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Fly Anatomy (FA): sensory system 
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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).
Jump to [ Top · Hierarchy · Annotations ]
Root: FA Hierarchy (fly anatomy from FlyBase anatomy ontology)
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) |
| RNase III catalytic domain-like | 0 | DIRECT |
| Eps15 homology domain (EH domain) | 0 | DIRECT |
| Phosphatidylinositol phosphate kinase IIbeta, PIPK IIbeta | 0 | DIRECT |
| Fibrinogen C-terminal domain-like | 0 | DIRECT |
| Rel/Dorsal transcription factors, DNA-binding domain | 0 | DIRECT |
| Metal cation-transporting ATPase, ATP-binding domain N | 0 | DIRECT |
| Frizzled cysteine-rich domain | 0 | DIRECT |
| VHS domain | 0 | DIRECT |
| Diacylglycerol kinase-like | 0 | DIRECT |
| NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain | 0 | DIRECT |
| Inositol polyphosphate 5-phosphatase (IPP5) | 0 | DIRECT |
| Sema domain | 0 | DIRECT |
| Laminin-type module | 0 | DIRECT |
| SAP domain | 0 | DIRECT |
| Integrin domains | 0 | DIRECT |
| Cell cycle control phosphatase, catalytic domain | 0 | DIRECT |
| Discoidin domain (FA58C, coagulation factor 5/8 C-terminal domain) | 0 | DIRECT |
| Arrestin/Vps26-like | 0 | DIRECT |
| Third domain of FERM | 0.03637 | INHERITED FROM: ommatidium |
| Laminin G-like module | 0.05323 | INHERITED FROM: photoreceptor cell R4 || rhabdomeric photoreceptor cell |
| Second domain of FERM | 0.05323 | INHERITED FROM: head bristle |
| POU-specific domain | 0.05913 | INHERITED FROM: adult olfactory receptor neuron Or42a || olfactory system || chemosensory system || olfactory system neuron || chemosensory neuron || chemosensory system neuron || olfactory receptor neuron || antennal sense organ || eo neuron || adult olfactory receptor neuron |
| PLC-like (P variant) | 0.0599 | INHERITED FROM: larval dorsal multidendritic neuron || larval dorsal multidendritic neuron ddaC |
| Growth factor receptor domain | 0.08202 | INHERITED FROM: ocellus |
| I set domains | 0.1007 | INHERITED FROM: gustatory system || gustatory system neuron || leg taste bristle chemosensory neuron || mechanosensory system neuron || gustatory receptor neuron || larval abdominal sensory neuron |
| SH2 domain | 0.1165 | INHERITED FROM: photoreceptor cell R7 || head sensillum || photoreceptor cell || ommatidium || rhabdomeric photoreceptor cell |
| Fibronectin type III | 0.1191 | INHERITED FROM: gustatory receptor neuron |
| Ankyrin repeat | 0.1223 | INHERITED FROM: ventral multidendritic neuron || Johnston organ neuron |
| Cadherin | 0.1867 | INHERITED FROM: photoreceptor cell R4 || outer photoreceptor cell |
| Protein kinases, catalytic subunit | 0.225 | INHERITED FROM: photoreceptor cell R8 of pale ommatidium |
| Transducin (alpha subunit), insertion domain | 0.3899 | INHERITED FROM: chemosensory system || eo neuron |
| Classic zinc finger, C2H2 | 0.6027 | INHERITED FROM: embryonic/larval head sensillum |
| HLH, helix-loop-helix DNA-binding domain | 0.6396 | INHERITED FROM: sensillum campaniformium || anterior orbital bristle |
| Homeodomain | 0.9144 | INHERITED FROM: terminal organ || head bristle || embryonic/larval sense organ || embryonic/larval labial organ || dorsal rim area || dorsal margin photoreceptor || embryonic/larval sensillum || maxillary palp olfactory receptor neuron || dorsal margin ommatidium |
| SCOP term |
FDR (all) |
Annotation (direct or inherited) |
| RNase III catalytic domain-like | 0 | Direct |
| Eps15 homology domain (EH domain) | 0 | Direct |
| Phosphatidylinositol phosphate kinase IIbeta, PIPK IIbeta | 0 | Direct |
| Fibrinogen C-terminal domain-like | 0 | Direct |
| Rel/Dorsal transcription factors, DNA-binding domain | 0 | Direct |
| Metal cation-transporting ATPase, ATP-binding domain N | 0 | Direct |
| Frizzled cysteine-rich domain | 0 | Direct |
| VHS domain | 0 | Direct |
| Diacylglycerol kinase-like | 0 | Direct |
| NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain | 0 | Direct |
| Inositol polyphosphate 5-phosphatase (IPP5) | 0 | Direct |
| Sema domain | 0 | Direct |
| Laminin-type module | 0 | Direct |
| SAP domain | 0 | Direct |
| Integrin domains | 0 | Direct |
| Cell cycle control phosphatase, catalytic domain | 0 | Direct |
| Discoidin domain (FA58C, coagulation factor 5/8 C-terminal domain) | 0 | Direct |
| Arrestin/Vps26-like | 0 | Direct |
| Third domain of FERM | 0.03637 | Inherited |
| Laminin G-like module | 0.05323 | Inherited |
| Second domain of FERM | 0.05323 | Inherited |
| POU-specific domain | 0.05913 | Inherited |
| PLC-like (P variant) | 0.0599 | Inherited |
| Growth factor receptor domain | 0.08202 | Inherited |
| I set domains | 0.1007 | Inherited |
| SH2 domain | 0.1165 | Inherited |
| Fibronectin type III | 0.1191 | Inherited |
| Ankyrin repeat | 0.1223 | Inherited |
| Cadherin | 0.1867 | Inherited |
| Protein kinases, catalytic subunit | 0.225 | Inherited |
| Transducin (alpha subunit), insertion domain | 0.3899 | Inherited |
| Classic zinc finger, C2H2 | 0.6027 | Inherited |
| HLH, helix-loop-helix DNA-binding domain | 0.6396 | Inherited |
| Homeodomain | 0.9144 | 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) |
57903,47370
57903 - FYVE/PHD zinc finger
47370 - Bromodomain | 0 | DIRECT |
51045,51045
51045 - WW domain
51045 - WW domain | 0 | DIRECT |
81660,56784
81660 - Metal cation-transporting ATPase, ATP-binding domain N
56784 - HAD-like | 0 | DIRECT |
49417,81296
49417 - p53-like transcription factors
81296 - E set domains | 0 | DIRECT |
57184,57184
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain | 0 | DIRECT |
101912,103575
101912 - Sema domain
103575 - Plexin repeat | 0 | DIRECT |
48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.01318 | INHERITED FROM: leg taste bristle chemosensory neuron |
52058,52058
52058 - L domain-like
52058 - L domain-like | 0.015 | INHERITED FROM: macrochaeta || mechanosensory system || mechanosensory sensory organ |
47413,46689
47413 - lambda repressor-like DNA-binding domains
46689 - Homeodomain-like | 0.02801 | INHERITED FROM: olfactory receptor neuron || sensory neuron || chemosensory system || olfactory system neuron || antennal sense organ || adult olfactory receptor neuron || eo neuron || chemosensory sensory organ || adult olfactory receptor neuron Or42a || larval multidendritic class IV neuron |
49899,49899
49899 - Concanavalin A-like lectins/glucanases
49899 - Concanavalin A-like lectins/glucanases | 0.02956 | INHERITED FROM: photoreceptor cell R4 || rhabdomeric photoreceptor cell || external compound sense organ || photoreceptor || compound sense organ |
57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.04887 | INHERITED FROM: secondary pigment cell || ocellus || rhabdomeric photoreceptor cell || tertiary pigment cell || eye photoreceptor cell stalk |
55550,50044
55550 - SH2 domain
50044 - SH3-domain | 0.09504 | INHERITED FROM: photoreceptor cell R7 || inner photoreceptor cell |
54236,47031
54236 - Ubiquitin-like
47031 - Second domain of FERM | 0.1069 | INHERITED FROM: head bristle |
48726,49265
48726 - Immunoglobulin
49265 - Fibronectin type III | 0.1159 | INHERITED FROM: mechanosensory neuron || gustatory receptor neuron || chemosensory system neuron || leg taste bristle chemosensory neuron || chemosensory neuron |
57196,57184
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.1383 | INHERITED FROM: mesothoracic bristle || adult thoracic sensillum || photoreceptor cell R7 || inner photoreceptor cell || adult mesothoracic sensillum || interommatidial bristle |
54928,54928
54928 - RNA-binding domain, RBD
54928 - RNA-binding domain, RBD | 0.1525 | INHERITED FROM: bristle of mesothoracic tergum |
49313,49313
49313 - Cadherin-like
49313 - Cadherin-like | 0.1647 | INHERITED FROM: photoreceptor cell R4 || outer photoreceptor cell |
49265,49265
49265 - Fibronectin type III
49265 - Fibronectin type III | 0.2486 | INHERITED FROM: dendritic arborizing neuron || larval abdominal sensory neuron || multidendritic neuron |
47895,52540
47895 - Transducin (alpha subunit), insertion domain
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.3633 | INHERITED FROM: chemosensory system || eo neuron |
50978,50978
50978 - WD40 repeat-like
50978 - WD40 repeat-like | 0.489 | INHERITED FROM: mechanosensory neuron || mechanosensory system neuron |
57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 0.9879 | INHERITED FROM: postalar bristle |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57903,47370
57903 - FYVE/PHD zinc finger
47370 - Bromodomain | 0 | Direct |
51045,51045
51045 - WW domain
51045 - WW domain | 0 | Direct |
81660,56784
81660 - Metal cation-transporting ATPase, ATP-binding domain N
56784 - HAD-like | 0 | Direct |
49417,81296
49417 - p53-like transcription factors
81296 - E set domains | 0 | Direct |
57184,57184
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain | 0 | Direct |
101912,103575
101912 - Sema domain
103575 - Plexin repeat | 0 | Direct |
48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.01318 | Inherited |
52058,52058
52058 - L domain-like
52058 - L domain-like | 0.015 | Inherited |
47413,46689
47413 - lambda repressor-like DNA-binding domains
46689 - Homeodomain-like | 0.02801 | Inherited |
49899,49899
49899 - Concanavalin A-like lectins/glucanases
49899 - Concanavalin A-like lectins/glucanases | 0.02956 | Inherited |
57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.04887 | Inherited |
55550,50044
55550 - SH2 domain
50044 - SH3-domain | 0.09504 | Inherited |
54236,47031
54236 - Ubiquitin-like
47031 - Second domain of FERM | 0.1069 | Inherited |
48726,49265
48726 - Immunoglobulin
49265 - Fibronectin type III | 0.1159 | Inherited |
57196,57184
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.1383 | Inherited |
54928,54928
54928 - RNA-binding domain, RBD
54928 - RNA-binding domain, RBD | 0.1525 | Inherited |
49313,49313
49313 - Cadherin-like
49313 - Cadherin-like | 0.1647 | Inherited |
49265,49265
49265 - Fibronectin type III
49265 - Fibronectin type III | 0.2486 | Inherited |
47895,52540
47895 - Transducin (alpha subunit), insertion domain
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.3633 | Inherited |
50978,50978
50978 - WD40 repeat-like
50978 - WD40 repeat-like | 0.489 | Inherited |
57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 0.9879 | 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) |
57196,49899,49899
57196 - EGF/Laminin
49899 - Concanavalin A-like lectins/glucanases
49899 - Concanavalin A-like lectins/glucanases | 0 | DIRECT |
81660,56784,81665
81660 - Metal cation-transporting ATPase, ATP-binding domain N
56784 - HAD-like
81665 - Calcium ATPase, transmembrane domain M | 0 | DIRECT |
57196,57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.0004735 | DIRECT |
46966,46966,46966
46966 - Spectrin repeat
46966 - Spectrin repeat
46966 - Spectrin repeat | 0.02801 | INHERITED FROM: sensory system neuron || sensory neuron |
48726,48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.04295 | INHERITED FROM: gustatory receptor neuron || leg taste bristle chemosensory neuron |
57196,57196,57184
57196 - EGF/Laminin
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.05203 | INHERITED FROM: bristle of mesothoracic tergum || adult thoracic mechanosensory chaeta |
48726,48726,49265
48726 - Immunoglobulin
48726 - Immunoglobulin
49265 - Fibronectin type III | 0.07143 | INHERITED FROM: mechanosensory neuron || gustatory receptor neuron || mechanosensory system neuron || chemosensory system neuron || eo neuron || leg taste bristle chemosensory neuron || chemosensory neuron |
54236,47031,50729
54236 - Ubiquitin-like
47031 - Second domain of FERM
50729 - PH domain-like | 0.08441 | INHERITED FROM: head bristle |
49313,49313,49313
49313 - Cadherin-like
49313 - Cadherin-like
49313 - Cadherin-like | 0.1647 | INHERITED FROM: photoreceptor cell R4 || outer photoreceptor cell |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57196,49899,49899
57196 - EGF/Laminin
49899 - Concanavalin A-like lectins/glucanases
49899 - Concanavalin A-like lectins/glucanases | 0 | Direct |
81660,56784,81665
81660 - Metal cation-transporting ATPase, ATP-binding domain N
56784 - HAD-like
81665 - Calcium ATPase, transmembrane domain M | 0 | Direct |
57196,57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.0004735 | Direct |
46966,46966,46966
46966 - Spectrin repeat
46966 - Spectrin repeat
46966 - Spectrin repeat | 0.02801 | Inherited |
48726,48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.04295 | Inherited |
57196,57196,57184
57196 - EGF/Laminin
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.05203 | Inherited |
48726,48726,49265
48726 - Immunoglobulin
48726 - Immunoglobulin
49265 - Fibronectin type III | 0.07143 | Inherited |
54236,47031,50729
54236 - Ubiquitin-like
47031 - Second domain of FERM
50729 - PH domain-like | 0.08441 | Inherited |
49313,49313,49313
49313 - Cadherin-like
49313 - Cadherin-like
49313 - Cadherin-like | 0.1647 | 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 FA 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 FA term
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Plot tree as:
| |
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 > sensory system
