Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module | 0 | Direct |
55550,55550 55550 - SH2 domain 55550 - SH2 domain | 0 | Direct |
48425,50729 48425 - Sec7 domain 50729 - PH domain-like | 0 | Direct |
52058,49265 52058 - L domain-like 49265 - Fibronectin type III | 0 | Direct |
54160,54160 54160 - Chromo domain-like 54160 - Chromo domain-like | 0 | Direct |
56968,48431 56968 - Lipovitellin-phosvitin complex; beta-sheet shell regions 48431 - Lipovitellin-phosvitin complex, superhelical domain | 0 | Direct |
81324,81324 81324 - Voltage-gated potassium channels 81324 - Voltage-gated potassium channels | 0 | Direct |
49785,57184 49785 - Galactose-binding domain-like 57184 - Growth factor receptor domain | 0 | Direct |
50729,47473 50729 - PH domain-like 47473 - EF-hand | 0 | Direct |
90193,90193 90193 - Notch domain 90193 - Notch domain | 0 | Direct |
47473,51695 47473 - EF-hand 51695 - PLC-like phosphodiesterases | 0 | Direct |
57362,57362 57362 - BPTI-like 57362 - BPTI-like | 0 | Direct |
46785,46785 46785 - "Winged helix" DNA-binding domain 46785 - "Winged helix" DNA-binding domain | 0 | Direct |
57196,63825 57196 - EGF/Laminin 63825 - YWTD domain | 0 | Direct |
141072,141072 141072 - CalX-like 141072 - CalX-like | 0 | Direct |
53300,53300 53300 - vWA-like 53300 - vWA-like | 0 | Direct |
46938,52087 46938 - CRAL/TRIO N-terminal domain 52087 - CRAL/TRIO domain | 0 | Direct |
55021,56534 55021 - ACT-like 56534 - Aromatic aminoacid monoxygenases, catalytic and oligomerization domains | 0 | Direct |
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0 | Direct |
57196,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases | 0 | Direct |
57903,47370 57903 - FYVE/PHD zinc finger 47370 - Bromodomain | 0 | Direct |
53067,100920 53067 - Actin-like ATPase domain 100920 - Heat shock protein 70kD (HSP70), peptide-binding domain | 0 | Direct |
57184,57603 57184 - Growth factor receptor domain 57603 - FnI-like domain | 0 | Direct |
54001,143791 54001 - Cysteine proteinases 143791 - DUSP-like | 0 | Direct |
50978,50998 50978 - WD40 repeat-like 50998 - Quinoprotein alcohol dehydrogenase-like | 0 | Direct |
50156,50044 50156 - PDZ domain-like 50044 - SH3-domain | 0 | Direct |
54791,54791 54791 - Eukaryotic type KH-domain (KH-domain type I) 54791 - Eukaryotic type KH-domain (KH-domain type I) | 0 | Direct |
52743,49785 52743 - Subtilisin-like 49785 - Galactose-binding domain-like | 0 | Direct |
50447,50465 50447 - Translation proteins 50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0 | Direct |
54585,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
52540,50447 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins | 0 | Direct |
51556,51338 51556 - Metallo-dependent hydrolases 51338 - Composite domain of metallo-dependent hydrolases | 0 | Direct |
90257,57997 90257 - Myosin rod fragments 57997 - Tropomyosin | 0 | Direct |
63825,57196 63825 - YWTD domain 57196 - EGF/Laminin | 0 | Direct |
57196,90193 57196 - EGF/Laminin 90193 - Notch domain | 0 | Direct |
49854,57196 49854 - Spermadhesin, CUB domain 57196 - EGF/Laminin | 0 | Direct |
50692,54585 50692 - ADC-like 54585 - Cdc48 domain 2-like | 0 | Direct |
49417,47719 49417 - p53-like transcription factors 47719 - p53 tetramerization domain | 0 | Direct |
57850,57850 57850 - RING/U-box 57850 - RING/U-box | 0 | Direct |
52490,55307 52490 - Tubulin nucleotide-binding domain-like 55307 - Tubulin C-terminal domain-like | 0 | Direct |
57903,57903 57903 - FYVE/PHD zinc finger 57903 - FYVE/PHD zinc finger | 0 | Direct |
50729,56112 50729 - PH domain-like 56112 - Protein kinase-like (PK-like) | 0 | Direct |
48452,81901 48452 - TPR-like 81901 - HCP-like | 0 | Direct |
54160,52540 54160 - Chromo domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
57440,57440 57440 - Kringle-like 57440 - Kringle-like | 0.3359 | Inherited |
57196,49854 57196 - EGF/Laminin 49854 - Spermadhesin, CUB domain | 0.3359 | Inherited |
49313,49313 49313 - Cadherin-like 49313 - Cadherin-like | 0.641 | Inherited |
50156,50156 50156 - PDZ domain-like 50156 - PDZ domain-like | 0.705 | Inherited |
(show details)
Supra-domains annotated to this ZA term (SPZA level: Least 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) |
50729,47473,51695 50729 - PH domain-like 47473 - EF-hand 51695 - PLC-like phosphodiesterases | 0 | DIRECT |
57196,63825,57196 57196 - EGF/Laminin 63825 - YWTD domain 57196 - EGF/Laminin | 0 | DIRECT |
52540,50447,50465 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins 50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0 | DIRECT |
57196,57184,57196 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57196 - EGF/Laminin | 0 | DIRECT |
57184,57184,57196 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57196 - EGF/Laminin | 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 | DIRECT |
57196,49899,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases | 0 | DIRECT |
54160,52540,52540 54160 - Chromo domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
54585,52540,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
49854,57196,49854 49854 - Spermadhesin, CUB domain 57196 - EGF/Laminin 49854 - Spermadhesin, CUB domain | 0 | DIRECT |
57196,57196,90193 57196 - EGF/Laminin 57196 - EGF/Laminin 90193 - Notch domain | 0 | DIRECT |
90193,90193,90193 90193 - Notch domain 90193 - Notch domain 90193 - Notch domain | 0 | DIRECT |
54160,54160,52540 54160 - Chromo domain-like 54160 - Chromo domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0 | DIRECT |
52743,49785,57184 52743 - Subtilisin-like 49785 - Galactose-binding domain-like 57184 - Growth factor receptor domain | 0 | DIRECT |
57184,57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0 | DIRECT |
50156,50044,52540 50156 - PDZ domain-like 50044 - SH3-domain 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
54897,52743,49785 54897 - Protease propeptides/inhibitors 52743 - Subtilisin-like 49785 - Galactose-binding domain-like | 0 | DIRECT |
57850,57850,57850 57850 - RING/U-box 57850 - RING/U-box 57850 - RING/U-box | 0 | DIRECT |
50692,54585,52540 50692 - ADC-like 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
75399,75399,75399 75399 - Plakin repeat 75399 - Plakin repeat 75399 - Plakin repeat | 0 | DIRECT |
57424,57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module 57424 - LDL receptor-like module | 0 | DIRECT |
47031,50729,50729 47031 - Second domain of FERM 50729 - PH domain-like 50729 - PH domain-like | 0 | DIRECT |
57184,52058,49265 57184 - Growth factor receptor domain 52058 - L domain-like 49265 - Fibronectin type III | 0 | DIRECT |
57196,90193,90193 57196 - EGF/Laminin 90193 - Notch domain 90193 - Notch domain | 0 | DIRECT |
52058,49265,49265 52058 - L domain-like 49265 - Fibronectin type III 49265 - Fibronectin type III | 0 | DIRECT |
49313,49313,49313 49313 - Cadherin-like 49313 - Cadherin-like 49313 - Cadherin-like | 0.5066 | INHERITED FROM: retinal ganglion cell layer |
Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
50729,47473,51695 50729 - PH domain-like 47473 - EF-hand 51695 - PLC-like phosphodiesterases | 0 | Direct |
57196,63825,57196 57196 - EGF/Laminin 63825 - YWTD domain 57196 - EGF/Laminin | 0 | Direct |
52540,50447,50465 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins 50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0 | Direct |
57196,57184,57196 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57196 - EGF/Laminin | 0 | Direct |
57184,57184,57196 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57196 - EGF/Laminin | 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 | Direct |
57196,49899,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases | 0 | Direct |
54160,52540,52540 54160 - Chromo domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
54585,52540,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
49854,57196,49854 49854 - Spermadhesin, CUB domain 57196 - EGF/Laminin 49854 - Spermadhesin, CUB domain | 0 | Direct |
57196,57196,90193 57196 - EGF/Laminin 57196 - EGF/Laminin 90193 - Notch domain | 0 | Direct |
90193,90193,90193 90193 - Notch domain 90193 - Notch domain 90193 - Notch domain | 0 | Direct |
54160,54160,52540 54160 - Chromo domain-like 54160 - Chromo domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0 | Direct |
52743,49785,57184 52743 - Subtilisin-like 49785 - Galactose-binding domain-like 57184 - Growth factor receptor domain | 0 | Direct |
57184,57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0 | Direct |
50156,50044,52540 50156 - PDZ domain-like 50044 - SH3-domain 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
54897,52743,49785 54897 - Protease propeptides/inhibitors 52743 - Subtilisin-like 49785 - Galactose-binding domain-like | 0 | Direct |
57850,57850,57850 57850 - RING/U-box 57850 - RING/U-box 57850 - RING/U-box | 0 | Direct |
50692,54585,52540 50692 - ADC-like 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
75399,75399,75399 75399 - Plakin repeat 75399 - Plakin repeat 75399 - Plakin repeat | 0 | Direct |
57424,57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module 57424 - LDL receptor-like module | 0 | Direct |
47031,50729,50729 47031 - Second domain of FERM 50729 - PH domain-like 50729 - PH domain-like | 0 | Direct |
57184,52058,49265 57184 - Growth factor receptor domain 52058 - L domain-like 49265 - Fibronectin type III | 0 | Direct |
57196,90193,90193 57196 - EGF/Laminin 90193 - Notch domain 90193 - Notch domain | 0 | Direct |
52058,49265,49265 52058 - L domain-like 49265 - Fibronectin type III 49265 - Fibronectin type III | 0 | Direct |
49313,49313,49313 49313 - Cadherin-like 49313 - Cadherin-like 49313 - Cadherin-like | 0.5066 | Inherited |
Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term
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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
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