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Xenopus DEvelopment stage (XDE): embryonic stage
(show info)
Phenotype Ontology
Like Gene Ontology (GO), phenotypy ontology classifies and organizes gene-mutant/null phenotypic information from the very general at the top to more specific terms in the directed acyclic graph (DAG) by viewing an individual term as a node and its relations to parental terms (allowing for multiple parents) as directed edges. To navigate this hierarchy, we display all parental phenotypic terms to the current phenotypic term of interest ordered by their shortest distances to the current term. Also, only direct children phenotypic terms of the current phenotypic term are listed. Phenotype ontologies we have incorporated are as follows:
- Disease Ontology (DO) Ontology (DO) DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI thesaurus, SNOMED and OMIM.
- Human Phenotype (HP) Ontology (HP) HP captures phenotypic abnormalities that are described in OMIM, along with the corresponding disease-causing genes. It includes three complementary biological concepts: Mode_of_Inheritance (MI), ONset_and_clinical_course (ON), and Phenotypic_Abnormality (PA).
- Mouse Phenotype (MP) Ontology (MP) MP describes phenotypes of the mouse after a specific gene is genetically disrupted. Using it, Mouse Genome Informatics (MGI) provides high-coverate gene-level phenotypes for the mouse.
- Worm Phenotype (WP) Ontology (WP) WP classifies and organizes phenotype descriptions for C. elegans and other nematodes. Using it, WormBase provides primary resource for phenotype annotations for C. elegans.
- Yeast Phenotype (YP) Ontology (YP) Based on YP which is the major contributor to the Ascomycete phenotype ontology, Saccharomyces Genome Database (SGD) provides single mutant phenotypes for every gene in the yeast genome.
- Fly Phenotype (FP) Ontology (FP) FP refers to FlyBase controlled vocabulary. Specifically, a structured controlled vocabulary is used for the annotation of alleles (for their mutagen etc) in FlyBase.
- Fly Anatomy (FA) Ontology (FA) FA is a structured controlled vocabulary of the anatomy of Drosophila melanogaster, used for the description of phenotypes and where a gene is expressed.
- Zebrafish Anatomy (ZA) Ontology (ZA) ZA displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
- Xenopus Anatomy (XA) Ontology (XA) XA represents the lineage of tissues and the timing of development for frogs (Xenopus laevis and Xenopus tropicalis). It is used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes.
- Arabidopsis Plant Ontology (AP) Ontology (AP) As a major contributor to Plant Ontology which describes plant anatomical and morphological structures (AN) and growth and developmental stages (DE), the Arabidopsis Information Resource (TAIR) provides arabidopsis plant ontology annotations for the model higher plant Arabidopsis thaliana.
- Enzyme Commission (EC) Ontology (EC) Each enzyme is allocated a four-digit EC number, the first three digits of which define the reaction catalysed and the fourth of which is a unique identifier (serial number). Each enzyme is also assigned a systematic name that uniquely defines the reaction catalysed.
- DrugBank ATC (DB) Ontology (DB) In the Anatomical Therapeutic Chemical (ATC) classification system, drugs are classified in groups at five different levels according to the organ or system (1st level, anatomical main group) on which they act and their therapeutic (2nd level, therapeutic subgroup), pharmacological (3rd level, pharmacological subgroup) and chemical properties (4th level, chemical subgroup; 5th level, chemical substance). Only drugs in DrugBank are considered.
- UniProtKB KeyWords (KW) Ontology (KW) Keywords in UniProtKB are controlled vocabulary, providing a summary of the entry content and are used to index UniProtKB/Swiss-Prot entries based on 10 categories (the category "Technical term" being excluded here). Each keyword is attributed manually to UniProtKB/Swiss-Prot entries and automatically to UniProtKB/TrEMBL entries (according to specific annotation rules).
- UniProtKB UniPathway (UP) Ontology (UP) UP is a fully manually curated resource for the representation and annotation of metabolic pathways, being used as controlled vocabulary for pathway annotation in UniProtKB.
Structural Domain Phenotype Ontology and its Annotations
Structural Classification of Proteins (SCOP) classifies evolutionary-related domains into Superfamily level and Family level. Using the phenotype ontologies above, we have generated the domain-centric phenotype annotations, and further identified those phenotype terms which are the most informative to annotate SCOP domains. Promisingly, domain-centric phenotypic annotations can serve as an alternative starting point to explore genotype-phenotype relationships. We provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.
- Structural Domain Disease Ontology (DO) Ontology (SDDO) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DO.txt, and the corresponding ontology:SDDO.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Human Phenotype (HP) Ontology (SDHP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2HP.txt, and the corresponding ontology:SDHP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Mouse Phenotype (MP) Ontology (SDMP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2MP.txt, and the corresponding ontology:SDMP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Worm Phenotype (WP) Ontology (SDWP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2WP.txt, and the corresponding ontology:SDWP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Yeast Phenotype (YP) Ontology (SDYP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2YP.txt, and the corresponding ontology:SDYP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Fly Phenotype (FP) Ontology (SDFP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FP.txt, and the corresponding ontology:SDFP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Fly Anatomy (FA) Ontology (SDFA) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FA.txt, and the corresponding ontology:SDFA.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Zebrafish Anatomy (ZA) Ontology (SDZA) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2ZA.txt, and the corresponding ontology:SDZA.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Xenopus Anatomy (XA) Ontology (SDXA) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2XA.txt, and the corresponding ontology:SDXA.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Arabidopsis Plant Ontology (AP) Ontology (SDAP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2AP.txt, and the corresponding ontology:SDAP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Enzyme Commission (EC) Ontology (SDEC) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2EC.txt, and the corresponding ontology:SDEC.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain DrugBank ATC (DB) Ontology (SDDB) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DB.txt, and the corresponding ontology:SDDB.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain UniProtKB KeyWords (KW) Ontology (SDKW) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2KW.txt, and the corresponding ontology:SDKW.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain UniProtKB UniPathway (UP) Ontology (SDUP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2UP.txt, and the corresponding ontology:SDUP.txt) and mysql tables (Domain2PO.sql.gz).
Supra-domain Phenotype Ontology and its Annotations
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are interested in domain combinations. Also, we provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.
- Supra-domain Domain Disease Ontology (DO) Ontology (SPDO) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DO.txt, and the corresponding ontology:SPDO.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Human Phenotype (HP) Ontology (SPHO) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2HP.txt, and the corresponding ontology:SPHO.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Mouse Phenotype (MP) Ontology (SPMP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2MP.txt, and the corresponding ontology:SPMP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Worm Phenotype (WP) Ontology (SPWP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2WP.txt, and the corresponding ontology:SPWP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Yeast Phenotype (YP) Ontology (SPYP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2YP.txt, and the corresponding ontology:SPYP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Fly Phenotype (FP) Ontology (SPFP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FP.txt, and the corresponding ontology:SPFP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Fly Anatomy (FA) Ontology (SPFA) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FA.txt, and the corresponding ontology:SPFA.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Zebrafish Anatomy (ZA) Ontology (SPZA) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2ZA.txt, and the corresponding ontology:SPZA.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Xenopus Anatomy (XA) Ontology (SPXA) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2XA.txt, and the corresponding ontology:SPXA.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Arabidopsis Plant Ontology (AP) Ontology (SPAP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2AP.txt, and the corresponding ontology:SPAP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Enzyme Commission (EC) Ontology (SPEC) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2EC.txt, and the corresponding ontology:SPEC.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain DrugBank ATC (DB) Ontology (SPDB) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DB.txt, and the corresponding ontology:SPDB.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain UniProtKB KeyWords (KW) Ontology (SPKW) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2KW.txt, and the corresponding ontology:SPKW.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain UniProtKB UniPathway (UP) Ontology (SPUP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2UP.txt, and the corresponding ontology:SPUP.txt) and mysql tables (SP2PO.sql.gz).
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Root: XA Hierarchy (Xenopus anatomy and development from Xenbase frog anatomy ontology)
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Superfamily(show details)
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Family(show details)
Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term
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Plot tree as:
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Download Newick format tree:
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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)
(show details)
(show details)
Supra-domains annotated to this XA term (SPXA level: Moderately Informative)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
46689,57667
46689 - Homeodomain-like
57667 - beta-beta-alpha zinc fingers | 0 | DIRECT |
49854,57424
49854 - Spermadhesin, CUB domain
57424 - LDL receptor-like module | 0 | DIRECT |
48371,101447
48371 - ARM repeat
101447 - Formin homology 2 domain (FH2 domain) | 0 | DIRECT |
57535,49854
57535 - Complement control module/SCR domain
49854 - Spermadhesin, CUB domain | 0 | DIRECT |
57196,50494
57196 - EGF/Laminin
50494 - Trypsin-like serine proteases | 0 | DIRECT |
52058,57184
52058 - L domain-like
57184 - Growth factor receptor domain | 0 | DIRECT |
57196,56436
57196 - EGF/Laminin
56436 - C-type lectin-like | 0 | DIRECT |
57535,57196
57535 - Complement control module/SCR domain
57196 - EGF/Laminin | 0 | DIRECT |
56487,56487
56487 - SRCR-like
56487 - SRCR-like | 0 | DIRECT |
47986,52129
47986 - DEATH domain
52129 - Caspase-like | 0 | DIRECT |
82615,82615
82615 - Polo-box domain
82615 - Polo-box domain | 0 | DIRECT |
52058,49265
52058 - L domain-like
49265 - Fibronectin type III | 0 | DIRECT |
56436,57535
56436 - C-type lectin-like
57535 - Complement control module/SCR domain | 0 | DIRECT |
57184,52058
57184 - Growth factor receptor domain
52058 - L domain-like | 0 | DIRECT |
89837,89837
89837 - Doublecortin (DC)
89837 - Doublecortin (DC) | 0 | DIRECT |
82895,57424
82895 - TSP-1 type 1 repeat
57424 - LDL receptor-like module | 0 | DIRECT |
46955,63763
46955 - Putative DNA-binding domain
63763 - SAND domain-like | 0 | DIRECT |
82185,82185
82185 - Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
82185 - Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain | 0 | DIRECT |
117839,117839
117839 - WWE domain
117839 - WWE domain | 0 | DIRECT |
50044,50156
50044 - SH3-domain
50156 - PDZ domain-like | 0 | DIRECT |
100895,48726
100895 - Kazal-type serine protease inhibitors
48726 - Immunoglobulin | 0 | DIRECT |
54236,48366
54236 - Ubiquitin-like
48366 - Ras GEF | 0 | DIRECT |
50044,47769
50044 - SH3-domain
47769 - SAM/Pointed domain | 0 | DIRECT |
52540,140990
52540 - P-loop containing nucleoside triphosphate hydrolases
140990 - FtsH protease domain-like | 0 | DIRECT |
57424,50494
57424 - LDL receptor-like module
50494 - Trypsin-like serine proteases | 0 | DIRECT |
48726,82895
48726 - Immunoglobulin
82895 - TSP-1 type 1 repeat | 0 | DIRECT |
103473,100895
103473 - MFS general substrate transporter
100895 - Kazal-type serine protease inhibitors | 0 | DIRECT |
117281,117281
117281 - Kelch motif
117281 - Kelch motif | 0 | DIRECT |
47576,48065
47576 - Calponin-homology domain, CH-domain
48065 - DBL homology domain (DH-domain) | 0 | DIRECT |
48350,50729
48350 - GTPase activation domain, GAP
50729 - PH domain-like | 0 | DIRECT |
101690,53098
101690 - PAZ domain
53098 - Ribonuclease H-like | 0 | DIRECT |
54236,50729
54236 - Ubiquitin-like
50729 - PH domain-like | 0 | DIRECT |
161111,160240
161111 - Cation efflux protein transmembrane domain-like
160240 - Cation efflux protein cytoplasmic domain-like | 0 | DIRECT |
48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.00003231 | DIRECT |
63712,90112
63712 - Nicotinic receptor ligand binding domain-like
90112 - Neurotransmitter-gated ion-channel transmembrane pore | 0.00005718 | DIRECT |
57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 0.00008696 | DIRECT |
47413,46689
47413 - lambda repressor-like DNA-binding domains
46689 - Homeodomain-like | 0.0002127 | DIRECT |
57603,57603
57603 - FnI-like domain
57603 - FnI-like domain | 0.01815 | INHERITED FROM: NF stage 10.5 |
50729,47473
50729 - PH domain-like
47473 - EF-hand | 0.02698 | INHERITED FROM: NF stage 29 and 30 |
51695,49562
51695 - PLC-like phosphodiesterases
49562 - C2 domain (Calcium/lipid-binding domain, CaLB) | 0.02698 | INHERITED FROM: NF stage 29 and 30 |
49313,49313
49313 - Cadherin-like
49313 - Cadherin-like | 0.02918 | INHERITED FROM: NF stage 35 and 36 |
57889,57889
57889 - Cysteine-rich domain
57889 - Cysteine-rich domain | 0.07181 | INHERITED FROM: gastrula stage |
55550,56112
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.5286 | INHERITED FROM: NF stage 31 |
55486,82895
55486 - Metalloproteases ("zincins"), catalytic domain
82895 - TSP-1 type 1 repeat | 1 | INHERITED FROM: NF stage 15 |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
46689,57667
46689 - Homeodomain-like
57667 - beta-beta-alpha zinc fingers | 0 | Direct |
49854,57424
49854 - Spermadhesin, CUB domain
57424 - LDL receptor-like module | 0 | Direct |
48371,101447
48371 - ARM repeat
101447 - Formin homology 2 domain (FH2 domain) | 0 | Direct |
57535,49854
57535 - Complement control module/SCR domain
49854 - Spermadhesin, CUB domain | 0 | Direct |
57196,50494
57196 - EGF/Laminin
50494 - Trypsin-like serine proteases | 0 | Direct |
52058,57184
52058 - L domain-like
57184 - Growth factor receptor domain | 0 | Direct |
57196,56436
57196 - EGF/Laminin
56436 - C-type lectin-like | 0 | Direct |
57535,57196
57535 - Complement control module/SCR domain
57196 - EGF/Laminin | 0 | Direct |
56487,56487
56487 - SRCR-like
56487 - SRCR-like | 0 | Direct |
47986,52129
47986 - DEATH domain
52129 - Caspase-like | 0 | Direct |
82615,82615
82615 - Polo-box domain
82615 - Polo-box domain | 0 | Direct |
52058,49265
52058 - L domain-like
49265 - Fibronectin type III | 0 | Direct |
56436,57535
56436 - C-type lectin-like
57535 - Complement control module/SCR domain | 0 | Direct |
57184,52058
57184 - Growth factor receptor domain
52058 - L domain-like | 0 | Direct |
89837,89837
89837 - Doublecortin (DC)
89837 - Doublecortin (DC) | 0 | Direct |
82895,57424
82895 - TSP-1 type 1 repeat
57424 - LDL receptor-like module | 0 | Direct |
46955,63763
46955 - Putative DNA-binding domain
63763 - SAND domain-like | 0 | Direct |
82185,82185
82185 - Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
82185 - Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain | 0 | Direct |
117839,117839
117839 - WWE domain
117839 - WWE domain | 0 | Direct |
50044,50156
50044 - SH3-domain
50156 - PDZ domain-like | 0 | Direct |
100895,48726
100895 - Kazal-type serine protease inhibitors
48726 - Immunoglobulin | 0 | Direct |
54236,48366
54236 - Ubiquitin-like
48366 - Ras GEF | 0 | Direct |
50044,47769
50044 - SH3-domain
47769 - SAM/Pointed domain | 0 | Direct |
52540,140990
52540 - P-loop containing nucleoside triphosphate hydrolases
140990 - FtsH protease domain-like | 0 | Direct |
57424,50494
57424 - LDL receptor-like module
50494 - Trypsin-like serine proteases | 0 | Direct |
48726,82895
48726 - Immunoglobulin
82895 - TSP-1 type 1 repeat | 0 | Direct |
103473,100895
103473 - MFS general substrate transporter
100895 - Kazal-type serine protease inhibitors | 0 | Direct |
117281,117281
117281 - Kelch motif
117281 - Kelch motif | 0 | Direct |
47576,48065
47576 - Calponin-homology domain, CH-domain
48065 - DBL homology domain (DH-domain) | 0 | Direct |
48350,50729
48350 - GTPase activation domain, GAP
50729 - PH domain-like | 0 | Direct |
101690,53098
101690 - PAZ domain
53098 - Ribonuclease H-like | 0 | Direct |
54236,50729
54236 - Ubiquitin-like
50729 - PH domain-like | 0 | Direct |
161111,160240
161111 - Cation efflux protein transmembrane domain-like
160240 - Cation efflux protein cytoplasmic domain-like | 0 | Direct |
48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.00003231 | Direct |
63712,90112
63712 - Nicotinic receptor ligand binding domain-like
90112 - Neurotransmitter-gated ion-channel transmembrane pore | 0.00005718 | Direct |
57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 0.00008696 | Direct |
47413,46689
47413 - lambda repressor-like DNA-binding domains
46689 - Homeodomain-like | 0.0002127 | Direct |
57603,57603
57603 - FnI-like domain
57603 - FnI-like domain | 0.01815 | Inherited |
50729,47473
50729 - PH domain-like
47473 - EF-hand | 0.02698 | Inherited |
51695,49562
51695 - PLC-like phosphodiesterases
49562 - C2 domain (Calcium/lipid-binding domain, CaLB) | 0.02698 | Inherited |
49313,49313
49313 - Cadherin-like
49313 - Cadherin-like | 0.02918 | Inherited |
57889,57889
57889 - Cysteine-rich domain
57889 - Cysteine-rich domain | 0.07181 | Inherited |
55550,56112
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.5286 | Inherited |
55486,82895
55486 - Metalloproteases ("zincins"), catalytic domain
82895 - TSP-1 type 1 repeat | 1 | 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) |
57184,52058,57184
57184 - Growth factor receptor domain
52058 - L domain-like
57184 - Growth factor receptor domain | 0 | DIRECT |
52058,49265,49265
52058 - L domain-like
49265 - Fibronectin type III
49265 - Fibronectin type III | 0 | DIRECT |
57630,57196,57196
57630 - GLA-domain
57196 - EGF/Laminin
57196 - EGF/Laminin | 0 | DIRECT |
57184,57196,57184
57184 - Growth factor receptor domain
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0 | DIRECT |
48726,48726,82895
48726 - Immunoglobulin
48726 - Immunoglobulin
82895 - TSP-1 type 1 repeat | 0 | DIRECT |
52058,48726,49265
52058 - L domain-like
48726 - Immunoglobulin
49265 - Fibronectin type III | 0 | DIRECT |
57196,57535,57535
57196 - EGF/Laminin
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0 | DIRECT |
141072,141072,141072
141072 - CalX-like
141072 - CalX-like
141072 - CalX-like | 0 | DIRECT |
57535,49854,57535
57535 - Complement control module/SCR domain
49854 - Spermadhesin, CUB domain
57535 - Complement control module/SCR domain | 0 | DIRECT |
52058,57184,52058
52058 - L domain-like
57184 - Growth factor receptor domain
52058 - L domain-like | 0 | DIRECT |
57184,52058,49265
57184 - Growth factor receptor domain
52058 - L domain-like
49265 - Fibronectin type III | 0 | DIRECT |
47576,48065,50729
47576 - Calponin-homology domain, CH-domain
48065 - DBL homology domain (DH-domain)
50729 - PH domain-like | 0 | DIRECT |
54511,57184,57184
54511 - GFP-like
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain | 0 | DIRECT |
48726,82895,82895
48726 - Immunoglobulin
82895 - TSP-1 type 1 repeat
82895 - TSP-1 type 1 repeat | 0 | DIRECT |
48726,48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.0001243 | DIRECT |
57667,57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 0.0006688 | DIRECT |
49313,49313,49313
49313 - Cadherin-like
49313 - Cadherin-like
49313 - Cadherin-like | 0.05167 | INHERITED FROM: NF stage 35 and 36 |
48065,50729,50044
48065 - DBL homology domain (DH-domain)
50729 - PH domain-like
50044 - SH3-domain | 0.1008 | INHERITED FROM: NF stage 10.5 |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57184,52058,57184
57184 - Growth factor receptor domain
52058 - L domain-like
57184 - Growth factor receptor domain | 0 | Direct |
52058,49265,49265
52058 - L domain-like
49265 - Fibronectin type III
49265 - Fibronectin type III | 0 | Direct |
57630,57196,57196
57630 - GLA-domain
57196 - EGF/Laminin
57196 - EGF/Laminin | 0 | Direct |
57184,57196,57184
57184 - Growth factor receptor domain
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0 | Direct |
48726,48726,82895
48726 - Immunoglobulin
48726 - Immunoglobulin
82895 - TSP-1 type 1 repeat | 0 | Direct |
52058,48726,49265
52058 - L domain-like
48726 - Immunoglobulin
49265 - Fibronectin type III | 0 | Direct |
57196,57535,57535
57196 - EGF/Laminin
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0 | Direct |
141072,141072,141072
141072 - CalX-like
141072 - CalX-like
141072 - CalX-like | 0 | Direct |
57535,49854,57535
57535 - Complement control module/SCR domain
49854 - Spermadhesin, CUB domain
57535 - Complement control module/SCR domain | 0 | Direct |
52058,57184,52058
52058 - L domain-like
57184 - Growth factor receptor domain
52058 - L domain-like | 0 | Direct |
57184,52058,49265
57184 - Growth factor receptor domain
52058 - L domain-like
49265 - Fibronectin type III | 0 | Direct |
47576,48065,50729
47576 - Calponin-homology domain, CH-domain
48065 - DBL homology domain (DH-domain)
50729 - PH domain-like | 0 | Direct |
54511,57184,57184
54511 - GFP-like
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain | 0 | Direct |
48726,82895,82895
48726 - Immunoglobulin
82895 - TSP-1 type 1 repeat
82895 - TSP-1 type 1 repeat | 0 | Direct |
48726,48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.0001243 | Direct |
57667,57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 0.0006688 | Direct |
49313,49313,49313
49313 - Cadherin-like
49313 - Cadherin-like
49313 - Cadherin-like | 0.05167 | Inherited |
48065,50729,50044
48065 - DBL homology domain (DH-domain)
50729 - PH domain-like
50044 - SH3-domain | 0.1008 | 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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