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Mammalian Phenotype (MP): abnormal embryonic tissue morphology 
(show info)
Biomedical Ontology
Like Gene Ontology (GO), biomedical ontology such as phenotype 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. Biomedical ontologies we have incorporated are as follows:
- Disease Ontology (DO) Ontology DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM.
- Human Phenotype (HP) Ontology 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 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 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 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 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 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 displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
- Xenopus Anatomy (XA) Ontology 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 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 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.
- UniProtKB KeyWords (KW) Ontology 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).
- CTD Diseases (CD) Ontology CD is MEDIC disease vocabulary that is modified by CTD from the "Diseases" [C] branch of Medical Subject Headings (MeSH), combined with genetic disorders from the Online Mendelian Inheritance in OMIM database.
- CTD Chemicals (CC) Ontology CC is chemical vocabulary that is adapted by CTD from the "Chemicals and Drugs" category and Supplementary Concept Records of Medical Subject Headings (MeSH, a hierarchical vocabulary used to index articles for MEDLINE/PubMed).
Jump to [ Top · Hierarchy · Annotations ]
Root: MP Hierarchy (mammalian/mouse phenotype from MGI_4.41)
Jump to [ Top · Hierarchy ]
Supra-domain (Single)( show details)
Highlighted in gray are those with FDR>0.001
LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm
Jump to [ Top · Hierarchy ]
Supra-domain (Duplex) in N- to C-terminal order( show details)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57196,57424
57196 - EGF/Laminin
57424 - LDL receptor-like module | 0 | DIRECT |
90193,90193
90193 - Notch domain
90193 - Notch domain | 0 | DIRECT |
57196,57184
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.0007739 | DIRECT |
57196,63825
57196 - EGF/Laminin
63825 - YWTD domain | 0.0008599 | DIRECT |
48452,81901
48452 - TPR-like
81901 - HCP-like | 0.001305 | INHERITED FROM: abnormal neural tube morphology |
63501,50242
63501 - Frizzled cysteine-rich domain
50242 - TIMP-like | 0.004476 | INHERITED FROM: abnormal somite development || fused somites || craniorachischisis || spina bifida || open neural tube || abnormal neural tube closure || incomplete somite formation || decreased somite size || abnormal neural tube morphology || abnormal somite size || impaired somite development |
52283,51735
52283 - Formate/glycerate dehydrogenase catalytic domain-like
51735 - NAD(P)-binding Rossmann-fold domains | 0.009896 | INHERITED FROM: abnormal embryonic neuroepithelium morphology |
57716,48508
57716 - Glucocorticoid receptor-like (DNA-binding domain)
48508 - Nuclear receptor ligand-binding domain | 0.07286 | INHERITED FROM: abnormal pharyngeal arch artery morphology || abnormal mesonephros morphology || rudimentary Mullerian ducts |
49313,49313
49313 - Cadherin-like
49313 - Cadherin-like | 0.09915 | INHERITED FROM: incomplete somite formation |
55550,56112
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.4465 | INHERITED FROM: delayed neural tube closure |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57196,57424
57196 - EGF/Laminin
57424 - LDL receptor-like module | 0 | Direct |
90193,90193
90193 - Notch domain
90193 - Notch domain | 0 | Direct |
57196,57184
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.0007739 | Direct |
57196,63825
57196 - EGF/Laminin
63825 - YWTD domain | 0.0008599 | Direct |
48452,81901
48452 - TPR-like
81901 - HCP-like | 0.001305 | Inherited |
63501,50242
63501 - Frizzled cysteine-rich domain
50242 - TIMP-like | 0.004476 | Inherited |
52283,51735
52283 - Formate/glycerate dehydrogenase catalytic domain-like
51735 - NAD(P)-binding Rossmann-fold domains | 0.009896 | Inherited |
57716,48508
57716 - Glucocorticoid receptor-like (DNA-binding domain)
48508 - Nuclear receptor ligand-binding domain | 0.07286 | Inherited |
49313,49313
49313 - Cadherin-like
49313 - Cadherin-like | 0.09915 | Inherited |
55550,56112
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.4465 | Inherited |
LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm
Jump to [ Top · Hierarchy ]
Supra-domain (Triple) in N- to C-terminal order( show details)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57196,57424,57424
57196 - EGF/Laminin
57424 - LDL receptor-like module
57424 - LDL receptor-like module | 0 | DIRECT |
57196,90193,90193
57196 - EGF/Laminin
90193 - Notch domain
90193 - Notch domain | 0 | DIRECT |
63825,57196,57424
63825 - YWTD domain
57196 - EGF/Laminin
57424 - LDL receptor-like module | 0 | DIRECT |
63825,57196,63825
63825 - YWTD domain
57196 - EGF/Laminin
63825 - YWTD domain | 0.00002967 | DIRECT |
57196,63825,57196
57196 - EGF/Laminin
63825 - YWTD domain
57196 - EGF/Laminin | 0.0008599 | DIRECT |
57184,49899,49899
57184 - Growth factor receptor domain
49899 - Concanavalin A-like lectins/glucanases
49899 - Concanavalin A-like lectins/glucanases | 0.004476 | INHERITED FROM: abnormal neural tube morphology |
49313,49313,49313
49313 - Cadherin-like
49313 - Cadherin-like
49313 - Cadherin-like | 0.0787 | INHERITED FROM: incomplete somite formation |
50044,55550,56112
50044 - SH3-domain
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.2595 | INHERITED FROM: delayed neural tube closure |
57667,57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 0.8145 | INHERITED FROM: absent floor plate |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57196,57424,57424
57196 - EGF/Laminin
57424 - LDL receptor-like module
57424 - LDL receptor-like module | 0 | Direct |
57196,90193,90193
57196 - EGF/Laminin
90193 - Notch domain
90193 - Notch domain | 0 | Direct |
63825,57196,57424
63825 - YWTD domain
57196 - EGF/Laminin
57424 - LDL receptor-like module | 0 | Direct |
63825,57196,63825
63825 - YWTD domain
57196 - EGF/Laminin
63825 - YWTD domain | 0.00002967 | Direct |
57196,63825,57196
57196 - EGF/Laminin
63825 - YWTD domain
57196 - EGF/Laminin | 0.0008599 | Direct |
57184,49899,49899
57184 - Growth factor receptor domain
49899 - Concanavalin A-like lectins/glucanases
49899 - Concanavalin A-like lectins/glucanases | 0.004476 | Inherited |
49313,49313,49313
49313 - Cadherin-like
49313 - Cadherin-like
49313 - Cadherin-like | 0.0787 | Inherited |
50044,55550,56112
50044 - SH3-domain
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.2595 | Inherited |
57667,57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 0.8145 | Inherited |
LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm
Plot distribution on species Tree Of Life (sTOL) for Superfamily and/or Family domains annotated by this MP term
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Plot tree as:
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Download Newick format tree:
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( 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.
Plot distribution on species Tree Of Life (sTOL) for single supra-domains annotated by this MP term
|
Plot tree as:
| |
Download Newick format tree:
| |
Browsing in TREE OF LIFE:
|
( 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.
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> BO Hierarchy > abnormal embryonic tissue morphology
