Fly Anatomy (FA): segment

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).

Superfamily

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Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
Orange domain-like	0	Direct
ARID-like	0	Direct
A DNA-binding domain in eukaryotic transcription factors	0	Direct
lambda repressor-like DNA-binding domains	0	Direct
TIMP-like	0	Direct
SAND domain-like	0	Direct
Cysteine-rich DNA binding domain, (DM domain)	0	Direct
Putative DNA-binding domain	0	Direct
Sema domain	0	Direct
Frizzled cysteine-rich domain	0	Direct
SMAD MH1 domain	0	Direct
cAMP-binding domain-like	0	Direct
Translation proteins SH3-like domain	0	Direct
Rhomboid-like	0	Direct
Cytokine	0	Direct
beta-beta-alpha zinc fingers	0.0000000007799	Direct
Homeodomain-like	0.00000001309	Direct
Glucocorticoid receptor-like (DNA-binding domain)	0.00001269	Direct
p53-like transcription factors	0.00009214	Direct
Nuclear receptor ligand-binding domain	0.001338	Inherited
HLH, helix-loop-helix DNA-binding domain	0.00315	Inherited
SH2 domain	0.04253	Inherited
Plexin repeat	0.04934	Inherited
Snake toxin-like	0.04934	Inherited
Cadherin-like	0.05495	Inherited
Fibronectin type III	0.06897	Inherited
dsRNA-binding domain-like	0.09817	Inherited
HMG-box	0.1002	Inherited
Immunoglobulin	0.1026	Inherited
Calponin-homology domain, CH-domain	0.1408	Inherited
EGF/Laminin	0.1476	Inherited
(Phosphotyrosine protein) phosphatases II	0.2285	Inherited
SET domain	0.3226	Inherited
Growth factor receptor domain	0.3795	Inherited
CoA-dependent acyltransferases	0.4562	Inherited
Cystine-knot cytokines	0.4839	Inherited
TPR-like	0.6586	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Family

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
Myb/SANT domain	0	Direct
RNase III catalytic domain-like	0	Direct
ets domain	0	Direct
Paired domain	0	Direct
BC ATP-binding domain-like	0	Direct
p120GAP domain-like	0	Direct
Rel/Dorsal transcription factors, DNA-binding domain	0	Direct
A DNA-binding domain in eukaryotic transcription factors	0	Direct
Dachshund-homology domain	0	Direct
Fibroblast growth factors (FGF)	0	Direct
Phoshoinositide 3-kinase (PI3K), catalytic domain	0	Direct
Frizzled cysteine-rich domain	0	Direct
SMAD MH1 domain	0	Direct
Class I glutamine amidotransferases (GAT)	0	Direct
Ubiquitin activating enzymes (UBA)	0	Direct
ARID domain	0	Direct
ZZ domain	0	Direct
Extracellular domain of cell surface receptors	0	Direct
BC N-terminal domain-like	0	Direct
Sema domain	0	Direct
Hairy Orange domain	0	Direct
Cysteine-rich DNA binding domain, (DM domain)	0	Direct
Laminin-type module	0	Direct
POU-specific domain	0	Direct
Rhomboid-like	0	Direct
Integrin domains	0	Direct
Cell cycle control phosphatase, catalytic domain	0	Direct
cAMP-binding domain	0	Direct
Phoshoinositide 3-kinase (PI3K) helical domain	0	Direct
Homeodomain	0.000000535	Direct
Classic zinc finger, C2H2	0.00007589	Direct
Nuclear receptor ligand-binding domain	0.00129	Inherited
Nuclear receptor	0.00171	Inherited
Laminin G-like module	0.002393	Inherited
HLH, helix-loop-helix DNA-binding domain	0.002466	Inherited
SH2 domain	0.03403	Inherited
Plexin repeat	0.04279	Inherited
Fibronectin type III	0.05804	Inherited
SMAD domain	0.07296	Inherited
Cadherin	0.078	Inherited
HMG-box	0.08445	Inherited
EGF-type module	0.1006	Inherited
BTB/POZ domain	0.1068	Inherited
Calponin-homology domain, CH-domain	0.1202	Inherited
Choline/Carnitine O-acyltransferase	0.1234	Inherited
I set domains	0.2029	Inherited
PLC-like (P variant)	0.2254	Inherited
Ngr ectodomain-like	0.2425	Inherited
Growth factor receptor domain	0.2901	Inherited
Histone lysine methyltransferases	0.2901	Inherited
SAM (sterile alpha motif) domain	0.3453	Inherited
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0.3453	Inherited
Transforming growth factor (TGF)-beta	0.3453	Inherited
G proteins	1	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Supra-domain (Single|Duplex|Triple)

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Supra-domain (Single)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Rhomboid-like	0	Direct
lambda repressor-like DNA-binding domains	0	Direct
TIMP-like	0	Direct
Cytokine	0	Direct
Cysteine-rich DNA binding domain, (DM domain)	0	Direct
Orange domain-like	0	Direct
ARID-like	0	Direct
A DNA-binding domain in eukaryotic transcription factors	0	Direct
Translation proteins SH3-like domain	0	Direct
SMAD MH1 domain	0	Direct
Frizzled cysteine-rich domain	0	Direct
cAMP-binding domain-like	0	Direct
SAND domain-like	0	Direct
Sema domain	0	Direct
Putative DNA-binding domain	0	Direct
beta-beta-alpha zinc fingers	0.0000000005599	Direct
Homeodomain-like	0.000000009433	Direct
Glucocorticoid receptor-like (DNA-binding domain)	0.000009239	Direct
p53-like transcription factors	0.00006753	Direct
Nuclear receptor ligand-binding domain	0.000965	Direct
HLH, helix-loop-helix DNA-binding domain	0.002275	Inherited
SH2 domain	0.0336	Inherited
Plexin repeat	0.03927	Inherited
Snake toxin-like	0.03927	Inherited
Cadherin-like	0.04408	Inherited
Fibronectin type III	0.05623	Inherited
dsRNA-binding domain-like	0.08177	Inherited
HMG-box	0.08368	Inherited
Immunoglobulin	0.08568	Inherited
Calponin-homology domain, CH-domain	0.1196	Inherited
EGF/Laminin	0.1258	Inherited
(Phosphotyrosine protein) phosphatases II	0.2006	Inherited
GTPase activation domain, GAP	0.2803	Inherited
SET domain	0.291	Inherited
Growth factor receptor domain	0.3471	Inherited
CoA-dependent acyltransferases	0.4238	Inherited
Cystine-knot cytokines	0.4518	Inherited
SMAD/FHA domain	0.5128	Inherited
TPR-like	0.6314	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

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Supra-domain (Duplex) in N- to C-terminal order

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like	0	Direct
57716,48508 57716 - Glucocorticoid receptor-like (DNA-binding domain) 48508 - Nuclear receptor ligand-binding domain	0	Direct
49265,48726 49265 - Fibronectin type III 48726 - Immunoglobulin	0	Direct
55550,50044 55550 - SH2 domain 50044 - SH3-domain	0	Direct
49899,49899 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0	Direct
48371,56112 48371 - ARM repeat 56112 - Protein kinase-like (PK-like)	0	Direct
50044,55550 50044 - SH3-domain 55550 - SH2 domain	0	Direct
49562,48371 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 48371 - ARM repeat	0	Direct
101912,103575 101912 - Sema domain 103575 - Plexin repeat	0	Direct
51206,51206 51206 - cAMP-binding domain-like 51206 - cAMP-binding domain-like	0	Direct
49417,81296 49417 - p53-like transcription factors 81296 - E set domains	0	Direct
47769,47769 47769 - SAM/Pointed domain 47769 - SAM/Pointed domain	0	Direct
47413,46689 47413 - lambda repressor-like DNA-binding domains 46689 - Homeodomain-like	0	Direct
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	0.000001002	Direct
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.03927	Inherited
46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat	0.07058	Inherited
49313,49313 49313 - Cadherin-like 49313 - Cadherin-like	0.07058	Inherited
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.08368	Inherited
52777,52777 52777 - CoA-dependent acyltransferases 52777 - CoA-dependent acyltransferases	0.1169	Inherited
52799,52799 52799 - (Phosphotyrosine protein) phosphatases II 52799 - (Phosphotyrosine protein) phosphatases II	0.1169	Inherited
48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin	0.1171	Inherited
54928,54928 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD	0.1196	Inherited
48726,49265 48726 - Immunoglobulin 49265 - Fibronectin type III	0.1745	Inherited
49265,49265 49265 - Fibronectin type III 49265 - Fibronectin type III	0.3486	Inherited
51045,51045 51045 - WW domain 51045 - WW domain	0.3486	Inherited
81296,81296 81296 - E set domains 81296 - E set domains	0.5028	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

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Supra-domain (Triple) in N- to C-terminal order

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
49265,48726,48726 49265 - Fibronectin type III 48726 - Immunoglobulin 48726 - Immunoglobulin	0	Direct
49562,48371,56112 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 48371 - ARM repeat 56112 - Protein kinase-like (PK-like)	0	Direct
49899,49899,49899 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0	Direct
57196,49899,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0	Direct
57667,57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	0.000000001662	Direct
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin	0.05263	Inherited
49313,49313,49313 49313 - Cadherin-like 49313 - Cadherin-like 49313 - Cadherin-like	0.07058	Inherited
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin	0.1432	Inherited
48726,48726,49265 48726 - Immunoglobulin 48726 - Immunoglobulin 49265 - Fibronectin type III	0.2314	Inherited
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.4182	Inherited
81296,81296,81296 81296 - E set domains 81296 - E set domains 81296 - E set domains	0.5028	Inherited