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Xenopus ANatomical entity (XAN): embryonic structure
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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: XA Hierarchy (Xenopus anatomy and development from Xenbase frog 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 XA term (SDXA level: Moderately Informative)
Highlighted in gray are those with FDR_all>0.001
SCOP term | FDR (all) | Annotation (direct or inherited) |
Alanine racemase-like, N-terminal domain | 0 | DIRECT |
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain | 0 | DIRECT |
SH3BGR (SH3-binding, glutamic acid-rich protein-like) | 0 | DIRECT |
Hedgehog (development protein), N-terminal signaling domain | 0 | DIRECT |
Guanido kinase N-terminal domain | 0 | DIRECT |
LysM domain | 0 | DIRECT |
Ran-binding domain | 0 | DIRECT |
SRF-like | 0 | DIRECT |
Cysteine-rich DNA binding domain, (DM domain) | 0 | DIRECT |
Fibroblast growth factors (FGF) | 0 | DIRECT |
Noggin | 0 | DIRECT |
Eukaryotic ODC-like | 0 | DIRECT |
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain | 0 | DIRECT |
Guanido kinase catalytic domain | 0 | DIRECT |
Pointed domain | 0 | DIRECT |
Homeodomain | 0 | DIRECT |
Extracellular domain of cell surface receptors | 0 | DIRECT |
Synuclein | 0 | DIRECT |
14-3-3 protein | 0 | DIRECT |
HLH, helix-loop-helix DNA-binding domain | 0.0000000000002587 | DIRECT |
Canonical RBD | 0.000000000001107 | DIRECT |
Forkhead DNA-binding domain | 0.000000000001163 | DIRECT |
ets domain | 0.00000005123 | DIRECT |
Transforming growth factor (TGF)-beta | 0.0000006152 | DIRECT |
Frizzled cysteine-rich domain | 0.000001489 | DIRECT |
HMG-box | 0.00006854 | DIRECT |
Sema domain | 0.0004016 | DIRECT |
T-box | 0.0004338 | DIRECT |
POU-specific domain | 0.001066 | INHERITED FROM: neural tube || presumptive midbrain-hindbrain boundary || neurogenic placode |
LIM domain | 0.003692 | INHERITED FROM: cranial placode |
Hairy Orange domain | 0.004263 | INHERITED FROM: neural tube || lateral plate mesoderm || cranial placode || presomitic mesoderm || chordoneural hinge || paraxial mesoderm |
Cell cycle control phosphatase, catalytic domain | 0.005767 | INHERITED FROM: neural tube |
P4 origin-binding domain-like | 0.005767 | INHERITED FROM: neural tube || optic vesicle || cranial placode || neurogenic placode || otic placode |
Group II chaperonin (CCT, TRIC), apical domain | 0.0105 | INHERITED FROM: anterior dorsal lateral plate region |
Group II chaperonin (CCT, TRIC), intermediate domain | 0.01557 | INHERITED FROM: anterior dorsal lateral plate region |
Plexin repeat | 0.01715 | INHERITED FROM: cranial placode || presumptive midbrain-hindbrain boundary || liver primordium || otic placode |
Erythroid transcription factor GATA-1 | 0.02477 | INHERITED FROM: cardiac mesoderm || hematopoietic stem cell || lateral plate mesoderm || anterior dorsal lateral plate region || primordium || liver diverticulum || cardiac progenitor cell |
Eukaryotic type KH-domain (KH-domain type I) | 0.02557 | INHERITED FROM: upper blastopore lip |
VWC domain | 0.03149 | INHERITED FROM: neural tube || prechordal plate |
Glutathione peroxidase-like | 0.06008 | INHERITED FROM: presumptive paraxial mesoderm || foregut || eye primordium || presomitic mesoderm || paraxial mesoderm |
Paired domain | 0.0614 | INHERITED FROM: posterior neural tube || neural tube || cranial placode || primordium || neurogenic placode || anterior neural tube |
Tandem AAA-ATPase domain | 0.08095 | INHERITED FROM: upper blastopore lip || blastopore || blastopore lip || marginal zone || vegetal yolk mass |
Transducin (alpha subunit), insertion domain | 0.1001 | INHERITED FROM: dorsal marginal zone |
Classic zinc finger, C2H2 | 0.1184 | INHERITED FROM: presumptive rhombomere || splanchnic layer of lateral plate mesoderm |
Class I aldolase | 0.1214 | INHERITED FROM: primordium |
Tropomyosin | 0.1946 | INHERITED FROM: cardiac mesoderm |
Mannose 6-phosphate receptor domain | 0.2053 | INHERITED FROM: cement gland primordium |
Arginine methyltransferase | 0.2261 | INHERITED FROM: optic vesicle |
Alpha-macroglobulin receptor domain | 0.2261 | INHERITED FROM: hindgut || foregut || midgut |
Globins | 0.2638 | INHERITED FROM: hematopoietic stem cell || anterior dorsal lateral plate region |
Complement components | 0.3386 | INHERITED FROM: hindgut || midgut |
LDL receptor-like module | 0.5887 | INHERITED FROM: hindgut |
I set domains | 0.7491 | INHERITED FROM: optic vesicle |
SCOP term | FDR (all) | Annotation (direct or inherited) |
Alanine racemase-like, N-terminal domain | 0 | Direct |
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain | 0 | Direct |
SH3BGR (SH3-binding, glutamic acid-rich protein-like) | 0 | Direct |
Hedgehog (development protein), N-terminal signaling domain | 0 | Direct |
Guanido kinase N-terminal domain | 0 | Direct |
LysM domain | 0 | Direct |
Ran-binding domain | 0 | Direct |
SRF-like | 0 | Direct |
Cysteine-rich DNA binding domain, (DM domain) | 0 | Direct |
Fibroblast growth factors (FGF) | 0 | Direct |
Noggin | 0 | Direct |
Eukaryotic ODC-like | 0 | Direct |
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain | 0 | Direct |
Guanido kinase catalytic domain | 0 | Direct |
Pointed domain | 0 | Direct |
Homeodomain | 0 | Direct |
Extracellular domain of cell surface receptors | 0 | Direct |
Synuclein | 0 | Direct |
14-3-3 protein | 0 | Direct |
HLH, helix-loop-helix DNA-binding domain | 0.0000000000002587 | Direct |
Canonical RBD | 0.000000000001107 | Direct |
Forkhead DNA-binding domain | 0.000000000001163 | Direct |
ets domain | 0.00000005123 | Direct |
Transforming growth factor (TGF)-beta | 0.0000006152 | Direct |
Frizzled cysteine-rich domain | 0.000001489 | Direct |
HMG-box | 0.00006854 | Direct |
Sema domain | 0.0004016 | Direct |
T-box | 0.0004338 | Direct |
POU-specific domain | 0.001066 | Inherited |
LIM domain | 0.003692 | Inherited |
Hairy Orange domain | 0.004263 | Inherited |
Cell cycle control phosphatase, catalytic domain | 0.005767 | Inherited |
P4 origin-binding domain-like | 0.005767 | Inherited |
Group II chaperonin (CCT, TRIC), apical domain | 0.0105 | Inherited |
Group II chaperonin (CCT, TRIC), intermediate domain | 0.01557 | Inherited |
Plexin repeat | 0.01715 | Inherited |
Erythroid transcription factor GATA-1 | 0.02477 | Inherited |
Eukaryotic type KH-domain (KH-domain type I) | 0.02557 | Inherited |
VWC domain | 0.03149 | Inherited |
Glutathione peroxidase-like | 0.06008 | Inherited |
Paired domain | 0.0614 | Inherited |
Tandem AAA-ATPase domain | 0.08095 | Inherited |
Transducin (alpha subunit), insertion domain | 0.1001 | Inherited |
Classic zinc finger, C2H2 | 0.1184 | Inherited |
Class I aldolase | 0.1214 | Inherited |
Tropomyosin | 0.1946 | Inherited |
Mannose 6-phosphate receptor domain | 0.2053 | Inherited |
Arginine methyltransferase | 0.2261 | Inherited |
Alpha-macroglobulin receptor domain | 0.2261 | Inherited |
Globins | 0.2638 | Inherited |
Complement components | 0.3386 | Inherited |
LDL receptor-like module | 0.5887 | Inherited |
I set domains | 0.7491 | 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 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) |
103647,103647 103647 - TSP type-3 repeat 103647 - TSP type-3 repeat | 0 | DIRECT |
53223,51735 53223 - Aminoacid dehydrogenase-like, N-terminal domain 51735 - NAD(P)-binding Rossmann-fold domains | 0 | DIRECT |
54534,54534 54534 - FKBP-like 54534 - FKBP-like | 0 | DIRECT |
47095,47095 47095 - HMG-box 47095 - HMG-box | 0 | DIRECT |
52540,53254 52540 - P-loop containing nucleoside triphosphate hydrolases 53254 - Phosphoglycerate mutase-like | 0 | DIRECT |
49899,48726 49899 - Concanavalin A-like lectins/glucanases 48726 - Immunoglobulin | 0 | DIRECT |
51419,50621 51419 - PLP-binding barrel 50621 - Alanine racemase C-terminal domain-like | 0 | DIRECT |
63501,50242 63501 - Frizzled cysteine-rich domain 50242 - TIMP-like | 0 | DIRECT |
48034,55931 48034 - Guanido kinase N-terminal domain 55931 - Glutamine synthetase/guanido kinase | 0 | DIRECT |
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.0000003013 | DIRECT |
54928,54928 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD | 0.0000299 | DIRECT |
101912,103575 101912 - Sema domain 103575 - Plexin repeat | 0.0006265 | DIRECT |
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like | 0.0006265 | DIRECT |
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like | 0.003255 | INHERITED FROM: presomitic mesoderm || chordoneural hinge || lateral plate mesoderm || neural tube || paraxial mesoderm || cranial placode |
90209,90209 90209 - Ran binding protein zinc finger-like 90209 - Ran binding protein zinc finger-like | 0.01302 | INHERITED FROM: blastopore || blastopore lip || marginal zone || upper blastopore lip || vegetal yolk mass |
103575,48726 103575 - Plexin repeat 48726 - Immunoglobulin | 0.02047 | INHERITED FROM: cranial placode |
57440,57440 57440 - Kringle-like 57440 - Kringle-like | 0.02047 | INHERITED FROM: neurogenic placode |
47413,46689 47413 - lambda repressor-like DNA-binding domains 46689 - Homeodomain-like | 0.02371 | INHERITED FROM: presumptive midbrain-hindbrain boundary || neurogenic placode |
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers | 0.06421 | INHERITED FROM: presumptive rhombomere || lateral plate mesoderm || splanchnic layer of lateral plate mesoderm |
55550,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) | 0.06647 | INHERITED FROM: non-involuting marginal zone |
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases | 0.083 | INHERITED FROM: dorsal marginal zone |
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.1053 | INHERITED FROM: dorsal marginal zone |
57850,49599 57850 - RING/U-box 49599 - TRAF domain-like | 0.1063 | INHERITED FROM: optic vesicle |
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain | 0.1116 | INHERITED FROM: circumblastoporal collar |
52540,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases | 0.1797 | INHERITED FROM: blastopore || blastopore lip || upper blastopore lip || vegetal yolk mass |
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.4783 | INHERITED FROM: presomitic mesoderm || dorsal marginal zone |
50044,55550 50044 - SH3-domain 55550 - SH2 domain | 0.5042 | INHERITED FROM: non-involuting marginal zone |
Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
103647,103647 103647 - TSP type-3 repeat 103647 - TSP type-3 repeat | 0 | Direct |
53223,51735 53223 - Aminoacid dehydrogenase-like, N-terminal domain 51735 - NAD(P)-binding Rossmann-fold domains | 0 | Direct |
54534,54534 54534 - FKBP-like 54534 - FKBP-like | 0 | Direct |
47095,47095 47095 - HMG-box 47095 - HMG-box | 0 | Direct |
52540,53254 52540 - P-loop containing nucleoside triphosphate hydrolases 53254 - Phosphoglycerate mutase-like | 0 | Direct |
49899,48726 49899 - Concanavalin A-like lectins/glucanases 48726 - Immunoglobulin | 0 | Direct |
51419,50621 51419 - PLP-binding barrel 50621 - Alanine racemase C-terminal domain-like | 0 | Direct |
63501,50242 63501 - Frizzled cysteine-rich domain 50242 - TIMP-like | 0 | Direct |
48034,55931 48034 - Guanido kinase N-terminal domain 55931 - Glutamine synthetase/guanido kinase | 0 | Direct |
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.0000003013 | Direct |
54928,54928 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD | 0.0000299 | Direct |
101912,103575 101912 - Sema domain 103575 - Plexin repeat | 0.0006265 | Direct |
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like | 0.0006265 | Direct |
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like | 0.003255 | Inherited |
90209,90209 90209 - Ran binding protein zinc finger-like 90209 - Ran binding protein zinc finger-like | 0.01302 | Inherited |
103575,48726 103575 - Plexin repeat 48726 - Immunoglobulin | 0.02047 | Inherited |
57440,57440 57440 - Kringle-like 57440 - Kringle-like | 0.02047 | Inherited |
47413,46689 47413 - lambda repressor-like DNA-binding domains 46689 - Homeodomain-like | 0.02371 | Inherited |
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers | 0.06421 | Inherited |
55550,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) | 0.06647 | Inherited |
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases | 0.083 | Inherited |
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.1053 | Inherited |
57850,49599 57850 - RING/U-box 49599 - TRAF domain-like | 0.1063 | Inherited |
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain | 0.1116 | Inherited |
52540,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases | 0.1797 | Inherited |
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.4783 | Inherited |
50044,55550 50044 - SH3-domain 55550 - SH2 domain | 0.5042 | 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) |
103647,103647,49899 103647 - TSP type-3 repeat 103647 - TSP type-3 repeat 49899 - Concanavalin A-like lectins/glucanases | 0 | DIRECT |
103647,103647,103647 103647 - TSP type-3 repeat 103647 - TSP type-3 repeat 103647 - TSP type-3 repeat | 0 | DIRECT |
47220,47220,47220 47220 - alpha-catenin/vinculin-like 47220 - alpha-catenin/vinculin-like 47220 - alpha-catenin/vinculin-like | 0 | DIRECT |
49899,48726,49265 49899 - Concanavalin A-like lectins/glucanases 48726 - Immunoglobulin 49265 - Fibronectin type III | 0 | DIRECT |
57603,57603,57603 57603 - FnI-like domain 57603 - FnI-like domain 57603 - FnI-like domain | 0.004661 | INHERITED FROM: circumblastoporal collar || neural tube |
50044,55550,56112 50044 - SH3-domain 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) | 0.01053 | INHERITED FROM: non-involuting marginal zone |
101912,103575,48726 101912 - Sema domain 103575 - Plexin repeat 48726 - Immunoglobulin | 0.02047 | INHERITED FROM: cranial placode |
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.03668 | INHERITED FROM: non-neurogenic ectodermal placode |
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain | 0.05133 | INHERITED FROM: presomitic mesoderm || dorsal marginal zone |
48371,48371,48371 48371 - ARM repeat 48371 - ARM repeat 48371 - ARM repeat | 0.05182 | INHERITED FROM: chordoneural hinge |
48726,49265,49265 48726 - Immunoglobulin 49265 - Fibronectin type III 49265 - Fibronectin type III | 0.1063 | INHERITED FROM: optic vesicle |
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.1072 | INHERITED FROM: presomitic mesoderm || dorsal marginal zone || paraxial mesoderm |
57667,57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers | 0.9571 | INHERITED FROM: splanchnic layer of lateral plate mesoderm |
Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
103647,103647,49899 103647 - TSP type-3 repeat 103647 - TSP type-3 repeat 49899 - Concanavalin A-like lectins/glucanases | 0 | Direct |
103647,103647,103647 103647 - TSP type-3 repeat 103647 - TSP type-3 repeat 103647 - TSP type-3 repeat | 0 | Direct |
47220,47220,47220 47220 - alpha-catenin/vinculin-like 47220 - alpha-catenin/vinculin-like 47220 - alpha-catenin/vinculin-like | 0 | Direct |
49899,48726,49265 49899 - Concanavalin A-like lectins/glucanases 48726 - Immunoglobulin 49265 - Fibronectin type III | 0 | Direct |
57603,57603,57603 57603 - FnI-like domain 57603 - FnI-like domain 57603 - FnI-like domain | 0.004661 | Inherited |
50044,55550,56112 50044 - SH3-domain 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) | 0.01053 | Inherited |
101912,103575,48726 101912 - Sema domain 103575 - Plexin repeat 48726 - Immunoglobulin | 0.02047 | Inherited |
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.03668 | Inherited |
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain | 0.05133 | Inherited |
48371,48371,48371 48371 - ARM repeat 48371 - ARM repeat 48371 - ARM repeat | 0.05182 | Inherited |
48726,49265,49265 48726 - Immunoglobulin 49265 - Fibronectin type III 49265 - Fibronectin type III | 0.1063 | Inherited |
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.1072 | Inherited |
57667,57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers | 0.9571 | 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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