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Mammalian Phenotype (MP): abnormal pulmonary alveolar system 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) |
52799,49562
52799 - (Phosphotyrosine protein) phosphatases II
49562 - C2 domain (Calcium/lipid-binding domain, CaLB) | 0.0001579 | DIRECT |
52058,57184
52058 - L domain-like
57184 - Growth factor receptor domain | 0.0003196 | DIRECT |
57184,52058
57184 - Growth factor receptor domain
52058 - L domain-like | 0.0003196 | DIRECT |
55785,55785
55785 - PYP-like sensor domain (PAS domain)
55785 - PYP-like sensor domain (PAS domain) | 0.0008914 | DIRECT |
50729,50729
50729 - PH domain-like
50729 - PH domain-like | 0.02032 | INHERITED FROM: abnormal pulmonary alveolus epithelium morphology || abnormal type II pneumocyte morphology || abnormal pulmonary alveolar parenchyma morphology || abnormal pulmonary alveolus epithelial cell morphology || increased type II pneumocyte number |
47459,55785
47459 - HLH, helix-loop-helix DNA-binding domain
55785 - PYP-like sensor domain (PAS domain) | 0.05525 | INHERITED FROM: abnormal pulmonary alveolus morphology || abnormal pulmonary acinus morphology |
57184,57196
57184 - Growth factor receptor domain
57196 - EGF/Laminin | 0.173 | INHERITED FROM: abnormal pulmonary alveolus morphology || emphysema || abnormal pulmonary acinus morphology |
47090,55486
47090 - PGBD-like
55486 - Metalloproteases ("zincins"), catalytic domain | 0.2315 | INHERITED FROM: overexpanded pulmonary alveoli |
57196,57184
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.3729 | INHERITED FROM: emphysema |
57184,57184
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain | 0.5077 | INHERITED FROM: emphysema || overexpanded pulmonary alveoli |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
52799,49562
52799 - (Phosphotyrosine protein) phosphatases II
49562 - C2 domain (Calcium/lipid-binding domain, CaLB) | 0.0001579 | Direct |
52058,57184
52058 - L domain-like
57184 - Growth factor receptor domain | 0.0003196 | Direct |
57184,52058
57184 - Growth factor receptor domain
52058 - L domain-like | 0.0003196 | Direct |
55785,55785
55785 - PYP-like sensor domain (PAS domain)
55785 - PYP-like sensor domain (PAS domain) | 0.0008914 | Direct |
50729,50729
50729 - PH domain-like
50729 - PH domain-like | 0.02032 | Inherited |
47459,55785
47459 - HLH, helix-loop-helix DNA-binding domain
55785 - PYP-like sensor domain (PAS domain) | 0.05525 | Inherited |
57184,57196
57184 - Growth factor receptor domain
57196 - EGF/Laminin | 0.173 | Inherited |
47090,55486
47090 - PGBD-like
55486 - Metalloproteases ("zincins"), catalytic domain | 0.2315 | Inherited |
57196,57184
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.3729 | Inherited |
57184,57184
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain | 0.5077 | 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) |
52058,57184,52058
52058 - L domain-like
57184 - Growth factor receptor domain
52058 - L domain-like | 0.0003196 | 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) | 0.0005585 | DIRECT |
57184,57196,57184
57184 - Growth factor receptor domain
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.1002 | INHERITED FROM: abnormal pulmonary alveolus morphology || abnormal pulmonary acinus morphology || overexpanded pulmonary alveoli |
57184,57184,57196
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain
57196 - EGF/Laminin | 0.1002 | INHERITED FROM: abnormal pulmonary alveolus morphology || emphysema || abnormal pulmonary acinus morphology || overexpanded pulmonary alveoli |
57196,57184,57196
57196 - EGF/Laminin
57184 - Growth factor receptor domain
57196 - EGF/Laminin | 0.2315 | INHERITED FROM: abnormal pulmonary alveolus morphology || emphysema |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
52058,57184,52058
52058 - L domain-like
57184 - Growth factor receptor domain
52058 - L domain-like | 0.0003196 | 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) | 0.0005585 | Direct |
57184,57196,57184
57184 - Growth factor receptor domain
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.1002 | Inherited |
57184,57184,57196
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain
57196 - EGF/Laminin | 0.1002 | Inherited |
57196,57184,57196
57196 - EGF/Laminin
57184 - Growth factor receptor domain
57196 - EGF/Laminin | 0.2315 | 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
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Plot tree as:
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Download Newick format tree:
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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 pulmonary alveolar system morphology
