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Xenopus ANatomical entity (XAN): mesoderm
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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)
Superfamily domains annotated to this XA term (SDXA level: Informative)
Highlighted in gray are those with FDR_all>0.001
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Family(show details)
Family domains annotated to this XA term (SDXA level: Informative)
Highlighted in gray are those with FDR_all>0.001
SCOP term | FDR (all) | Annotation (direct or inherited) |
Hedgehog (development protein), N-terminal signaling domain | 0 | DIRECT |
Guanido kinase catalytic domain | 0 | DIRECT |
Pointed domain | 0 | DIRECT |
Extracellular domain of cell surface receptors | 0 | DIRECT |
Guanido kinase N-terminal domain | 0 | DIRECT |
Noggin | 0 | DIRECT |
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain | 0 | DIRECT |
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain | 0 | DIRECT |
Homeodomain | 0.000000000009037 | DIRECT |
HLH, helix-loop-helix DNA-binding domain | 0.00000000003797 | DIRECT |
Frizzled cysteine-rich domain | 0.0000000001584 | DIRECT |
ets domain | 0.00000000239 | DIRECT |
Fibroblast growth factors (FGF) | 0.000003687 | DIRECT |
Transforming growth factor (TGF)-beta | 0.000004979 | DIRECT |
Hairy Orange domain | 0.00001897 | DIRECT |
Growth factor receptor domain | 0.00003559 | DIRECT |
L domain | 0.00008865 | DIRECT |
Paired domain | 0.000183 | DIRECT |
VWC domain | 0.0002408 | DIRECT |
Erythroid transcription factor GATA-1 | 0.0005116 | DIRECT |
T-box | 0.0005213 | DIRECT |
Hypoxia-inducible factor Hif2a, C-terminal domain | 0.0006021 | DIRECT |
SMAD MH1 domain | 0.0006252 | DIRECT |
Forkhead DNA-binding domain | 0.0008211 | DIRECT |
14-3-3 protein | 0.002104 | INHERITED FROM: somite |
Parvalbumin | 0.002505 | INHERITED FROM: somite |
Actin/HSP70 | 0.005196 | INHERITED FROM: head mesoderm || head somite || trunk somite |
Matrix metalloproteases, catalytic domain | 0.01137 | INHERITED FROM: fibroblast || mesodermal cell |
Protein kinases, catalytic subunit | 0.0144 | INHERITED FROM: head mesoderm |
SRF-like | 0.02151 | INHERITED FROM: head mesoderm || dermomyotome || myotome || trunk somite |
Glutathione peroxidase-like | 0.02459 | INHERITED FROM: presomitic mesoderm || paraxial mesoderm || presumptive paraxial mesoderm |
Classic zinc finger, C2H2 | 0.03015 | INHERITED FROM: splanchnic layer of lateral plate mesoderm |
Group II chaperonin (CCT, TRIC), apical domain | 0.06354 | INHERITED FROM: anterior dorsal lateral plate region |
Globins | 0.06546 | INHERITED FROM: anterior dorsal lateral plate region || hematopoietic stem cell |
Group II chaperonin (CCT, TRIC), intermediate domain | 0.06962 | INHERITED FROM: anterior dorsal lateral plate region |
Tropomyosin | 0.07112 | INHERITED FROM: dermomyotome || myotome |
Hemopexin-like domain | 0.07257 | INHERITED FROM: fibroblast || mesodermal cell |
Integrin domains | 0.2672 | INHERITED FROM: fibroblast || mesodermal cell |
SCOP term | FDR (all) | Annotation (direct or inherited) |
Hedgehog (development protein), N-terminal signaling domain | 0 | Direct |
Guanido kinase catalytic domain | 0 | Direct |
Pointed domain | 0 | Direct |
Extracellular domain of cell surface receptors | 0 | Direct |
Guanido kinase N-terminal domain | 0 | Direct |
Noggin | 0 | Direct |
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain | 0 | Direct |
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain | 0 | Direct |
Homeodomain | 0.000000000009037 | Direct |
HLH, helix-loop-helix DNA-binding domain | 0.00000000003797 | Direct |
Frizzled cysteine-rich domain | 0.0000000001584 | Direct |
ets domain | 0.00000000239 | Direct |
Fibroblast growth factors (FGF) | 0.000003687 | Direct |
Transforming growth factor (TGF)-beta | 0.000004979 | Direct |
Hairy Orange domain | 0.00001897 | Direct |
Growth factor receptor domain | 0.00003559 | Direct |
L domain | 0.00008865 | Direct |
Paired domain | 0.000183 | Direct |
VWC domain | 0.0002408 | Direct |
Erythroid transcription factor GATA-1 | 0.0005116 | Direct |
T-box | 0.0005213 | Direct |
Hypoxia-inducible factor Hif2a, C-terminal domain | 0.0006021 | Direct |
SMAD MH1 domain | 0.0006252 | Direct |
Forkhead DNA-binding domain | 0.0008211 | Direct |
14-3-3 protein | 0.002104 | Inherited |
Parvalbumin | 0.002505 | Inherited |
Actin/HSP70 | 0.005196 | Inherited |
Matrix metalloproteases, catalytic domain | 0.01137 | Inherited |
Protein kinases, catalytic subunit | 0.0144 | Inherited |
SRF-like | 0.02151 | Inherited |
Glutathione peroxidase-like | 0.02459 | Inherited |
Classic zinc finger, C2H2 | 0.03015 | Inherited |
Group II chaperonin (CCT, TRIC), apical domain | 0.06354 | Inherited |
Globins | 0.06546 | Inherited |
Group II chaperonin (CCT, TRIC), intermediate domain | 0.06962 | Inherited |
Tropomyosin | 0.07112 | Inherited |
Hemopexin-like domain | 0.07257 | Inherited |
Integrin domains | 0.2672 | Inherited |
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: 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) |
52540,53254 52540 - P-loop containing nucleoside triphosphate hydrolases 53254 - Phosphoglycerate mutase-like | 0 | DIRECT |
48034,55931 48034 - Guanido kinase N-terminal domain 55931 - Glutamine synthetase/guanido kinase | 0 | DIRECT |
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like | 0.00001101 | DIRECT |
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain | 0.0000588 | DIRECT |
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like | 0.0000588 | DIRECT |
63501,50242 63501 - Frizzled cysteine-rich domain 50242 - TIMP-like | 0.0003686 | DIRECT |
50729,56112 50729 - PH domain-like 56112 - Protein kinase-like (PK-like) | 0.0003686 | DIRECT |
47459,55785 47459 - HLH, helix-loop-helix DNA-binding domain 55785 - PYP-like sensor domain (PAS domain) | 0.001583 | INHERITED FROM: somite |
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers | 0.007319 | INHERITED FROM: lateral plate mesoderm || splanchnic layer of lateral plate mesoderm |
55785,55785 55785 - PYP-like sensor domain (PAS domain) 55785 - PYP-like sensor domain (PAS domain) | 0.007579 | INHERITED FROM: somite |
53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain | 0.01156 | INHERITED FROM: head somite |
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.02989 | INHERITED FROM: anterior dorsal lateral plate region |
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.1255 | INHERITED FROM: presomitic mesoderm |
Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
52540,53254 52540 - P-loop containing nucleoside triphosphate hydrolases 53254 - Phosphoglycerate mutase-like | 0 | Direct |
48034,55931 48034 - Guanido kinase N-terminal domain 55931 - Glutamine synthetase/guanido kinase | 0 | Direct |
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like | 0.00001101 | Direct |
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain | 0.0000588 | Direct |
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like | 0.0000588 | Direct |
63501,50242 63501 - Frizzled cysteine-rich domain 50242 - TIMP-like | 0.0003686 | Direct |
50729,56112 50729 - PH domain-like 56112 - Protein kinase-like (PK-like) | 0.0003686 | Direct |
47459,55785 47459 - HLH, helix-loop-helix DNA-binding domain 55785 - PYP-like sensor domain (PAS domain) | 0.001583 | Inherited |
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers | 0.007319 | Inherited |
55785,55785 55785 - PYP-like sensor domain (PAS domain) 55785 - PYP-like sensor domain (PAS domain) | 0.007579 | Inherited |
53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain | 0.01156 | Inherited |
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.02989 | Inherited |
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.1255 | Inherited |
(show details)
Supra-domains annotated to this XA term (SPXA level: 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 |
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like | 0.0003686 | DIRECT |
50044,55550,56112 50044 - SH3-domain 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) | 0.000664 | DIRECT |
47459,55785,55785 47459 - HLH, helix-loop-helix DNA-binding domain 55785 - PYP-like sensor domain (PAS domain) 55785 - PYP-like sensor domain (PAS domain) | 0.007579 | INHERITED FROM: somite |
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.01782 | INHERITED FROM: presomitic mesoderm || paraxial mesoderm |
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain | 0.02103 | INHERITED FROM: presomitic mesoderm |
48371,48371,48371 48371 - ARM repeat 48371 - ARM repeat 48371 - ARM repeat | 0.02177 | INHERITED FROM: trunk somite || tail somite |
57667,57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers | 0.6541 | INHERITED FROM: splanchnic layer of lateral plate mesoderm |
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 |
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like | 0.0003686 | Direct |
50044,55550,56112 50044 - SH3-domain 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) | 0.000664 | Direct |
47459,55785,55785 47459 - HLH, helix-loop-helix DNA-binding domain 55785 - PYP-like sensor domain (PAS domain) 55785 - PYP-like sensor domain (PAS domain) | 0.007579 | Inherited |
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.01782 | Inherited |
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain | 0.02103 | Inherited |
48371,48371,48371 48371 - ARM repeat 48371 - ARM repeat 48371 - ARM repeat | 0.02177 | Inherited |
57667,57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers | 0.6541 | Inherited |
Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term
 |
Plot tree as:
| |
Download Newick format tree:
|
(show help)
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.
|