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Mammalian Phenotype (MP): abnormal skin adnexa morphology
(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: MP Hierarchy (mammalian/mouse phenotype from MGI_4.41)
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Superfamily(show details)
Superfamily domains annotated to this MP term (Not in SDMP)
Highlighted in gray are those with FDR_all>0.001
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
 |
Plot tree as:
| |
Download Newick format tree:
|
(show help)
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)
Supra-domains annotated to this MP term (Not in SPMP)
Highlighted in gray are those with FDR>0.001
(show details)
Supra-domains annotated to this MP term (Not in SPMP)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
49417,47719
49417 - p53-like transcription factors
47719 - p53 tetramerization domain | 0 | DIRECT |
48092,47655
48092 - Transcription factor STAT-4 N-domain
47655 - STAT | 0.000177 | DIRECT |
52058,57184
52058 - L domain-like
57184 - Growth factor receptor domain | 0.000177 | DIRECT |
57184,52058
57184 - Growth factor receptor domain
52058 - L domain-like | 0.000177 | DIRECT |
49417,55550
49417 - p53-like transcription factors
55550 - SH2 domain | 0.000177 | DIRECT |
47655,49417
47655 - STAT
49417 - p53-like transcription factors | 0.000177 | DIRECT |
57903,51197
57903 - FYVE/PHD zinc finger
51197 - Clavaminate synthase-like | 0.0002351 | DIRECT |
57196,90193
57196 - EGF/Laminin
90193 - Notch domain | 0.001444 | INHERITED FROM: absent sebaceous gland || abnormal sebaceous gland morphology || abnormal hair follicle morphology |
46579,64593
46579 - Prefoldin
64593 - Intermediate filament protein, coiled coil region | 0.001444 | INHERITED FROM: abnormal hair follicle morphology |
50729,56112
50729 - PH domain-like
56112 - Protein kinase-like (PK-like) | 0.005066 | INHERITED FROM: increased mammary gland tumor incidence || decreased hair follicle number || increased mammary adenocarcinoma incidence |
55785,55785
55785 - PYP-like sensor domain (PAS domain)
55785 - PYP-like sensor domain (PAS domain) | 0.008917 | INHERITED FROM: abnormal mammary gland morphology |
47459,55785
47459 - HLH, helix-loop-helix DNA-binding domain
55785 - PYP-like sensor domain (PAS domain) | 0.03427 | INHERITED FROM: abnormal mammary gland morphology |
57184,57184
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain | 0.05313 | INHERITED FROM: abnormal coat/ hair morphology || abnormal coat appearance |
57716,48508
57716 - Glucocorticoid receptor-like (DNA-binding domain)
48508 - Nuclear receptor ligand-binding domain | 0.05926 | INHERITED FROM: abnormal mammary gland lobule morphology || abnormal mammary gland development || abnormal mammary gland alveolus morphology |
57424,57424
57424 - LDL receptor-like module
57424 - LDL receptor-like module | 0.1487 | INHERITED FROM: abnormal coat/ hair morphology || abnormal coat appearance |
64593,64593
64593 - Intermediate filament protein, coiled coil region
64593 - Intermediate filament protein, coiled coil region | 0.2058 | INHERITED FROM: abnormal nail morphology |
57196,69687
57196 - EGF/Laminin
69687 - Integrin beta tail domain | 0.288 | INHERITED FROM: abnormal hair growth || alopecia |
57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.3906 | INHERITED FROM: absent sebaceous gland || abnormal mammary gland duct morphology |
53300,69179
53300 - vWA-like
69179 - Integrin domains | 0.3929 | INHERITED FROM: abnormal hair growth || alopecia || abnormal hair follicle morphology |
55550,55550
55550 - SH2 domain
55550 - SH2 domain | 0.3929 | INHERITED FROM: abnormal hair growth |
49265,49265
49265 - Fibronectin type III
49265 - Fibronectin type III | 0.6618 | INHERITED FROM: increased subcutaneous adipose tissue amount |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
49417,47719
49417 - p53-like transcription factors
47719 - p53 tetramerization domain | 0 | Direct |
48092,47655
48092 - Transcription factor STAT-4 N-domain
47655 - STAT | 0.000177 | Direct |
52058,57184
52058 - L domain-like
57184 - Growth factor receptor domain | 0.000177 | Direct |
57184,52058
57184 - Growth factor receptor domain
52058 - L domain-like | 0.000177 | Direct |
49417,55550
49417 - p53-like transcription factors
55550 - SH2 domain | 0.000177 | Direct |
47655,49417
47655 - STAT
49417 - p53-like transcription factors | 0.000177 | Direct |
57903,51197
57903 - FYVE/PHD zinc finger
51197 - Clavaminate synthase-like | 0.0002351 | Direct |
57196,90193
57196 - EGF/Laminin
90193 - Notch domain | 0.001444 | Inherited |
46579,64593
46579 - Prefoldin
64593 - Intermediate filament protein, coiled coil region | 0.001444 | Inherited |
50729,56112
50729 - PH domain-like
56112 - Protein kinase-like (PK-like) | 0.005066 | Inherited |
55785,55785
55785 - PYP-like sensor domain (PAS domain)
55785 - PYP-like sensor domain (PAS domain) | 0.008917 | Inherited |
47459,55785
47459 - HLH, helix-loop-helix DNA-binding domain
55785 - PYP-like sensor domain (PAS domain) | 0.03427 | Inherited |
57184,57184
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain | 0.05313 | Inherited |
57716,48508
57716 - Glucocorticoid receptor-like (DNA-binding domain)
48508 - Nuclear receptor ligand-binding domain | 0.05926 | Inherited |
57424,57424
57424 - LDL receptor-like module
57424 - LDL receptor-like module | 0.1487 | Inherited |
64593,64593
64593 - Intermediate filament protein, coiled coil region
64593 - Intermediate filament protein, coiled coil region | 0.2058 | Inherited |
57196,69687
57196 - EGF/Laminin
69687 - Integrin beta tail domain | 0.288 | Inherited |
57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.3906 | Inherited |
53300,69179
53300 - vWA-like
69179 - Integrin domains | 0.3929 | Inherited |
55550,55550
55550 - SH2 domain
55550 - SH2 domain | 0.3929 | Inherited |
49265,49265
49265 - Fibronectin type III
49265 - Fibronectin type III | 0.6618 | Inherited |
(show details)
Supra-domains annotated to this MP term (Not in SPMP)
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 |
48092,47655,49417
48092 - Transcription factor STAT-4 N-domain
47655 - STAT
49417 - p53-like transcription factors | 0.000177 | DIRECT |
47655,49417,55550
47655 - STAT
49417 - p53-like transcription factors
55550 - SH2 domain | 0.000177 | DIRECT |
52058,57184,52058
52058 - L domain-like
57184 - Growth factor receptor domain
52058 - L domain-like | 0.000177 | 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) | 0.005066 | INHERITED FROM: abnormal mammary gland morphology |
57196,57196,57184
57196 - EGF/Laminin
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.08157 | INHERITED FROM: absent sebaceous gland || diluted coat color |
57424,57424,57424
57424 - LDL receptor-like module
57424 - LDL receptor-like module
57424 - LDL receptor-like module | 0.1487 | INHERITED FROM: abnormal coat/ hair morphology || abnormal coat appearance |
57196,57196,69687
57196 - EGF/Laminin
57196 - EGF/Laminin
69687 - Integrin beta tail domain | 0.288 | INHERITED FROM: abnormal hair growth || alopecia |
57196,57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.4485 | INHERITED FROM: absent sebaceous gland |
57184,57196,57196
57184 - Growth factor receptor domain
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.5032 | INHERITED FROM: absent sebaceous gland || diluted coat color |
| 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 |
48092,47655,49417
48092 - Transcription factor STAT-4 N-domain
47655 - STAT
49417 - p53-like transcription factors | 0.000177 | Direct |
47655,49417,55550
47655 - STAT
49417 - p53-like transcription factors
55550 - SH2 domain | 0.000177 | Direct |
52058,57184,52058
52058 - L domain-like
57184 - Growth factor receptor domain
52058 - L domain-like | 0.000177 | 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) | 0.005066 | Inherited |
57196,57196,57184
57196 - EGF/Laminin
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.08157 | Inherited |
57424,57424,57424
57424 - LDL receptor-like module
57424 - LDL receptor-like module
57424 - LDL receptor-like module | 0.1487 | Inherited |
57196,57196,69687
57196 - EGF/Laminin
57196 - EGF/Laminin
69687 - Integrin beta tail domain | 0.288 | Inherited |
57196,57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.4485 | Inherited |
57184,57196,57196
57184 - Growth factor receptor domain
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.5032 | 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.
|
