|
|
Mammalian Phenotype (MP): decreased lymphocyte cell number 
(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 ]
Family( show details)
Highlighted in gray are those with FDR_all>0.001
| SCOP term |
FDR (all) |
Annotation (direct or inherited) |
| Proteasome subunits | 0 | DIRECT |
| RUNT domain | 0 | DIRECT |
| DNA polymerase beta-like | 0 | DIRECT |
| DNA polymerase beta-like, second domain | 0 | DIRECT |
| Rel/Dorsal transcription factors, DNA-binding domain | 0.00000108 | DIRECT |
| NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain | 0.000007619 | DIRECT |
| Phoshoinositide 3-kinase (PI3K), catalytic domain | 0.0000382 | DIRECT |
| Pointed domain | 0.0002373 | DIRECT |
| DNA polymerase beta, N-terminal domain-like | 0.0003046 | DIRECT |
| Bcl-2 inhibitors of programmed cell death | 0.001565 | INHERITED FROM: decreased mature B cell number |
| Interferon regulatory factor | 0.001565 | INHERITED FROM: decreased T cell number || decreased mature B cell number |
| WWE domain | 0.013 | INHERITED FROM: decreased marginal zone B cell number || decreased mature B cell number |
| Interferon regulatory factor 3 (IRF3), transactivation domain | 0.023 | INHERITED FROM: absent lymphocyte || decreased mature B cell number || absent B cells |
| SH2 domain | 0.03687 | INHERITED FROM: decreased single-positive T cell number || decreased thymocyte number || decreased immature B cell number |
| PLC-like (P variant) | 0.0416 | INHERITED FROM: decreased B-2 B cell number |
| Protein kinase cysteine-rich domain (cys2, phorbol-binding domain) | 0.05483 | INHERITED FROM: decreased thymocyte number |
| Integrin domains | 0.07219 | INHERITED FROM: decreased CD4-positive, alpha beta T cell number || decreased T cell number |
| Pleckstrin-homology domain (PH domain) | 0.07316 | INHERITED FROM: decreased transitional stage B cell number |
| SH3-domain | 0.09099 | INHERITED FROM: decreased single-positive T cell number |
| Ran binding protein zinc finger-like | 0.1234 | INHERITED FROM: decreased B-1a cell number || decreased B cell number |
| DBL homology domain (DH-domain) | 0.1604 | INHERITED FROM: decreased transitional stage B cell number || decreased transitional stage T2 B cell number |
| C1 set domains (antibody constant domain-like) | 0.2531 | INHERITED FROM: absent CD8-positive, alpha-beta T cells |
| Calponin-homology domain, CH-domain | 0.2987 | INHERITED FROM: decreased transitional stage T2 B cell number |
| E2F dimerization segment | 0.3548 | INHERITED FROM: decreased double-positive T cell number |
| Cell cycle transcription factor e2f-dp | 0.3548 | INHERITED FROM: decreased double-positive T cell number |
| ets domain | 0.3566 | INHERITED FROM: decreased thymocyte number |
| MHC antigen-recognition domain | 0.4868 | INHERITED FROM: absent CD8-positive, alpha-beta T cells |
| Toll/Interleukin receptor TIR domain | 0.4868 | INHERITED FROM: decreased mature B cell number |
LINKTO: Domain2BO Download and Domain2BO Algorithm
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) |
81585,81301
81585 - PsbU/PolX domain-like
81301 - Nucleotidyltransferase | 0 | DIRECT |
47802,81585
47802 - DNA polymerase beta, N-terminal domain-like
81585 - PsbU/PolX domain-like | 0 | DIRECT |
47576,48065
47576 - Calponin-homology domain, CH-domain
48065 - DBL homology domain (DH-domain) | 0 | DIRECT |
49417,81296
49417 - p53-like transcription factors
81296 - E set domains | 0.0000006781 | DIRECT |
50729,56112
50729 - PH domain-like
56112 - Protein kinase-like (PK-like) | 0.00003091 | DIRECT |
50729,55550
50729 - PH domain-like
55550 - SH2 domain | 0.001011 | INHERITED FROM: decreased B cell number |
69179,69179
69179 - Integrin domains
69179 - Integrin domains | 0.003247 | INHERITED FROM: decreased T cell number |
69318,69179
69318 - Integrin alpha N-terminal domain
69179 - Integrin domains | 0.003247 | INHERITED FROM: decreased T cell number |
57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 0.00456 | INHERITED FROM: decreased DN2 thymocyte number |
53300,69318
53300 - vWA-like
69318 - Integrin alpha N-terminal domain | 0.03134 | INHERITED FROM: decreased CD4-positive, alpha beta T cell number |
50044,55550
50044 - SH3-domain
55550 - SH2 domain | 0.1029 | INHERITED FROM: decreased immature B cell number || decreased single-positive T cell number |
48065,50729
48065 - DBL homology domain (DH-domain)
50729 - PH domain-like | 0.1417 | INHERITED FROM: decreased transitional stage B cell number || decreased transitional stage T2 B cell number |
55550,55550
55550 - SH2 domain
55550 - SH2 domain | 0.1925 | INHERITED FROM: decreased mature B cell number || decreased immature B cell number |
55550,50044
55550 - SH2 domain
50044 - SH3-domain | 0.1925 | INHERITED FROM: decreased mature B cell number || decreased double-negative T cell number || decreased immature B cell number || decreased follicular B cell number || decreased transitional stage B cell number || decreased single-positive T cell number |
46785,144074
46785 - "Winged helix" DNA-binding domain
144074 - E2F-DP heterodimerization region | 0.3339 | INHERITED FROM: decreased double-positive T cell number |
54452,48726
54452 - MHC antigen-recognition domain
48726 - Immunoglobulin | 0.4547 | INHERITED FROM: absent CD8-positive, alpha-beta T cells |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
81585,81301
81585 - PsbU/PolX domain-like
81301 - Nucleotidyltransferase | 0 | Direct |
47802,81585
47802 - DNA polymerase beta, N-terminal domain-like
81585 - PsbU/PolX domain-like | 0 | Direct |
47576,48065
47576 - Calponin-homology domain, CH-domain
48065 - DBL homology domain (DH-domain) | 0 | Direct |
49417,81296
49417 - p53-like transcription factors
81296 - E set domains | 0.0000006781 | Direct |
50729,56112
50729 - PH domain-like
56112 - Protein kinase-like (PK-like) | 0.00003091 | Direct |
50729,55550
50729 - PH domain-like
55550 - SH2 domain | 0.001011 | Inherited |
69179,69179
69179 - Integrin domains
69179 - Integrin domains | 0.003247 | Inherited |
69318,69179
69318 - Integrin alpha N-terminal domain
69179 - Integrin domains | 0.003247 | Inherited |
57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 0.00456 | Inherited |
53300,69318
53300 - vWA-like
69318 - Integrin alpha N-terminal domain | 0.03134 | Inherited |
50044,55550
50044 - SH3-domain
55550 - SH2 domain | 0.1029 | Inherited |
48065,50729
48065 - DBL homology domain (DH-domain)
50729 - PH domain-like | 0.1417 | Inherited |
55550,55550
55550 - SH2 domain
55550 - SH2 domain | 0.1925 | Inherited |
55550,50044
55550 - SH2 domain
50044 - SH3-domain | 0.1925 | Inherited |
46785,144074
46785 - "Winged helix" DNA-binding domain
144074 - E2F-DP heterodimerization region | 0.3339 | Inherited |
54452,48726
54452 - MHC antigen-recognition domain
48726 - Immunoglobulin | 0.4547 | 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) |
47802,81585,81301
47802 - DNA polymerase beta, N-terminal domain-like
81585 - PsbU/PolX domain-like
81301 - Nucleotidyltransferase | 0 | DIRECT |
47576,48065,50729
47576 - Calponin-homology domain, CH-domain
48065 - DBL homology domain (DH-domain)
50729 - PH domain-like | 0 | DIRECT |
50729,50044,55550
50729 - PH domain-like
50044 - SH3-domain
55550 - SH2 domain | 0 | DIRECT |
55550,56112,56112
55550 - SH2 domain
56112 - Protein kinase-like (PK-like)
56112 - Protein kinase-like (PK-like) | 0.001486 | INHERITED FROM: decreased T cell number || decreased B cell number |
50729,55550,56112
50729 - PH domain-like
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.001486 | INHERITED FROM: decreased T cell number || decreased B cell number |
69318,69179,69179
69318 - Integrin alpha N-terminal domain
69179 - Integrin domains
69179 - Integrin domains | 0.003247 | INHERITED FROM: decreased T cell number |
53300,69318,69179
53300 - vWA-like
69318 - Integrin alpha N-terminal domain
69179 - Integrin domains | 0.03134 | INHERITED FROM: decreased CD4-positive, alpha beta T cell number |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
47802,81585,81301
47802 - DNA polymerase beta, N-terminal domain-like
81585 - PsbU/PolX domain-like
81301 - Nucleotidyltransferase | 0 | Direct |
47576,48065,50729
47576 - Calponin-homology domain, CH-domain
48065 - DBL homology domain (DH-domain)
50729 - PH domain-like | 0 | Direct |
50729,50044,55550
50729 - PH domain-like
50044 - SH3-domain
55550 - SH2 domain | 0 | Direct |
55550,56112,56112
55550 - SH2 domain
56112 - Protein kinase-like (PK-like)
56112 - Protein kinase-like (PK-like) | 0.001486 | Inherited |
50729,55550,56112
50729 - PH domain-like
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.001486 | Inherited |
69318,69179,69179
69318 - Integrin alpha N-terminal domain
69179 - Integrin domains
69179 - Integrin domains | 0.003247 | Inherited |
53300,69318,69179
53300 - vWA-like
69318 - Integrin alpha N-terminal domain
69179 - Integrin domains | 0.03134 | 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
 |
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.
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.
|
|
> BO Hierarchy > decreased lymphocyte cell number
