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Xenopus DEvelopment stage (XDE): embryonic stage
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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)
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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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) |
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 |
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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 (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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