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Worm Phenotype (WP): organelle organization biogenesis variant 
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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).
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Root: WP Hierarchy (worm phenotype from Wormbase Release WS226)
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Family( show details)
Highlighted in gray are those with FDR_all>0.001
| SCOP term |
FDR (all) |
Annotation (direct or inherited) |
| beta-sandwich domain of Sec23/24 | 0 | DIRECT |
| Heme-dependent catalases | 0 | DIRECT |
| Helical domain of Sec23/24 | 0 | DIRECT |
| Zn-finger domain of Sec23/24 | 0 | DIRECT |
| Trunk domain of Sec23/24 | 0 | DIRECT |
| Skp1 dimerisation domain-like | 0 | DIRECT |
| C-terminal, gelsolin-like domain of Sec23/24 | 0 | DIRECT |
| BTB/POZ domain | 0.00000005534 | DIRECT |
| Motor proteins | 0.000001186 | DIRECT |
| Pumilio repeat | 0.00000133 | DIRECT |
| DEP domain | 0.0001995 | DIRECT |
| PDZ domain | 0.0003478 | DIRECT |
| Tropomyosin | 0.0008623 | DIRECT |
| G proteins | 0.008065 | INHERITED FROM: mitotic spindle defective early emb || actin organization biogenesis variant || nuclear positioning variant || spindle position orientation defective early emb || microtubule organization biogenesis variant |
| Protein kinases, catalytic subunit | 0.0459 | INHERITED FROM: mitochondrial content variant |
| Group II chaperonin (CCT, TRIC), apical domain | 0.125 | INHERITED FROM: germline nuclear positioning variant || nuclear positioning variant |
| Actin/HSP70 | 0.125 | INHERITED FROM: germline nuclear positioning variant |
| Group II chaperonin (CCT, TRIC), ATPase domain | 0.125 | INHERITED FROM: germline nuclear positioning variant || nuclear positioning variant |
| Calponin-homology domain, CH-domain | 0.125 | INHERITED FROM: actin organization biogenesis variant |
| SH3-domain | 0.2305 | INHERITED FROM: actin organization biogenesis variant |
| Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain | 0.2928 | INHERITED FROM: germline nuclear positioning variant |
| Tubulin, GTPase domain | 0.3507 | INHERITED FROM: mitotic spindle defective early emb || cytoskeleton organization biogenesis variant || microtubule organization biogenesis variant || spindle assembly defective |
| Spectrin repeat | 0.3861 | INHERITED FROM: cytoskeleton organization biogenesis variant |
| Group II chaperonin (CCT, TRIC), intermediate domain | 0.3861 | INHERITED FROM: nuclear fallout || germline nuclear positioning variant || nuclear positioning variant |
| Armadillo repeat | 0.4255 | INHERITED FROM: spindle orientation defective early emb || mitotic spindle defective early emb || cytoskeleton organization biogenesis variant || spindle variant || microtubule organization biogenesis variant |
| Extended AAA-ATPase domain | 0.5659 | INHERITED FROM: meiotic spindle defective early emb || microtubule organization biogenesis variant || nucleus reforms cell division remnant early emb |
| Tubulin, C-terminal domain | 0.5824 | INHERITED FROM: mitotic spindle defective early emb || cytoskeleton organization biogenesis variant || microtubule organization biogenesis variant || spindle assembly defective |
| Prefoldin | 0.7113 | INHERITED FROM: mitotic spindle defective early emb || cytoskeleton organization biogenesis variant || spindle variant || microtubule organization biogenesis variant |
| DNA replication initiator (cdc21/cdc54) N-terminal domain | 0.7113 | INHERITED FROM: nuclear position defective early emb || nucleus reforms cell division remnant early emb |
| SCOP term |
FDR (all) |
Annotation (direct or inherited) |
| beta-sandwich domain of Sec23/24 | 0 | Direct |
| Heme-dependent catalases | 0 | Direct |
| Helical domain of Sec23/24 | 0 | Direct |
| Zn-finger domain of Sec23/24 | 0 | Direct |
| Trunk domain of Sec23/24 | 0 | Direct |
| Skp1 dimerisation domain-like | 0 | Direct |
| C-terminal, gelsolin-like domain of Sec23/24 | 0 | Direct |
| BTB/POZ domain | 0.00000005534 | Direct |
| Motor proteins | 0.000001186 | Direct |
| Pumilio repeat | 0.00000133 | Direct |
| DEP domain | 0.0001995 | Direct |
| PDZ domain | 0.0003478 | Direct |
| Tropomyosin | 0.0008623 | Direct |
| G proteins | 0.008065 | Inherited |
| Protein kinases, catalytic subunit | 0.0459 | Inherited |
| Group II chaperonin (CCT, TRIC), apical domain | 0.125 | Inherited |
| Actin/HSP70 | 0.125 | Inherited |
| Group II chaperonin (CCT, TRIC), ATPase domain | 0.125 | Inherited |
| Calponin-homology domain, CH-domain | 0.125 | Inherited |
| SH3-domain | 0.2305 | Inherited |
| Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain | 0.2928 | Inherited |
| Tubulin, GTPase domain | 0.3507 | Inherited |
| Spectrin repeat | 0.3861 | Inherited |
| Group II chaperonin (CCT, TRIC), intermediate domain | 0.3861 | Inherited |
| Armadillo repeat | 0.4255 | Inherited |
| Extended AAA-ATPase domain | 0.5659 | Inherited |
| Tubulin, C-terminal domain | 0.5824 | Inherited |
| Prefoldin | 0.7113 | Inherited |
| DNA replication initiator (cdc21/cdc54) N-terminal domain | 0.7113 | Inherited |
LINKTO: Domain2BO Download and Domain2BO Algorithm
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Supra-domain (Single)( show details)
Highlighted in gray are those with FDR>0.001
LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm
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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) |
54695,81382
54695 - POZ domain
81382 - Skp1 dimerisation domain-like | 0 | DIRECT |
81811,82754
81811 - Helical domain of Sec23/24
82754 - C-terminal, gelsolin-like domain of Sec23/24 | 0 | DIRECT |
82919,53300
82919 - Zn-finger domain of Sec23/24
53300 - vWA-like | 0 | DIRECT |
53067,53067
53067 - Actin-like ATPase domain
53067 - Actin-like ATPase domain | 0.09086 | INHERITED FROM: germline nuclear positioning variant |
48592,54849
48592 - GroEL equatorial domain-like
54849 - GroEL-intermediate domain like | 0.1222 | INHERITED FROM: germline nuclear positioning variant || nuclear positioning variant |
54849,52029
54849 - GroEL-intermediate domain like
52029 - GroEL apical domain-like | 0.1222 | INHERITED FROM: germline nuclear positioning variant || nuclear positioning variant |
52540,52540
52540 - P-loop containing nucleoside triphosphate hydrolases
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.2177 | INHERITED FROM: meiotic spindle defective early emb |
48452,48452
48452 - TPR-like
48452 - TPR-like | 0.2893 | INHERITED FROM: mitotic spindle defective early emb || cytoskeleton organization biogenesis variant || microtubule organization biogenesis variant |
52490,55307
52490 - Tubulin nucleotide-binding domain-like
55307 - Tubulin C-terminal domain-like | 0.3416 | INHERITED FROM: mitotic spindle defective early emb || spindle assembly defective || cytoskeleton organization biogenesis variant || microtubule organization biogenesis variant |
48371,48371
48371 - ARM repeat
48371 - ARM repeat | 0.5966 | INHERITED FROM: cytoskeleton organization biogenesis variant || microtubule organization biogenesis variant |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
54695,81382
54695 - POZ domain
81382 - Skp1 dimerisation domain-like | 0 | Direct |
81811,82754
81811 - Helical domain of Sec23/24
82754 - C-terminal, gelsolin-like domain of Sec23/24 | 0 | Direct |
82919,53300
82919 - Zn-finger domain of Sec23/24
53300 - vWA-like | 0 | Direct |
53067,53067
53067 - Actin-like ATPase domain
53067 - Actin-like ATPase domain | 0.09086 | Inherited |
48592,54849
48592 - GroEL equatorial domain-like
54849 - GroEL-intermediate domain like | 0.1222 | Inherited |
54849,52029
54849 - GroEL-intermediate domain like
52029 - GroEL apical domain-like | 0.1222 | Inherited |
52540,52540
52540 - P-loop containing nucleoside triphosphate hydrolases
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.2177 | Inherited |
48452,48452
48452 - TPR-like
48452 - TPR-like | 0.2893 | Inherited |
52490,55307
52490 - Tubulin nucleotide-binding domain-like
55307 - Tubulin C-terminal domain-like | 0.3416 | Inherited |
48371,48371
48371 - ARM repeat
48371 - ARM repeat | 0.5966 | 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
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 WP 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 WP term
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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 > organelle organization biogenesis variant
