|
Disease Ontology (DO): cell type cancer  
(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: DO Hierarchy (disease ontology from University of Maryland)
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) |
DEATH effector domain, DED | 0 | DIRECT |
Hsp90 middle domain | 0 | DIRECT |
Tissue inhibitor of metalloproteinases, TIMP | 0 | DIRECT |
L domain | 0 | DIRECT |
p53 tetramerization domain | 0 | DIRECT |
Retinoblastoma tumor suppressor domains | 0 | DIRECT |
p53 DNA-binding domain-like | 0 | DIRECT |
FAS1 domain | 0 | DIRECT |
Transferrin | 0 | DIRECT |
Neurotrophin | 0 | DIRECT |
Purine and uridine phosphorylases | 0 | DIRECT |
Synuclein | 0 | DIRECT |
HSP90 C-terminal domain | 0 | DIRECT |
Integrin beta EGF-like domains | 0 | DIRECT |
Nuclear receptor coactivator interlocking domain | 0 | DIRECT |
Insulin-like | 0 | DIRECT |
Integrin beta tail domain | 0 | DIRECT |
Lesion bypass DNA polymerase (Y-family), catalytic domain | 0 | DIRECT |
PAS domain of steroid receptor coactivator 1A, NCo-A1 | 0 | DIRECT |
Gelsolin-like | 0 | DIRECT |
Uteroglobin-like | 0 | DIRECT |
Heat shock protein 90, HSP90, N-terminal domain | 0 | DIRECT |
S100 proteins | 0.00005537 | DIRECT |
MMP N-terminal domain | 0.0003793 | DIRECT |
Growth factor receptor domain | 0.0004214 | DIRECT |
Matrix metalloproteases, catalytic domain | 0.0008824 | DIRECT |
Hemopexin-like domain | 0.001417 | INHERITED FROM: carcinoma || adult astrocytic tumour |
Ephrin receptor ligand binding domain | 0.003064 | INHERITED FROM: carcinoma |
Bcl-2 inhibitors of programmed cell death | 0.005064 | INHERITED FROM: carcinoma |
Platelet-derived growth factor-like | 0.02213 | INHERITED FROM: carcinoma || malignant mesothelioma |
Caspase catalytic domain | 0.03269 | INHERITED FROM: melanoma |
Hexokinase | 0.04575 | INHERITED FROM: adenocarcinoma |
Intermediate filament protein, coiled coil region | 0.06599 | INHERITED FROM: neuroendocrine carcinoma |
Protein kinases, catalytic subunit | 0.07784 | INHERITED FROM: malignant glioma |
Phoshoinositide 3-kinase (PI3K), catalytic domain | 0.1144 | INHERITED FROM: astrocytoma |
Protein kinase cysteine-rich domain (cys2, phorbol-binding domain) | 0.1158 | INHERITED FROM: papillary carcinoma |
C5 cytosine-specific DNA methylase, DCM | 0.1596 | INHERITED FROM: squamous cell carcinoma |
Ras-binding domain, RBD | 0.2432 | INHERITED FROM: pilocytic astrocytoma |
Ran binding protein zinc finger-like | 0.8246 | INHERITED FROM: sarcoma |
HMG-box | 0.8859 | INHERITED FROM: embryonal cancer || seminoma |
SCOP term |
FDR (all) |
Annotation (direct or inherited) |
DEATH effector domain, DED | 0 | Direct |
Hsp90 middle domain | 0 | Direct |
Tissue inhibitor of metalloproteinases, TIMP | 0 | Direct |
L domain | 0 | Direct |
p53 tetramerization domain | 0 | Direct |
Retinoblastoma tumor suppressor domains | 0 | Direct |
p53 DNA-binding domain-like | 0 | Direct |
FAS1 domain | 0 | Direct |
Transferrin | 0 | Direct |
Neurotrophin | 0 | Direct |
Purine and uridine phosphorylases | 0 | Direct |
Synuclein | 0 | Direct |
HSP90 C-terminal domain | 0 | Direct |
Integrin beta EGF-like domains | 0 | Direct |
Nuclear receptor coactivator interlocking domain | 0 | Direct |
Insulin-like | 0 | Direct |
Integrin beta tail domain | 0 | Direct |
Lesion bypass DNA polymerase (Y-family), catalytic domain | 0 | Direct |
PAS domain of steroid receptor coactivator 1A, NCo-A1 | 0 | Direct |
Gelsolin-like | 0 | Direct |
Uteroglobin-like | 0 | Direct |
Heat shock protein 90, HSP90, N-terminal domain | 0 | Direct |
S100 proteins | 0.00005537 | Direct |
MMP N-terminal domain | 0.0003793 | Direct |
Growth factor receptor domain | 0.0004214 | Direct |
Matrix metalloproteases, catalytic domain | 0.0008824 | Direct |
Hemopexin-like domain | 0.001417 | Inherited |
Ephrin receptor ligand binding domain | 0.003064 | Inherited |
Bcl-2 inhibitors of programmed cell death | 0.005064 | Inherited |
Platelet-derived growth factor-like | 0.02213 | Inherited |
Caspase catalytic domain | 0.03269 | Inherited |
Hexokinase | 0.04575 | Inherited |
Intermediate filament protein, coiled coil region | 0.06599 | Inherited |
Protein kinases, catalytic subunit | 0.07784 | Inherited |
Phoshoinositide 3-kinase (PI3K), catalytic domain | 0.1144 | Inherited |
Protein kinase cysteine-rich domain (cys2, phorbol-binding domain) | 0.1158 | Inherited |
C5 cytosine-specific DNA methylase, DCM | 0.1596 | Inherited |
Ras-binding domain, RBD | 0.2432 | Inherited |
Ran binding protein zinc finger-like | 0.8246 | Inherited |
HMG-box | 0.8859 | Inherited |
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) |
53300,69179 53300 - vWA-like 69179 - Integrin domains | 0 | DIRECT |
90188,53649 90188 - Somatomedin B domain 53649 - Alkaline phosphatase-like | 0 | DIRECT |
57603,82895 57603 - FnI-like domain 82895 - TSP-1 type 1 repeat | 0 | DIRECT |
54236,57889 54236 - Ubiquitin-like 57889 - Cysteine-rich domain | 0 | DIRECT |
53850,53850 53850 - Periplasmic binding protein-like II 53850 - Periplasmic binding protein-like II | 0 | DIRECT |
47576,48065 47576 - Calponin-homology domain, CH-domain 48065 - DBL homology domain (DH-domain) | 0 | DIRECT |
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain | 0 | DIRECT |
57184,49265 57184 - Growth factor receptor domain 49265 - Fibronectin type III | 0 | DIRECT |
49562,57889 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 57889 - Cysteine-rich domain | 0 | DIRECT |
57362,57362 57362 - BPTI-like 57362 - BPTI-like | 0 | DIRECT |
57302,57302 57302 - Snake toxin-like 57302 - Snake toxin-like | 0 | DIRECT |
49417,47719 49417 - p53-like transcription factors 47719 - p53 tetramerization domain | 0 | DIRECT |
55753,55753 55753 - Actin depolymerizing proteins 55753 - Actin depolymerizing proteins | 0 | DIRECT |
57196,69687 57196 - EGF/Laminin 69687 - Integrin beta tail domain | 0 | DIRECT |
57184,57603 57184 - Growth factor receptor domain 57603 - FnI-like domain | 0 | DIRECT |
82153,82153 82153 - FAS1 domain 82153 - FAS1 domain | 0 | DIRECT |
56672,100879 56672 - DNA/RNA polymerases 100879 - Lesion bypass DNA polymerase (Y-family), little finger domain | 0 | DIRECT |
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like | 0 | DIRECT |
90193,90193 90193 - Notch domain 90193 - Notch domain | 0 | DIRECT |
57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat | 0 | DIRECT |
57196,90193 57196 - EGF/Laminin 90193 - Notch domain | 0 | DIRECT |
47090,55486 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain | 0.0003056 | DIRECT |
56112,47769 56112 - Protein kinase-like (PK-like) 47769 - SAM/Pointed domain | 0.002666 | INHERITED FROM: carcinoma |
55486,50923 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain | 0.004915 | INHERITED FROM: carcinoma |
49785,57184 49785 - Galactose-binding domain-like 57184 - Growth factor receptor domain | 0.007422 | INHERITED FROM: carcinoma |
46579,64593 46579 - Prefoldin 64593 - Intermediate filament protein, coiled coil region | 0.01389 | INHERITED FROM: neuroendocrine carcinoma |
47986,52129 47986 - DEATH domain 52129 - Caspase-like | 0.02019 | INHERITED FROM: melanoma |
Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
53300,69179 53300 - vWA-like 69179 - Integrin domains | 0 | Direct |
90188,53649 90188 - Somatomedin B domain 53649 - Alkaline phosphatase-like | 0 | Direct |
57603,82895 57603 - FnI-like domain 82895 - TSP-1 type 1 repeat | 0 | Direct |
54236,57889 54236 - Ubiquitin-like 57889 - Cysteine-rich domain | 0 | Direct |
53850,53850 53850 - Periplasmic binding protein-like II 53850 - Periplasmic binding protein-like II | 0 | Direct |
47576,48065 47576 - Calponin-homology domain, CH-domain 48065 - DBL homology domain (DH-domain) | 0 | Direct |
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain | 0 | Direct |
57184,49265 57184 - Growth factor receptor domain 49265 - Fibronectin type III | 0 | Direct |
49562,57889 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 57889 - Cysteine-rich domain | 0 | Direct |
57362,57362 57362 - BPTI-like 57362 - BPTI-like | 0 | Direct |
57302,57302 57302 - Snake toxin-like 57302 - Snake toxin-like | 0 | Direct |
49417,47719 49417 - p53-like transcription factors 47719 - p53 tetramerization domain | 0 | Direct |
55753,55753 55753 - Actin depolymerizing proteins 55753 - Actin depolymerizing proteins | 0 | Direct |
57196,69687 57196 - EGF/Laminin 69687 - Integrin beta tail domain | 0 | Direct |
57184,57603 57184 - Growth factor receptor domain 57603 - FnI-like domain | 0 | Direct |
82153,82153 82153 - FAS1 domain 82153 - FAS1 domain | 0 | Direct |
56672,100879 56672 - DNA/RNA polymerases 100879 - Lesion bypass DNA polymerase (Y-family), little finger domain | 0 | Direct |
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like | 0 | Direct |
90193,90193 90193 - Notch domain 90193 - Notch domain | 0 | Direct |
57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat | 0 | Direct |
57196,90193 57196 - EGF/Laminin 90193 - Notch domain | 0 | Direct |
47090,55486 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain | 0.0003056 | Direct |
56112,47769 56112 - Protein kinase-like (PK-like) 47769 - SAM/Pointed domain | 0.002666 | Inherited |
55486,50923 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain | 0.004915 | Inherited |
49785,57184 49785 - Galactose-binding domain-like 57184 - Growth factor receptor domain | 0.007422 | Inherited |
46579,64593 46579 - Prefoldin 64593 - Intermediate filament protein, coiled coil region | 0.01389 | Inherited |
47986,52129 47986 - DEATH domain 52129 - Caspase-like | 0.02019 | 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) |
90188,90188,53649 90188 - Somatomedin B domain 90188 - Somatomedin B domain 53649 - Alkaline phosphatase-like | 0 | DIRECT |
57924,57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat | 0 | DIRECT |
49562,57889,57889 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 57889 - Cysteine-rich domain 57889 - Cysteine-rich domain | 0 | DIRECT |
55753,55753,55753 55753 - Actin depolymerizing proteins 55753 - Actin depolymerizing proteins 55753 - Actin depolymerizing proteins | 0 | DIRECT |
53067,53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain | 0 | DIRECT |
49785,57184,49265 49785 - Galactose-binding domain-like 57184 - Growth factor receptor domain 49265 - Fibronectin type III | 0 | DIRECT |
47986,47986,52129 47986 - DEATH domain 47986 - DEATH domain 52129 - Caspase-like | 0 | DIRECT |
57196,57196,90193 57196 - EGF/Laminin 57196 - EGF/Laminin 90193 - Notch domain | 0 | DIRECT |
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like | 0 | DIRECT |
57196,57196,69687 57196 - EGF/Laminin 57196 - EGF/Laminin 69687 - Integrin beta tail domain | 0 | DIRECT |
52058,48726,48726 52058 - L domain-like 48726 - Immunoglobulin 48726 - Immunoglobulin | 0 | DIRECT |
57184,52058,57184 57184 - Growth factor receptor domain 52058 - L domain-like 57184 - Growth factor receptor domain | 0 | DIRECT |
47576,48065,50729 47576 - Calponin-homology domain, CH-domain 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like | 0 | DIRECT |
47090,55486,50923 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain | 0.001571 | INHERITED FROM: carcinoma |
50729,55550,56112 50729 - PH domain-like 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) | 0.1504 | INHERITED FROM: melanoma |
55550,56112,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) 56112 - Protein kinase-like (PK-like) | 0.1504 | INHERITED FROM: melanoma |
57440,57440,57440 57440 - Kringle-like 57440 - Kringle-like 57440 - Kringle-like | 0.5165 | INHERITED FROM: glioblastoma multiforme || astrocytoma |
Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
90188,90188,53649 90188 - Somatomedin B domain 90188 - Somatomedin B domain 53649 - Alkaline phosphatase-like | 0 | Direct |
57924,57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat | 0 | Direct |
49562,57889,57889 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 57889 - Cysteine-rich domain 57889 - Cysteine-rich domain | 0 | Direct |
55753,55753,55753 55753 - Actin depolymerizing proteins 55753 - Actin depolymerizing proteins 55753 - Actin depolymerizing proteins | 0 | Direct |
53067,53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain | 0 | Direct |
49785,57184,49265 49785 - Galactose-binding domain-like 57184 - Growth factor receptor domain 49265 - Fibronectin type III | 0 | Direct |
47986,47986,52129 47986 - DEATH domain 47986 - DEATH domain 52129 - Caspase-like | 0 | Direct |
57196,57196,90193 57196 - EGF/Laminin 57196 - EGF/Laminin 90193 - Notch domain | 0 | Direct |
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like | 0 | Direct |
57196,57196,69687 57196 - EGF/Laminin 57196 - EGF/Laminin 69687 - Integrin beta tail domain | 0 | Direct |
52058,48726,48726 52058 - L domain-like 48726 - Immunoglobulin 48726 - Immunoglobulin | 0 | Direct |
57184,52058,57184 57184 - Growth factor receptor domain 52058 - L domain-like 57184 - Growth factor receptor domain | 0 | Direct |
47576,48065,50729 47576 - Calponin-homology domain, CH-domain 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like | 0 | Direct |
47090,55486,50923 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain | 0.001571 | Inherited |
50729,55550,56112 50729 - PH domain-like 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) | 0.1504 | Inherited |
55550,56112,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) 56112 - Protein kinase-like (PK-like) | 0.1504 | Inherited |
57440,57440,57440 57440 - Kringle-like 57440 - Kringle-like 57440 - Kringle-like | 0.5165 | 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 DO 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 DO 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.
|
  
|