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Mammalian Phenotype (MP): digestive/alimentary phenotype
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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)
Family domains annotated to this MP term (Not in SDMP)
Highlighted in gray are those with FDR_all>0.001
SCOP term | FDR (all) | Annotation (direct or inherited) |
Hedgehog (development protein), N-terminal signaling domain | 0 | DIRECT |
p53 DNA-binding domain-like | 0 | DIRECT |
Nitric oxide (NO) synthase oxygenase domain | 0 | DIRECT |
Hedgehog C-terminal (Hog) autoprocessing domain | 0 | DIRECT |
p53 tetramerization domain | 0 | DIRECT |
N-acetylmuramoyl-L-alanine amidase-like | 0 | DIRECT |
Forkhead DNA-binding domain | 0.00000002744 | DIRECT |
Homeodomain | 0.000001203 | DIRECT |
Rel/Dorsal transcription factors, DNA-binding domain | 0.00001086 | DIRECT |
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain | 0.00008289 | DIRECT |
Transforming growth factor (TGF)-beta | 0.0002072 | DIRECT |
SMAD MH1 domain | 0.0002288 | DIRECT |
SMAD domain | 0.0002288 | DIRECT |
Nuclear receptor ligand-binding domain | 0.0005149 | DIRECT |
Nuclear receptor | 0.0008569 | DIRECT |
Interleukin 17F, IL-17F | 0.0009958 | DIRECT |
EGF-type module | 0.001886 | INHERITED FROM: duodenal lesions |
T-box | 0.003366 | INHERITED FROM: cleft secondary palate || cleft palate || abnormal digestive system morphology || abnormal secondary palate development || abnormal secondary palate morphology |
Kringle modules | 0.003572 | INHERITED FROM: rectal prolapse || abnormal rectum morphology |
HMG-box | 0.003898 | INHERITED FROM: abnormal digestive system morphology |
Cytochrome p450 reductase N-terminal domain-like | 0.004475 | INHERITED FROM: abnormal stomach morphology || abnormal pyloric sphincter morphology || abnormal digestive system physiology || abnormal stomach pyloric region morphology || pyloric sphincter hypertrophy || enlarged stomach |
Integrin beta tail domain | 0.0092 | INHERITED FROM: abnormal digestive system physiology |
Pyrin domain, PYD | 0.0092 | INHERITED FROM: abnormal digestive system physiology || colitis || abnormal susceptibility to induced colitis || large intestinal inflammation || abnormal intestine physiology |
VWC domain | 0.009972 | INHERITED FROM: cleft secondary palate || abnormal secondary palate development || abnormal hard palate morphology || cleft hard palate |
Notch domain | 0.01408 | INHERITED FROM: abnormal exocrine pancreas morphology || abnormal pancreatic acinus morphology |
NADPH-cytochrome p450 reductase-like | 0.01408 | INHERITED FROM: abnormal stomach morphology || abnormal pyloric sphincter morphology || abnormal stomach pyloric region morphology || pyloric sphincter hypertrophy || enlarged stomach |
NADPH-cytochrome p450 reductase FAD-binding domain-like | 0.01408 | INHERITED FROM: abnormal stomach morphology || abnormal pyloric sphincter morphology || abnormal stomach pyloric region morphology || pyloric sphincter hypertrophy || enlarged stomach |
DNA repair protein MutS, domain III | 0.01408 | INHERITED FROM: increased intestinal adenocarcinoma incidence || increased alimentary system tumor incidence || increased gastrointestinal tumor incidence |
Paired domain | 0.02894 | INHERITED FROM: abnormal secondary palate morphology |
Interferons/interleukin-10 (IL-10) | 0.02894 | INHERITED FROM: abnormal colon morphology || increased susceptibility to induced colitis || colitis || abnormal susceptibility to induced colitis || abnormal intestine physiology || abnormal large intestine morphology |
Pyridoxal-dependent decarboxylase | 0.02913 | INHERITED FROM: cleft palate || abnormal palate morphology |
Trefoil | 0.02913 | INHERITED FROM: abnormal intestinal epithelium morphology |
Short-chain cytokines | 0.03675 | INHERITED FROM: abnormal intestinal goblet cell morphology || abnormal intestinal mucosa morphology || abnormal intestinal epithelium morphology |
HLH, helix-loop-helix DNA-binding domain | 0.03749 | INHERITED FROM: abnormal pancreatic acinus morphology || abnormal pancreatic acinar cell morphology |
Ephrin ectodomain | 0.04985 | INHERITED FROM: cleft palate || abnormal palate morphology |
Caspase recruitment domain, CARD | 0.08382 | INHERITED FROM: increased susceptibility to induced colitis || abnormal susceptibility to induced colitis |
Calponin-homology domain, CH-domain | 0.08585 | INHERITED FROM: intestinal ulcer |
Intermediate filament protein, coiled coil region | 0.09436 | INHERITED FROM: abnormal esophagus morphology || abnormal tongue morphology |
Phoshoinositide 3-kinase (PI3K), catalytic domain | 0.107 | INHERITED FROM: abnormal intestinal epithelium morphology |
Toll/Interleukin receptor TIR domain | 0.1168 | INHERITED FROM: increased susceptibility to induced colitis || rectal hemorrhage || colitis || large intestinal inflammation || abnormal intestine physiology || gastrointestinal hemorrhage |
ABC transporter ATPase domain-like | 0.1632 | INHERITED FROM: abnormal intestinal absorption || abnormal intestinal cholesterol absorption |
Cell cycle control phosphatase, catalytic domain | 0.1721 | INHERITED FROM: abnormal small intestinal crypt cell physiology || abnormal crypts of Lieberkuhn morphology || abnormal small intestine crypts of Lieberkuhn morphology || abnormal small intestinal crypt cell proliferation || increased enterocyte apoptosis || abnormal small intestinal villus morphology || decreased small intestine length || abnormal enterocyte physiology || abnormal intestinal epithelium physiology || decreased small intestinal villus size || abnormal enterocyte differentiation || abnormal intestine development || abnormal enterocyte apoptosis || decreased small intestinal villus height || abnormal digestive system development || decreased intestine length |
28-residue LRR | 0.1913 | INHERITED FROM: colitis || abnormal susceptibility to induced colitis || large intestinal inflammation |
Papain-like | 0.2475 | INHERITED FROM: salivary gland inflammation || abnormal salivary gland physiology |
Classic zinc finger, C2H2 | 0.7102 | INHERITED FROM: abnormal anal canal morphology |
DBL homology domain (DH-domain) | 0.829 | INHERITED FROM: abnormal enterocyte morphology || intestinal ulcer |
SCOP term | FDR (all) | Annotation (direct or inherited) |
Hedgehog (development protein), N-terminal signaling domain | 0 | Direct |
p53 DNA-binding domain-like | 0 | Direct |
Nitric oxide (NO) synthase oxygenase domain | 0 | Direct |
Hedgehog C-terminal (Hog) autoprocessing domain | 0 | Direct |
p53 tetramerization domain | 0 | Direct |
N-acetylmuramoyl-L-alanine amidase-like | 0 | Direct |
Forkhead DNA-binding domain | 0.00000002744 | Direct |
Homeodomain | 0.000001203 | Direct |
Rel/Dorsal transcription factors, DNA-binding domain | 0.00001086 | Direct |
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain | 0.00008289 | Direct |
Transforming growth factor (TGF)-beta | 0.0002072 | Direct |
SMAD MH1 domain | 0.0002288 | Direct |
SMAD domain | 0.0002288 | Direct |
Nuclear receptor ligand-binding domain | 0.0005149 | Direct |
Nuclear receptor | 0.0008569 | Direct |
Interleukin 17F, IL-17F | 0.0009958 | Direct |
EGF-type module | 0.001886 | Inherited |
T-box | 0.003366 | Inherited |
Kringle modules | 0.003572 | Inherited |
HMG-box | 0.003898 | Inherited |
Cytochrome p450 reductase N-terminal domain-like | 0.004475 | Inherited |
Integrin beta tail domain | 0.0092 | Inherited |
Pyrin domain, PYD | 0.0092 | Inherited |
VWC domain | 0.009972 | Inherited |
Notch domain | 0.01408 | Inherited |
NADPH-cytochrome p450 reductase-like | 0.01408 | Inherited |
NADPH-cytochrome p450 reductase FAD-binding domain-like | 0.01408 | Inherited |
DNA repair protein MutS, domain III | 0.01408 | Inherited |
Paired domain | 0.02894 | Inherited |
Interferons/interleukin-10 (IL-10) | 0.02894 | Inherited |
Pyridoxal-dependent decarboxylase | 0.02913 | Inherited |
Trefoil | 0.02913 | Inherited |
Short-chain cytokines | 0.03675 | Inherited |
HLH, helix-loop-helix DNA-binding domain | 0.03749 | Inherited |
Ephrin ectodomain | 0.04985 | Inherited |
Caspase recruitment domain, CARD | 0.08382 | Inherited |
Calponin-homology domain, CH-domain | 0.08585 | Inherited |
Intermediate filament protein, coiled coil region | 0.09436 | Inherited |
Phoshoinositide 3-kinase (PI3K), catalytic domain | 0.107 | Inherited |
Toll/Interleukin receptor TIR domain | 0.1168 | Inherited |
ABC transporter ATPase domain-like | 0.1632 | Inherited |
Cell cycle control phosphatase, catalytic domain | 0.1721 | Inherited |
28-residue LRR | 0.1913 | Inherited |
Papain-like | 0.2475 | Inherited |
Classic zinc finger, C2H2 | 0.7102 | Inherited |
DBL homology domain (DH-domain) | 0.829 | Inherited |
Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term
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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.
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Supra-domain (including individual superfamily)
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(show details)
Supra-domains annotated to this MP term (SPMP level: Moderately Informative)
Highlighted in gray are those with FDR>0.001
Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
55166,51294 55166 - Hedgehog/DD-peptidase 51294 - Hedgehog/intein (Hint) domain | 0 | DIRECT |
49417,47719 49417 - p53-like transcription factors 47719 - p53 tetramerization domain | 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 | 0.000006314 | DIRECT |
57440,50494 57440 - Kringle-like 50494 - Trypsin-like serine proteases | 0.0001574 | DIRECT |
55550,50044 55550 - SH2 domain 50044 - SH3-domain | 0.0005014 | DIRECT |
57716,48508 57716 - Glucocorticoid receptor-like (DNA-binding domain) 48508 - Nuclear receptor ligand-binding domain | 0.0006211 | DIRECT |
57586,57586 57586 - TNF receptor-like 57586 - TNF receptor-like | 0.0007196 | DIRECT |
47986,52540 47986 - DEATH domain 52540 - P-loop containing nucleoside triphosphate hydrolases | 0.001963 | INHERITED FROM: large intestinal inflammation || colitis || intestinal inflammation || abnormal intestine physiology || abnormal susceptibility to induced colitis |
57440,57440 57440 - Kringle-like 57440 - Kringle-like | 0.001963 | INHERITED FROM: large intestinal inflammation || colitis |
57196,69687 57196 - EGF/Laminin 69687 - Integrin beta tail domain | 0.00721 | INHERITED FROM: abnormal digestive system physiology |
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.009468 | INHERITED FROM: abnormal rectum morphology |
55550,50729 55550 - SH2 domain 50729 - PH domain-like | 0.01143 | INHERITED FROM: abnormal intestine morphology |
48334,52540 48334 - DNA repair protein MutS, domain III 52540 - P-loop containing nucleoside triphosphate hydrolases | 0.01143 | INHERITED FROM: increased gastrointestinal tumor incidence || increased alimentary system tumor incidence || increased intestinal adenocarcinoma incidence |
64593,64593 64593 - Intermediate filament protein, coiled coil region 64593 - Intermediate filament protein, coiled coil region | 0.02028 | INHERITED FROM: abnormal esophagus morphology || abnormal tongue epithelium morphology || abnormal tongue morphology |
52058,52058 52058 - L domain-like 52058 - L domain-like | 0.03987 | INHERITED FROM: abnormal intestine development || abnormal intestine physiology |
52540,90123 52540 - P-loop containing nucleoside triphosphate hydrolases 90123 - ABC transporter transmembrane region | 0.04185 | INHERITED FROM: abnormal intestine physiology |
51045,51045 51045 - WW domain 51045 - WW domain | 0.08997 | INHERITED FROM: abnormal intestinal epithelium physiology |
48065,50729 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like | 0.7515 | INHERITED FROM: abnormal enterocyte morphology || gastrointestinal ulcer || intestinal ulcer |
Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
55166,51294 55166 - Hedgehog/DD-peptidase 51294 - Hedgehog/intein (Hint) domain | 0 | Direct |
49417,47719 49417 - p53-like transcription factors 47719 - p53 tetramerization domain | 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 | 0.000006314 | Direct |
57440,50494 57440 - Kringle-like 50494 - Trypsin-like serine proteases | 0.0001574 | Direct |
55550,50044 55550 - SH2 domain 50044 - SH3-domain | 0.0005014 | Direct |
57716,48508 57716 - Glucocorticoid receptor-like (DNA-binding domain) 48508 - Nuclear receptor ligand-binding domain | 0.0006211 | Direct |
57586,57586 57586 - TNF receptor-like 57586 - TNF receptor-like | 0.0007196 | Direct |
47986,52540 47986 - DEATH domain 52540 - P-loop containing nucleoside triphosphate hydrolases | 0.001963 | Inherited |
57440,57440 57440 - Kringle-like 57440 - Kringle-like | 0.001963 | Inherited |
57196,69687 57196 - EGF/Laminin 69687 - Integrin beta tail domain | 0.00721 | Inherited |
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain | 0.009468 | Inherited |
55550,50729 55550 - SH2 domain 50729 - PH domain-like | 0.01143 | Inherited |
48334,52540 48334 - DNA repair protein MutS, domain III 52540 - P-loop containing nucleoside triphosphate hydrolases | 0.01143 | Inherited |
64593,64593 64593 - Intermediate filament protein, coiled coil region 64593 - Intermediate filament protein, coiled coil region | 0.02028 | Inherited |
52058,52058 52058 - L domain-like 52058 - L domain-like | 0.03987 | Inherited |
52540,90123 52540 - P-loop containing nucleoside triphosphate hydrolases 90123 - ABC transporter transmembrane region | 0.04185 | Inherited |
51045,51045 51045 - WW domain 51045 - WW domain | 0.08997 | Inherited |
48065,50729 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like | 0.7515 | Inherited |
(show details)
Supra-domains annotated to this MP term (SPMP level: Moderately Informative)
Highlighted in gray are those with FDR>0.001
Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
47576,48065,50729 47576 - Calponin-homology domain, CH-domain 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like | 0 | DIRECT |
57586,57586,57586 57586 - TNF receptor-like 57586 - TNF receptor-like 57586 - TNF receptor-like | 0.0007562 | DIRECT |
57440,57440,50494 57440 - Kringle-like 57440 - Kringle-like 50494 - Trypsin-like serine proteases | 0.0007562 | DIRECT |
57184,52058,57184 57184 - Growth factor receptor domain 52058 - L domain-like 57184 - Growth factor receptor domain | 0.003579 | INHERITED FROM: abnormal intestine morphology |
57196,57196,69687 57196 - EGF/Laminin 57196 - EGF/Laminin 69687 - Integrin beta tail domain | 0.00721 | INHERITED FROM: abnormal digestive system physiology |
57440,57440,57440 57440 - Kringle-like 57440 - Kringle-like 57440 - Kringle-like | 0.01143 | INHERITED FROM: large intestinal inflammation || colitis || abnormal intestine physiology |
52540,90123,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 90123 - ABC transporter transmembrane region 52540 - P-loop containing nucleoside triphosphate hydrolases | 0.04185 | INHERITED FROM: abnormal intestine physiology |
90123,52540,90123 90123 - ABC transporter transmembrane region 52540 - P-loop containing nucleoside triphosphate hydrolases 90123 - ABC transporter transmembrane region | 0.04185 | INHERITED FROM: abnormal intestine physiology |
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin | 0.04887 | INHERITED FROM: abnormal secondary palate development |
Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
47576,48065,50729 47576 - Calponin-homology domain, CH-domain 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like | 0 | Direct |
57586,57586,57586 57586 - TNF receptor-like 57586 - TNF receptor-like 57586 - TNF receptor-like | 0.0007562 | Direct |
57440,57440,50494 57440 - Kringle-like 57440 - Kringle-like 50494 - Trypsin-like serine proteases | 0.0007562 | Direct |
57184,52058,57184 57184 - Growth factor receptor domain 52058 - L domain-like 57184 - Growth factor receptor domain | 0.003579 | Inherited |
57196,57196,69687 57196 - EGF/Laminin 57196 - EGF/Laminin 69687 - Integrin beta tail domain | 0.00721 | Inherited |
57440,57440,57440 57440 - Kringle-like 57440 - Kringle-like 57440 - Kringle-like | 0.01143 | Inherited |
52540,90123,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 90123 - ABC transporter transmembrane region 52540 - P-loop containing nucleoside triphosphate hydrolases | 0.04185 | Inherited |
90123,52540,90123 90123 - ABC transporter transmembrane region 52540 - P-loop containing nucleoside triphosphate hydrolases 90123 - ABC transporter transmembrane region | 0.04185 | Inherited |
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin | 0.04887 | Inherited |
Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term
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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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