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Zebrafish Anatomy (ZA): cell
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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)
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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) |
Arrestin/Vps26-like | 0 | DIRECT |
FAD-linked reductases, N-terminal domain | 0 | DIRECT |
NHL repeat | 0 | DIRECT |
Platelet-derived growth factor-like | 0 | DIRECT |
Cdc48 domain 2-like | 0 | DIRECT |
Hydantoinase (dihydropyrimidinase) | 0 | DIRECT |
Aquaporin-like | 0 | DIRECT |
FYVE, a phosphatidylinositol-3-phosphate binding domain | 0 | DIRECT |
28-residue LRR | 0 | DIRECT |
Adenylyl and guanylyl cyclase catalytic domain | 0 | DIRECT |
Tudor domain | 0 | DIRECT |
Ras-binding domain, RBD | 0 | DIRECT |
Plakophilin 1 helical region | 0 | DIRECT |
Caspase recruitment domain, CARD | 0 | DIRECT |
Cell cycle control phosphatase, catalytic domain | 0 | DIRECT |
Myeloperoxidase-like | 0 | DIRECT |
Nucleoplasmin-like core domain | 0 | DIRECT |
LCCL domain | 0 | DIRECT |
Connexin43 | 0 | DIRECT |
Papain-like | 0 | DIRECT |
Filamin repeat (rod domain) | 0 | DIRECT |
Troponin T | 0 | DIRECT |
Hormone receptor domain | 0 | DIRECT |
Heat shock protein 70kD (HSP70), peptide-binding domain | 0 | DIRECT |
FAS1 domain | 0 | DIRECT |
Hydantoinase (dihydropyrimidinase), catalytic domain | 0 | DIRECT |
Erythroid transcription factor GATA-1 | 0 | DIRECT |
Long-chain cytokines | 0 | DIRECT |
Myotubularin-like phosphatases | 0 | DIRECT |
Clathrin adaptor core protein | 0 | DIRECT |
Notch domain | 0 | DIRECT |
Cdc48 N-terminal domain-like | 0 | DIRECT |
GABA-aminotransferase-like | 0 | DIRECT |
Ovomucoid domain III-like | 0 | DIRECT |
Single strand DNA-binding domain, SSB | 0 | DIRECT |
BRK domain-like | 0 | DIRECT |
Paired domain | 0.03472 | INHERITED FROM: mechanoreceptor cell |
Myb/SANT domain | 0.04145 | INHERITED FROM: hematopoietic cell || granulocyte || neutrophil |
SMAD MH1 domain | 0.05224 | INHERITED FROM: mononuclear phagocyte || professional antigen presenting cell || mononuclear cell |
SMAD domain | 0.07722 | INHERITED FROM: mononuclear phagocyte || professional antigen presenting cell || mononuclear cell |
Myosin rod fragments | 0.08191 | INHERITED FROM: muscle cell |
Leucine zipper domain | 0.1121 | INHERITED FROM: myeloid lineage restricted progenitor cell |
Laminin-type module | 0.1121 | INHERITED FROM: slow muscle cell |
Group II chaperonin (CCT, TRIC), ATPase domain | 0.1125 | INHERITED FROM: skeletal muscle cell || muscle cell || striated muscle cell |
WD40-repeat | 0.1236 | INHERITED FROM: retinal cone cell |
SH2 domain | 0.1288 | INHERITED FROM: hematopoietic cell || nucleate erythrocyte || monocyte || lymphoid progenitor cell |
ets domain | 0.1529 | INHERITED FROM: granulocyte || myeloid leukocyte |
Homeodomain | 0.1531 | INHERITED FROM: pancreatic A cell || endocrine cell |
Phenylalanine metabolism regulatory domain | 0.1645 | INHERITED FROM: hematopoietic multipotent progenitor cell |
Aromatic aminoacid monoxygenases, catalytic and oligomerization domains | 0.1645 | INHERITED FROM: hematopoietic multipotent progenitor cell |
Short-chain cytokines | 0.1645 | INHERITED FROM: pigment cell |
Multidrug efflux transporter AcrB transmembrane domain | 0.1645 | INHERITED FROM: skeletal muscle cell || slow muscle cell |
Group II chaperonin (CCT, TRIC), intermediate domain | 0.1645 | INHERITED FROM: skeletal muscle cell || muscle cell || striated muscle cell |
Motor proteins | 0.2594 | INHERITED FROM: pronephric podocyte |
Group II chaperonin (CCT, TRIC), apical domain | 0.2784 | INHERITED FROM: skeletal muscle cell || muscle cell || striated muscle cell |
Bromodomain | 0.3575 | INHERITED FROM: hematopoietic cell |
Ankyrin repeat | 0.4137 | INHERITED FROM: radial glial cell |
Sema domain | 0.4357 | INHERITED FROM: CaP motoneuron || primary neuron || neuron neural crest derived || primary motor neuron |
L domain | 0.4566 | INHERITED FROM: neuron neural crest derived || motor neuron |
HLH, helix-loop-helix DNA-binding domain | 0.4893 | INHERITED FROM: Kolmer-Agduhr neuron |
DBL homology domain (DH-domain) | 0.4919 | INHERITED FROM: blood vessel endothelial cell |
Plexin repeat | 0.5755 | INHERITED FROM: CaP motoneuron || primary neuron || neuron neural crest derived || primary motor neuron |
MIR domain | 0.6711 | INHERITED FROM: skeletal muscle cell |
Extracellular domain of cell surface receptors | 0.6711 | INHERITED FROM: lining cell || endothelial cell || barrier cell |
Classic zinc finger, C2H2 | 0.7622 | INHERITED FROM: xanthoblast |
Frizzled cysteine-rich domain | 0.7754 | INHERITED FROM: stromal cell |
WW domain | 0.9233 | INHERITED FROM: striated muscle cell |
Tetratricopeptide repeat (TPR) | 1 | INHERITED FROM: retinal rod cell |
SCOP term | FDR (all) | Annotation (direct or inherited) |
Arrestin/Vps26-like | 0 | Direct |
FAD-linked reductases, N-terminal domain | 0 | Direct |
NHL repeat | 0 | Direct |
Platelet-derived growth factor-like | 0 | Direct |
Cdc48 domain 2-like | 0 | Direct |
Hydantoinase (dihydropyrimidinase) | 0 | Direct |
Aquaporin-like | 0 | Direct |
FYVE, a phosphatidylinositol-3-phosphate binding domain | 0 | Direct |
28-residue LRR | 0 | Direct |
Adenylyl and guanylyl cyclase catalytic domain | 0 | Direct |
Tudor domain | 0 | Direct |
Ras-binding domain, RBD | 0 | Direct |
Plakophilin 1 helical region | 0 | Direct |
Caspase recruitment domain, CARD | 0 | Direct |
Cell cycle control phosphatase, catalytic domain | 0 | Direct |
Myeloperoxidase-like | 0 | Direct |
Nucleoplasmin-like core domain | 0 | Direct |
LCCL domain | 0 | Direct |
Connexin43 | 0 | Direct |
Papain-like | 0 | Direct |
Filamin repeat (rod domain) | 0 | Direct |
Troponin T | 0 | Direct |
Hormone receptor domain | 0 | Direct |
Heat shock protein 70kD (HSP70), peptide-binding domain | 0 | Direct |
FAS1 domain | 0 | Direct |
Hydantoinase (dihydropyrimidinase), catalytic domain | 0 | Direct |
Erythroid transcription factor GATA-1 | 0 | Direct |
Long-chain cytokines | 0 | Direct |
Myotubularin-like phosphatases | 0 | Direct |
Clathrin adaptor core protein | 0 | Direct |
Notch domain | 0 | Direct |
Cdc48 N-terminal domain-like | 0 | Direct |
GABA-aminotransferase-like | 0 | Direct |
Ovomucoid domain III-like | 0 | Direct |
Single strand DNA-binding domain, SSB | 0 | Direct |
BRK domain-like | 0 | Direct |
Paired domain | 0.03472 | Inherited |
Myb/SANT domain | 0.04145 | Inherited |
SMAD MH1 domain | 0.05224 | Inherited |
SMAD domain | 0.07722 | Inherited |
Myosin rod fragments | 0.08191 | Inherited |
Leucine zipper domain | 0.1121 | Inherited |
Laminin-type module | 0.1121 | Inherited |
Group II chaperonin (CCT, TRIC), ATPase domain | 0.1125 | Inherited |
WD40-repeat | 0.1236 | Inherited |
SH2 domain | 0.1288 | Inherited |
ets domain | 0.1529 | Inherited |
Homeodomain | 0.1531 | Inherited |
Phenylalanine metabolism regulatory domain | 0.1645 | Inherited |
Aromatic aminoacid monoxygenases, catalytic and oligomerization domains | 0.1645 | Inherited |
Short-chain cytokines | 0.1645 | Inherited |
Multidrug efflux transporter AcrB transmembrane domain | 0.1645 | Inherited |
Group II chaperonin (CCT, TRIC), intermediate domain | 0.1645 | Inherited |
Motor proteins | 0.2594 | Inherited |
Group II chaperonin (CCT, TRIC), apical domain | 0.2784 | Inherited |
Bromodomain | 0.3575 | Inherited |
Ankyrin repeat | 0.4137 | Inherited |
Sema domain | 0.4357 | Inherited |
L domain | 0.4566 | Inherited |
HLH, helix-loop-helix DNA-binding domain | 0.4893 | Inherited |
DBL homology domain (DH-domain) | 0.4919 | Inherited |
Plexin repeat | 0.5755 | Inherited |
MIR domain | 0.6711 | Inherited |
Extracellular domain of cell surface receptors | 0.6711 | Inherited |
Classic zinc finger, C2H2 | 0.7622 | Inherited |
Frizzled cysteine-rich domain | 0.7754 | Inherited |
WW domain | 0.9233 | Inherited |
Tetratricopeptide repeat (TPR) | 1 | 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.
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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) |
55486,50923 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain | 0 | DIRECT |
103575,81296 103575 - Plexin repeat 81296 - E set domains | 0 | DIRECT |
111418,81321 111418 - Hormone receptor domain 81321 - Family A G protein-coupled receptor-like | 0 | DIRECT |
49854,49785 49854 - Spermadhesin, CUB domain 49785 - Galactose-binding domain-like | 0 | DIRECT |
51905,54373 51905 - FAD/NAD(P)-binding domain 54373 - FAD-linked reductases, C-terminal domain | 0 | DIRECT |
90193,90193 90193 - Notch domain 90193 - Notch domain | 0 | DIRECT |
53300,53300 53300 - vWA-like 53300 - vWA-like | 0 | DIRECT |
49785,49899 49785 - Galactose-binding domain-like 49899 - Concanavalin A-like lectins/glucanases | 0 | DIRECT |
53067,100920 53067 - Actin-like ATPase domain 100920 - Heat shock protein 70kD (HSP70), peptide-binding 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 |
100909,49899 100909 - IP3 receptor type 1 binding core, domain 2 49899 - Concanavalin A-like lectins/glucanases | 0 | DIRECT |
54585,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases | 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 |
52799,49562 52799 - (Phosphotyrosine protein) phosphatases II 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) | 0 | DIRECT |
57196,90193 57196 - EGF/Laminin 90193 - Notch domain | 0 | DIRECT |
82109,82109 82109 - MIR domain 82109 - MIR domain | 0 | DIRECT |
50692,54585 50692 - ADC-like 54585 - Cdc48 domain 2-like | 0 | DIRECT |
82153,82153 82153 - FAS1 domain 82153 - FAS1 domain | 0 | DIRECT |
90257,90257 90257 - Myosin rod fragments 90257 - Myosin rod fragments | 0.07243 | INHERITED FROM: muscle cell |
81296,81296 81296 - E set domains 81296 - E set domains | 0.07243 | INHERITED FROM: primary neuron || CaP motoneuron || primary motor neuron |
55550,55550 55550 - SH2 domain 55550 - SH2 domain | 0.1599 | INHERITED FROM: motile cell || leukocyte |
55021,56534 55021 - ACT-like 56534 - Aromatic aminoacid monoxygenases, catalytic and oligomerization domains | 0.1599 | INHERITED FROM: hematopoietic multipotent progenitor cell |
82109,100909 82109 - MIR domain 100909 - IP3 receptor type 1 binding core, domain 2 | 0.2342 | INHERITED FROM: muscle cell || striated muscle cell || skeletal muscle cell |
49265,48726 49265 - Fibronectin type III 48726 - Immunoglobulin | 0.2342 | INHERITED FROM: muscle cell || striated muscle cell || skeletal muscle cell |
54849,52029 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like | 0.2721 | INHERITED FROM: muscle cell || striated muscle cell || skeletal muscle cell |
48592,54849 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like | 0.2721 | INHERITED FROM: muscle cell || striated muscle cell || skeletal muscle cell |
48065,50729 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like | 0.3496 | INHERITED FROM: blood vessel endothelial cell || squamous epithelial cell |
46689,46689 46689 - Homeodomain-like 46689 - Homeodomain-like | 0.3606 | INHERITED FROM: myeloid lineage restricted progenitor cell |
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.3838 | INHERITED FROM: VeLD || Kolmer-Agduhr neuron |
101912,103575 101912 - Sema domain 103575 - Plexin repeat | 0.4263 | INHERITED FROM: primary neuron || CaP motoneuron || neuron neural crest derived || primary motor neuron |
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain | 0.4478 | INHERITED FROM: neuron neural crest derived || motor neuron |
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like | 0.4478 | INHERITED FROM: neuron neural crest derived || motor neuron |
50156,50156 50156 - PDZ domain-like 50156 - PDZ domain-like | 0.7399 | INHERITED FROM: eye photoreceptor cell |
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers | 0.8877 | INHERITED FROM: xanthoblast |
Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
55486,50923 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain | 0 | Direct |
103575,81296 103575 - Plexin repeat 81296 - E set domains | 0 | Direct |
111418,81321 111418 - Hormone receptor domain 81321 - Family A G protein-coupled receptor-like | 0 | Direct |
49854,49785 49854 - Spermadhesin, CUB domain 49785 - Galactose-binding domain-like | 0 | Direct |
51905,54373 51905 - FAD/NAD(P)-binding domain 54373 - FAD-linked reductases, C-terminal domain | 0 | Direct |
90193,90193 90193 - Notch domain 90193 - Notch domain | 0 | Direct |
53300,53300 53300 - vWA-like 53300 - vWA-like | 0 | Direct |
49785,49899 49785 - Galactose-binding domain-like 49899 - Concanavalin A-like lectins/glucanases | 0 | Direct |
53067,100920 53067 - Actin-like ATPase domain 100920 - Heat shock protein 70kD (HSP70), peptide-binding 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 |
100909,49899 100909 - IP3 receptor type 1 binding core, domain 2 49899 - Concanavalin A-like lectins/glucanases | 0 | Direct |
54585,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases | 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 |
52799,49562 52799 - (Phosphotyrosine protein) phosphatases II 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) | 0 | Direct |
57196,90193 57196 - EGF/Laminin 90193 - Notch domain | 0 | Direct |
82109,82109 82109 - MIR domain 82109 - MIR domain | 0 | Direct |
50692,54585 50692 - ADC-like 54585 - Cdc48 domain 2-like | 0 | Direct |
82153,82153 82153 - FAS1 domain 82153 - FAS1 domain | 0 | Direct |
90257,90257 90257 - Myosin rod fragments 90257 - Myosin rod fragments | 0.07243 | Inherited |
81296,81296 81296 - E set domains 81296 - E set domains | 0.07243 | Inherited |
55550,55550 55550 - SH2 domain 55550 - SH2 domain | 0.1599 | Inherited |
55021,56534 55021 - ACT-like 56534 - Aromatic aminoacid monoxygenases, catalytic and oligomerization domains | 0.1599 | Inherited |
82109,100909 82109 - MIR domain 100909 - IP3 receptor type 1 binding core, domain 2 | 0.2342 | Inherited |
49265,48726 49265 - Fibronectin type III 48726 - Immunoglobulin | 0.2342 | Inherited |
54849,52029 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like | 0.2721 | Inherited |
48592,54849 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like | 0.2721 | Inherited |
48065,50729 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like | 0.3496 | Inherited |
46689,46689 46689 - Homeodomain-like 46689 - Homeodomain-like | 0.3606 | Inherited |
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.3838 | Inherited |
101912,103575 101912 - Sema domain 103575 - Plexin repeat | 0.4263 | Inherited |
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain | 0.4478 | Inherited |
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like | 0.4478 | Inherited |
50156,50156 50156 - PDZ domain-like 50156 - PDZ domain-like | 0.7399 | Inherited |
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers | 0.8877 | 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) |
49854,49785,49785 49854 - Spermadhesin, CUB domain 49785 - Galactose-binding domain-like 49785 - Galactose-binding domain-like | 0 | DIRECT |
57196,57184,57196 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57196 - EGF/Laminin | 0 | DIRECT |
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain | 0 | DIRECT |
82109,100909,49899 82109 - MIR domain 100909 - IP3 receptor type 1 binding core, domain 2 49899 - Concanavalin A-like lectins/glucanases | 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 |
54585,52540,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
57196,57196,90193 57196 - EGF/Laminin 57196 - EGF/Laminin 90193 - Notch domain | 0 | DIRECT |
49785,49785,49899 49785 - Galactose-binding domain-like 49785 - Galactose-binding domain-like 49899 - Concanavalin A-like lectins/glucanases | 0 | DIRECT |
90193,90193,90193 90193 - Notch domain 90193 - Notch domain 90193 - Notch domain | 0 | DIRECT |
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0 | DIRECT |
82109,82109,100909 82109 - MIR domain 82109 - MIR domain 100909 - IP3 receptor type 1 binding core, domain 2 | 0 | DIRECT |
50692,54585,52540 50692 - ADC-like 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
47090,55486,50923 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain | 0 | DIRECT |
103575,81296,81296 103575 - Plexin repeat 81296 - E set domains 81296 - E set domains | 0 | DIRECT |
57196,90193,90193 57196 - EGF/Laminin 90193 - Notch domain 90193 - Notch domain | 0 | DIRECT |
81296,81296,81296 81296 - E set domains 81296 - E set domains 81296 - E set domains | 0.07243 | INHERITED FROM: primary neuron || CaP motoneuron || primary motor neuron |
48726,48726,49265 48726 - Immunoglobulin 48726 - Immunoglobulin 49265 - Fibronectin type III | 0.2265 | INHERITED FROM: skeletal muscle cell |
57184,52058,57184 57184 - Growth factor receptor domain 52058 - L domain-like 57184 - Growth factor receptor domain | 0.2342 | INHERITED FROM: neuron neural crest derived |
48726,49265,48726 48726 - Immunoglobulin 49265 - Fibronectin type III 48726 - Immunoglobulin | 0.2342 | INHERITED FROM: muscle cell || striated muscle cell || skeletal muscle cell |
48592,54849,52029 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like | 0.2721 | INHERITED FROM: muscle cell || striated muscle cell || skeletal muscle cell |
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like | 0.4478 | INHERITED FROM: neuron neural crest derived || motor neuron |
Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
49854,49785,49785 49854 - Spermadhesin, CUB domain 49785 - Galactose-binding domain-like 49785 - Galactose-binding domain-like | 0 | Direct |
57196,57184,57196 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57196 - EGF/Laminin | 0 | Direct |
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain | 0 | Direct |
82109,100909,49899 82109 - MIR domain 100909 - IP3 receptor type 1 binding core, domain 2 49899 - Concanavalin A-like lectins/glucanases | 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 |
54585,52540,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
57196,57196,90193 57196 - EGF/Laminin 57196 - EGF/Laminin 90193 - Notch domain | 0 | Direct |
49785,49785,49899 49785 - Galactose-binding domain-like 49785 - Galactose-binding domain-like 49899 - Concanavalin A-like lectins/glucanases | 0 | Direct |
90193,90193,90193 90193 - Notch domain 90193 - Notch domain 90193 - Notch domain | 0 | Direct |
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0 | Direct |
82109,82109,100909 82109 - MIR domain 82109 - MIR domain 100909 - IP3 receptor type 1 binding core, domain 2 | 0 | Direct |
50692,54585,52540 50692 - ADC-like 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
47090,55486,50923 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain | 0 | Direct |
103575,81296,81296 103575 - Plexin repeat 81296 - E set domains 81296 - E set domains | 0 | Direct |
57196,90193,90193 57196 - EGF/Laminin 90193 - Notch domain 90193 - Notch domain | 0 | Direct |
81296,81296,81296 81296 - E set domains 81296 - E set domains 81296 - E set domains | 0.07243 | Inherited |
48726,48726,49265 48726 - Immunoglobulin 48726 - Immunoglobulin 49265 - Fibronectin type III | 0.2265 | Inherited |
57184,52058,57184 57184 - Growth factor receptor domain 52058 - L domain-like 57184 - Growth factor receptor domain | 0.2342 | Inherited |
48726,49265,48726 48726 - Immunoglobulin 49265 - Fibronectin type III 48726 - Immunoglobulin | 0.2342 | Inherited |
48592,54849,52029 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like | 0.2721 | Inherited |
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like | 0.4478 | 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
large tree. This produces a higher quality topology than if the trees had been produced
on their own, and allows the trees to be displayed instantly.
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