•  SEARCH

  • Keyword search
  • Sequence search
• 
  

•  BROWSE

  •   Organisms
  • Taxonomy
  • Statistics
  •   SCOP
  • Hierarchy
  •   Ontologies
  • GO
  • EC
  • Phenotype
• 
  

•  TOOLS

  • Compare genomes
  • Phylogenetic trees
  • Web services
  • Downloads
• 
  

•  ABOUT

  • Description
  • Publications
  • Documentation
• 
  

•  HELP

  • User support
  • Contact us
  • Email list
  • Sitemap

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).
  

Superfamily domains annotated to this WP term (Not in SDWP)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
Aromatic aminoacid monoxygenases, catalytic and oligomerization domains	0	DIRECT
Transducin (heterotrimeric G protein), gamma chain	0	DIRECT
Skp1 dimerisation domain-like	0.0000000000009406	DIRECT
Nicotinic receptor ligand binding domain-like	0.000000000001228	DIRECT
Neurotransmitter-gated ion-channel transmembrane pore	0.000000000002387	DIRECT
Cullin repeat-like	0.000000009891	DIRECT
Cullin homology domain	0.0000007544	DIRECT
Protein kinase-like (PK-like)	0.0000009624	DIRECT
cAMP-binding domain-like	0.00001046	DIRECT
C2 domain (Calcium/lipid-binding domain, CaLB)	0.00001394	DIRECT
Transducin (alpha subunit), insertion domain	0.0002654	DIRECT
Periplasmic binding protein-like I	0.002462	INHERITED FROM: magnesium chemotaxis defective || iodide chemotaxis variant || bromide chemotaxis variant || chemotaxis variant || benzaldehyde chemotaxis variant || aqueous chemosensory response variant || alkaline pH chemotaxis variant || diacetyl chemotaxis variant || AWC odorant chemotaxis defective || AWC odorant chemotaxis variant || chemosensory behavior variant || chemosensory response variant || bromide chemotaxis defective || lithium chemotaxis defective || iodide chemotaxis defective || aqueous positive chemotaxis variant
Myosin rod fragments	0.003839	INHERITED FROM: drug resistant
Quinoprotein alcohol dehydrogenase-like	0.007825	INHERITED FROM: drug response variant
Voltage-gated potassium channels	0.01824	INHERITED FROM: adrenergic receptor antagonist response variant || positive chemotaxis defective || serotonin resistant || serotonin response variant
Multidrug efflux transporter AcrB transmembrane domain	0.0217	INHERITED FROM: odorant positive chemotaxis defective || odorant chemosensory response variant || positive chemotaxis defective
EF-hand	0.02244	INHERITED FROM: aldicarb response variant
Tryptophan synthase beta subunit-like PLP-dependent enzymes	0.02287	INHERITED FROM: drug hypersensitive
Immunoglobulin	0.02522	INHERITED FROM: aldicarb response variant
PRTase-like	0.02693	INHERITED FROM: drug resistant || Fluorouracil resistant
Lipovitellin-phosvitin complex; beta-sheet shell regions	0.03135	INHERITED FROM: unfolded protein response variant
Spectrin repeat	0.03135	INHERITED FROM: drug response variant || aldicarb resistant || aldicarb response variant
Lipovitellin-phosvitin complex, superhelical domain	0.03135	INHERITED FROM: unfolded protein response variant
ENTH/VHS domain	0.03137	INHERITED FROM: acetylcholinesterase inhibitor resistant || aldicarb resistant
TPR-like	0.03146	INHERITED FROM: ivermectin resistant || positive chemotaxis defective || ivermectin response variant
Calcium ATPase, transmembrane domain M	0.03687	INHERITED FROM: nicotine hypersensitive
Calcium ATPase, transduction domain A	0.03687	INHERITED FROM: nicotine hypersensitive
Metal cation-transporting ATPase, ATP-binding domain N	0.03687	INHERITED FROM: nicotine hypersensitive
Periplasmic binding protein-like II	0.03784	INHERITED FROM: response to food variant || chemotaxis variant || chemosensory behavior variant || chemosensory response variant || positive chemotaxis defective || aqueous positive chemotaxis defective || sodium chloride chemotaxis variant || sodium chloride chemotaxis defective || aqueous positive chemotaxis variant
PDZ domain-like	0.04229	INHERITED FROM: aldicarb response variant || acetylcholinesterase inhibitor response variant
WD40 repeat-like	0.0456	INHERITED FROM: aldicarb response variant || osmotic avoidance variant
Troponin coil-coiled subunits	0.05919	INHERITED FROM: nicotine response variant || drug response variant
SMAD/FHA domain	0.05989	INHERITED FROM: aldicarb response variant
Glutathione synthetase ATP-binding domain-like	0.05989	INHERITED FROM: negative chemotaxis variant || chemotaxis variant || chemosensory behavior variant || chemosensory response variant || osmotic avoidance variant
SAM/Pointed domain	0.06482	INHERITED FROM: aldicarb response variant
Regulator of G-protein signaling, RGS	0.06482	INHERITED FROM: negative chemotaxis variant || chemotaxis variant
Nucleotide cyclase	0.06505	INHERITED FROM: anion positive chemotaxis defective || magnesium chemotaxis defective || iodide chemotaxis variant || bromide chemotaxis variant || chemotaxis variant || aqueous chemosensory response variant || cation positive chemotaxis variant || alkaline pH chemotaxis variant || diacetyl chemotaxis variant || cation positive chemotaxis defective || positive chemotaxis variant || AWC odorant chemotaxis defective || AWC odorant chemotaxis variant || chemosensory behavior variant || chemosensory response variant || anion positive chemotaxis variant || osmotic avoidance variant || bromide chemotaxis defective || lithium chemotaxis defective || iodide chemotaxis defective
Cysteine-rich domain	0.06797	INHERITED FROM: odorant chemosensory response variant || positive chemotaxis variant || odorant positive chemotaxis variant || aldicarb response variant
EGF/Laminin	0.08499	INHERITED FROM: octanol chemotaxis variant || octanol chemotaxis defective || odorant negative chemotaxis defective
SH3-domain	0.1106	INHERITED FROM: aldicarb response variant
t-snare proteins	0.1108	INHERITED FROM: drug hypersensitive
SNARE-like	0.1148	INHERITED FROM: acetylcholinesterase inhibitor resistant || aldicarb resistant
SNF-like	0.1797	INHERITED FROM: drug hypersensitive
PH domain-like	0.2133	INHERITED FROM: aldicarb response variant
P-loop containing nucleoside triphosphate hydrolases	0.2219	INHERITED FROM: hydroxyurea response variant
Cystine-knot cytokines	0.2225	INHERITED FROM: nicotine response variant || levamisole response variant
GroEL equatorial domain-like	0.2274	INHERITED FROM: unfolded protein response variant
GroEL-intermediate domain like	0.2274	INHERITED FROM: unfolded protein response variant
GroEL apical domain-like	0.2274	INHERITED FROM: unfolded protein response variant
Tubulin nucleotide-binding domain-like	0.262	INHERITED FROM: nicotine response variant
HAD-like	0.2669	INHERITED FROM: nicotine hypersensitive
POZ domain	0.2708	INHERITED FROM: chemical hypersensitive
Bromodomain	0.334	INHERITED FROM: anesthetic response variant || ethanol resistant || acute functional tolerance to alcohol defective || anesthetic resistant || drug adaptation variant
Tubulin C-terminal domain-like	0.3887	INHERITED FROM: nicotine response variant
Sm-like ribonucleoproteins	0.4719	INHERITED FROM: unfolded protein response variant
"Winged helix" DNA-binding domain	0.48	INHERITED FROM: anesthetic response variant || chemical hypersensitive
ABC transporter transmembrane region	0.6253	INHERITED FROM: colchicine hypersensitive
Leucine zipper domain	0.6309	INHERITED FROM: pore forming toxin response variant
Glucocorticoid receptor-like (DNA-binding domain)	0.6983	INHERITED FROM: SDS sensitive dauer
Homeodomain-like	0.8081	INHERITED FROM: egg laying imipramine resistant || imipramine resistant || adrenergic receptor antagonist response variant || inhibitor of serotonin uptake variant
DBL homology domain (DH-domain)	0.8339	INHERITED FROM: aldicarb response variant
Nucleic acid-binding proteins	0.8566	INHERITED FROM: hydroxyurea hypersensitive || hydroxyurea response variant
HLH, helix-loop-helix DNA-binding domain	0.9049	INHERITED FROM: lysine chemotaxis defective || aqueous positive chemotaxis defective
Nuclear receptor ligand-binding domain	1	INHERITED FROM: SDS sensitive dauer
Ankyrin repeat	1	INHERITED FROM: chemotaxis variant || octanol chemotaxis variant || octanol chemotaxis defective || odorant negative chemotaxis defective
Family A G protein-coupled receptor-like	1	INHERITED FROM: locomotion rate serotonin variant || serotonin induced fat reduction variant || male tail curling serotonin variant || serotonin induced pumping variant
beta-beta-alpha zinc fingers	1	INHERITED FROM: egg laying imipramine resistant || imipramine resistant || inhibitor of serotonin uptake variant

Family domains annotated to this WP term (SDWP level: Moderately Informative)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
Transducin (heterotrimeric G protein), gamma chain	0	DIRECT
Quinoprotein alcohol dehydrogenase-like	0	DIRECT
SCF ubiquitin ligase complex WHB domain	0	DIRECT
Cullin repeat	0	DIRECT
Aromatic aminoacid monoxygenases, catalytic and oligomerization domains	0	DIRECT
Neurotransmitter-gated ion-channel transmembrane pore	0.000000000007123	DIRECT
Nicotinic receptor ligand binding domain-like	0.000000000007123	DIRECT
Skp1 dimerisation domain-like	0.0000000001108	DIRECT
Protein kinases, catalytic subunit	0.0000002225	DIRECT
Cullin homology domain	0.000002233	DIRECT
cAMP-binding domain	0.00001692	DIRECT
Transducin (alpha subunit), insertion domain	0.0003371	DIRECT
DNA replication initiator (cdc21/cdc54) N-terminal domain	0.0005541	DIRECT
Eps15 homology domain (EH domain)	0.0007548	DIRECT
BTB/POZ domain	0.001715	INHERITED FROM: chemical hypersensitive
Transforming growth factor (TGF)-beta	0.003158	INHERITED FROM: nicotine response variant || drug response variant || levamisole response variant
PLC-like (P variant)	0.004607	INHERITED FROM: positive chemotaxis variant || aldicarb resistant || aldicarb response variant
Synaptotagmin-like (S variant)	0.006387	INHERITED FROM: drug resistant || drug response variant || acetylcholinesterase inhibitor resistant || acetylcholinesterase inhibitor response variant
G proteins	0.01033	INHERITED FROM: chemotaxis variant || chemosensory behavior variant || chemosensory response variant || aldicarb response variant
L-arabinose binding protein-like	0.01278	INHERITED FROM: anion positive chemotaxis defective || magnesium chemotaxis defective || iodide chemotaxis variant || bromide chemotaxis variant || chemotaxis variant || cation positive chemotaxis variant || alkaline pH chemotaxis variant || cation positive chemotaxis defective || chemosensory behavior variant || chemosensory response variant || anion positive chemotaxis variant || bromide chemotaxis defective || lithium chemotaxis defective || iodide chemotaxis defective || aqueous positive chemotaxis variant
I set domains	0.01302	INHERITED FROM: aldicarb resistant || aldicarb response variant
Clathrin coat assembly domain	0.01605	INHERITED FROM: drug resistant || acetylcholinesterase inhibitor resistant || aldicarb resistant || aldicarb response variant || acetylcholinesterase inhibitor response variant
Phosphoribosyltransferases (PRTases)	0.01605	INHERITED FROM: drug resistant || Fluorouracil resistant
Multidrug efflux transporter AcrB transmembrane domain	0.02276	INHERITED FROM: odorant positive chemotaxis defective || odorant chemosensory response variant || positive chemotaxis defective
Spectrin repeat	0.0311	INHERITED FROM: drug response variant || aldicarb resistant || aldicarb response variant
Lipovitellin-phosvitin complex; beta-sheet shell regions	0.0311	INHERITED FROM: unfolded protein response variant
Lipovitellin-phosvitin complex, superhelical domain	0.0311	INHERITED FROM: unfolded protein response variant
Pleckstrin-homology domain (PH domain)	0.0377	INHERITED FROM: egg laying imipramine resistant || diacetyl chemotaxis variant || egg laying serotonin variant || AWA odorant chemotaxis variant || aldicarb response variant
Phosphate binding protein-like	0.03905	INHERITED FROM: response to food variant || chemotaxis variant || chemosensory behavior variant || chemosensory response variant || positive chemotaxis defective || aqueous positive chemotaxis defective || sodium chloride chemotaxis variant || sodium chloride chemotaxis defective || aqueous positive chemotaxis variant
Calcium ATPase, transduction domain A	0.03932	INHERITED FROM: nicotine hypersensitive || drug hypersensitive
Metal cation-transporting ATPase, ATP-binding domain N	0.03932	INHERITED FROM: nicotine hypersensitive || drug hypersensitive
PDZ domain	0.03932	INHERITED FROM: egg laying serotonin variant || drug response variant || aldicarb response variant
Tryptophan synthase beta subunit-like PLP-dependent enzymes	0.04116	INHERITED FROM: drug hypersensitive
Regulator of G-protein signaling, RGS	0.0662	INHERITED FROM: negative chemotaxis variant || chemotaxis variant
Adenylyl and guanylyl cyclase catalytic domain	0.07647	INHERITED FROM: anion positive chemotaxis defective || magnesium chemotaxis defective || iodide chemotaxis variant || bromide chemotaxis variant || chemotaxis variant || aqueous chemosensory response variant || cation positive chemotaxis variant || alkaline pH chemotaxis variant || diacetyl chemotaxis variant || cation positive chemotaxis defective || positive chemotaxis variant || AWC odorant chemotaxis defective || AWC odorant chemotaxis variant || chemosensory behavior variant || chemosensory response variant || osmotic avoidance variant || bromide chemotaxis defective || lithium chemotaxis defective || iodide chemotaxis defective
Meta-cation ATPase, catalytic domain P	0.09926	INHERITED FROM: nicotine hypersensitive
t-snare proteins	0.1078	INHERITED FROM: drug hypersensitive
Group II chaperonin (CCT, TRIC), intermediate domain	0.1078	INHERITED FROM: unfolded protein response variant
SH3-domain	0.1245	INHERITED FROM: aldicarb response variant
Protein kinase cysteine-rich domain (cys2, phorbol-binding domain)	0.1296	INHERITED FROM: drug resistant || odorant positive chemotaxis variant || aldicarb response variant
WD40-repeat	0.1634	INHERITED FROM: ivermectin resistant || ivermectin response variant || osmotic avoidance variant
SNF-like	0.1799	INHERITED FROM: drug hypersensitive
Pyridoxal-dependent decarboxylase	0.1799	INHERITED FROM: egg laying response to drug variant
Voltage-gated potassium channels	0.2009	INHERITED FROM: adrenergic receptor antagonist response variant || serotonin resistant || serotonin response variant
Calcium ATPase, transmembrane domain M	0.2318	INHERITED FROM: nicotine hypersensitive || drug response variant
Tubulin, GTPase domain	0.2713	INHERITED FROM: nicotine response variant
FYVE, a phosphatidylinositol-3-phosphate binding domain	0.2859	INHERITED FROM: aldicarb resistant
Group II chaperonin (CCT, TRIC), ATPase domain	0.339	INHERITED FROM: unfolded protein response variant
Group II chaperonin (CCT, TRIC), apical domain	0.339	INHERITED FROM: unfolded protein response variant
Bromodomain	0.339	INHERITED FROM: anesthetic response variant || ethanol resistant || acute functional tolerance to alcohol defective || anesthetic resistant || drug adaptation variant
Tubulin, C-terminal domain	0.4017	INHERITED FROM: nicotine response variant
Leucine zipper domain	0.6477	INHERITED FROM: pore forming toxin response variant
Rhodopsin-like	0.7108	INHERITED FROM: egg laying response to drug variant || locomotion rate serotonin variant || serotonin hypersensitive || serotonin induced fat reduction variant || male tail curling serotonin variant || serotonin induced pumping variant || aqueous adaptation defective || biogenic amine receptor antagonist resistant || serotonin resistant || drug withdrawal response variant || serotonin response variant
ABC transporter transmembrane region	0.7465	INHERITED FROM: colchicine hypersensitive
DBL homology domain (DH-domain)	0.8488	INHERITED FROM: aldicarb response variant
ABC transporter ATPase domain-like	0.8659	INHERITED FROM: colchicine hypersensitive
HLH, helix-loop-helix DNA-binding domain	0.9153	INHERITED FROM: lysine chemotaxis defective || aqueous positive chemotaxis defective
Nuclear receptor ligand-binding domain	1	INHERITED FROM: SDS sensitive dauer
Ankyrin repeat	1	INHERITED FROM: octanol chemotaxis variant || octanol chemotaxis defective || odorant negative chemotaxis defective
Nuclear receptor	1	INHERITED FROM: SDS sensitive dauer

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.

Supra-domains annotated to this WP term (SPWP level: Moderately Informative)
Highlighted in gray are those with FDR>0.001

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Aromatic aminoacid monoxygenases, catalytic and oligomerization domains	0	DIRECT
Transducin (heterotrimeric G protein), gamma chain	0	DIRECT
Skp1 dimerisation domain-like	0.0000000000007435	DIRECT
Nicotinic receptor ligand binding domain-like	0.0000000000009712	DIRECT
Neurotransmitter-gated ion-channel transmembrane pore	0.000000000001889	DIRECT
Cullin repeat-like	0.000000007914	DIRECT
Cullin homology domain	0.0000006109	DIRECT
Protein kinase-like (PK-like)	0.0000007801	DIRECT
cAMP-binding domain-like	0.00000853	DIRECT
C2 domain (Calcium/lipid-binding domain, CaLB)	0.00001139	DIRECT
Transducin (alpha subunit), insertion domain	0.0002193	DIRECT
Periplasmic binding protein-like I	0.002076	INHERITED FROM: AWC odorant chemotaxis variant || benzaldehyde chemotaxis variant || lithium chemotaxis defective || bromide chemotaxis defective || iodide chemotaxis defective || AWC odorant chemotaxis defective || chemotaxis variant || aqueous chemosensory response variant || magnesium chemotaxis defective || iodide chemotaxis variant || chemosensory behavior variant || aqueous positive chemotaxis variant || bromide chemotaxis variant || diacetyl chemotaxis variant || alkaline pH chemotaxis variant || chemosensory response variant
Myosin rod fragments	0.003255	INHERITED FROM: drug resistant
Quinoprotein alcohol dehydrogenase-like	0.006707	INHERITED FROM: drug response variant
Voltage-gated potassium channels	0.01583	INHERITED FROM: adrenergic receptor antagonist response variant || serotonin response variant || positive chemotaxis defective || serotonin resistant
Multidrug efflux transporter AcrB transmembrane domain	0.01892	INHERITED FROM: odorant chemosensory response variant || odorant positive chemotaxis defective || positive chemotaxis defective
EF-hand	0.01958	INHERITED FROM: aldicarb response variant
Tryptophan synthase beta subunit-like PLP-dependent enzymes	0.01997	INHERITED FROM: drug hypersensitive
Immunoglobulin	0.02207	INHERITED FROM: aldicarb response variant
PRTase-like	0.0236	INHERITED FROM: drug resistant || Fluorouracil resistant
Spectrin repeat	0.02756	INHERITED FROM: aldicarb resistant || drug response variant || aldicarb response variant
Lipovitellin-phosvitin complex; beta-sheet shell regions	0.02756	INHERITED FROM: unfolded protein response variant
Lipovitellin-phosvitin complex, superhelical domain	0.02756	INHERITED FROM: unfolded protein response variant
ENTH/VHS domain	0.02758	INHERITED FROM: aldicarb resistant || acetylcholinesterase inhibitor resistant
TPR-like	0.02767	INHERITED FROM: ivermectin resistant || ivermectin response variant || positive chemotaxis defective
Calcium ATPase, transduction domain A	0.03253	INHERITED FROM: nicotine hypersensitive
Metal cation-transporting ATPase, ATP-binding domain N	0.03253	INHERITED FROM: nicotine hypersensitive
Calcium ATPase, transmembrane domain M	0.03253	INHERITED FROM: nicotine hypersensitive
Periplasmic binding protein-like II	0.0334	INHERITED FROM: sodium chloride chemotaxis variant || chemotaxis variant || aqueous positive chemotaxis defective || positive chemotaxis defective || chemosensory behavior variant || aqueous positive chemotaxis variant || response to food variant || sodium chloride chemotaxis defective || chemosensory response variant
PDZ domain-like	0.03739	INHERITED FROM: acetylcholinesterase inhibitor response variant || drug resistant || aldicarb response variant
WD40 repeat-like	0.04039	INHERITED FROM: aldicarb response variant || osmotic avoidance variant
Troponin coil-coiled subunits	0.05273	INHERITED FROM: nicotine response variant || drug response variant
Glutathione synthetase ATP-binding domain-like	0.05338	INHERITED FROM: chemotaxis variant || negative chemotaxis variant || chemosensory behavior variant || osmotic avoidance variant || chemosensory response variant
SMAD/FHA domain	0.05338	INHERITED FROM: aldicarb response variant
Regulator of G-protein signaling, RGS	0.05786	INHERITED FROM: chemotaxis variant || negative chemotaxis variant || chemosensory behavior variant || chemosensory response variant
SAM/Pointed domain	0.05786	INHERITED FROM: aldicarb response variant
Nucleotide cyclase	0.05809	INHERITED FROM: cation positive chemotaxis defective || AWC odorant chemotaxis variant || lithium chemotaxis defective || bromide chemotaxis defective || positive chemotaxis variant || iodide chemotaxis defective || AWC odorant chemotaxis defective || chemotaxis variant || aqueous chemosensory response variant || magnesium chemotaxis defective || iodide chemotaxis variant || cation positive chemotaxis variant || anion positive chemotaxis defective || chemosensory behavior variant || anion positive chemotaxis variant || bromide chemotaxis variant || diacetyl chemotaxis variant || osmotic avoidance variant || alkaline pH chemotaxis variant || chemosensory response variant
Cysteine-rich domain	0.06076	INHERITED FROM: odorant chemosensory response variant || positive chemotaxis variant || odorant positive chemotaxis variant || acetylcholinesterase inhibitor response variant || aldicarb response variant
EGF/Laminin	0.07653	INHERITED FROM: octanol chemotaxis defective || odorant negative chemotaxis defective || octanol chemotaxis variant
SH3-domain	0.1001	INHERITED FROM: aldicarb response variant
t-snare proteins	0.1003	INHERITED FROM: drug hypersensitive
SNARE-like	0.1041	INHERITED FROM: aldicarb resistant || acetylcholinesterase inhibitor resistant
SNF-like	0.165	INHERITED FROM: drug hypersensitive
PH domain-like	0.197	INHERITED FROM: aldicarb response variant || diacetyl chemotaxis variant
P-loop containing nucleoside triphosphate hydrolases	0.2052	INHERITED FROM: hydroxyurea response variant
Cystine-knot cytokines	0.2058	INHERITED FROM: nicotine response variant || levamisole response variant
WW domain	0.2105	INHERITED FROM: aldicarb resistant
GroEL apical domain-like	0.2105	INHERITED FROM: unfolded protein response variant
GroEL equatorial domain-like	0.2105	INHERITED FROM: unfolded protein response variant
GroEL-intermediate domain like	0.2105	INHERITED FROM: unfolded protein response variant
Tubulin nucleotide-binding domain-like	0.244	INHERITED FROM: nicotine response variant
HAD-like	0.2488	INHERITED FROM: nicotine hypersensitive
POZ domain	0.2525	INHERITED FROM: chemical hypersensitive
Bromodomain	0.3142	INHERITED FROM: ethanol resistant || anesthetic resistant || anesthetic response variant || acute functional tolerance to alcohol defective || drug adaptation variant
Tubulin C-terminal domain-like	0.3681	INHERITED FROM: nicotine response variant
Sm-like ribonucleoproteins	0.4507	INHERITED FROM: unfolded protein response variant
"Winged helix" DNA-binding domain	0.4589	INHERITED FROM: chemical hypersensitive || anesthetic response variant
ABC transporter transmembrane region	0.6035	INHERITED FROM: colchicine hypersensitive
Leucine zipper domain	0.6092	INHERITED FROM: pore forming toxin response variant
Glucocorticoid receptor-like (DNA-binding domain)	0.6775	INHERITED FROM: SDS sensitive dauer
Homeodomain-like	0.7897	INHERITED FROM: adrenergic receptor antagonist response variant || inhibitor of serotonin uptake variant || egg laying imipramine resistant || imipramine resistant
DBL homology domain (DH-domain)	0.8163	INHERITED FROM: aldicarb response variant
Nucleic acid-binding proteins	0.8402	INHERITED FROM: hydroxyurea response variant || hydroxyurea hypersensitive
HLH, helix-loop-helix DNA-binding domain	0.8899	INHERITED FROM: lysine chemotaxis defective || aqueous positive chemotaxis defective
Family A G protein-coupled receptor-like	1	INHERITED FROM: serotonin induced pumping variant || serotonin induced fat reduction variant || male tail curling serotonin variant || locomotion rate serotonin variant
Nuclear receptor ligand-binding domain	1	INHERITED FROM: SDS sensitive dauer
Ankyrin repeat	1	INHERITED FROM: octanol chemotaxis defective || chemotaxis variant || odorant negative chemotaxis defective || octanol chemotaxis variant
beta-beta-alpha zinc fingers	1	INHERITED FROM: inhibitor of serotonin uptake variant || egg laying imipramine resistant || imipramine resistant || egg laying serotonin resistant

Supra-domains annotated to this WP term (SPWP 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)
74788,75632 74788 - Cullin repeat-like 75632 - Cullin homology domain	0	DIRECT
75632,46785 75632 - Cullin homology domain 46785 - "Winged helix" DNA-binding domain	0	DIRECT
63712,90112 63712 - Nicotinic receptor ligand binding domain-like 90112 - Neurotransmitter-gated ion-channel transmembrane pore	0.000000000001889	DIRECT
54695,81382 54695 - POZ domain 81382 - Skp1 dimerisation domain-like	0.00000000003856	DIRECT
56112,55073 56112 - Protein kinase-like (PK-like) 55073 - Nucleotide cyclase	0.0000001014	DIRECT
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0.0002193	DIRECT
48452,48452 48452 - TPR-like 48452 - TPR-like	0.000255	DIRECT
49265,48726 49265 - Fibronectin type III 48726 - Immunoglobulin	0.0003767	DIRECT
48726,49265 48726 - Immunoglobulin 49265 - Fibronectin type III	0.0005462	DIRECT
50044,50044 50044 - SH3-domain 50044 - SH3-domain	0.0007086	DIRECT
49562,49562 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 49562 - C2 domain (Calcium/lipid-binding domain, CaLB)	0.01997	INHERITED FROM: drug resistant
56968,48431 56968 - Lipovitellin-phosvitin complex; beta-sheet shell regions 48431 - Lipovitellin-phosvitin complex, superhelical domain	0.02756	INHERITED FROM: unfolded protein response variant
47473,47473 47473 - EF-hand 47473 - EF-hand	0.02756	INHERITED FROM: drug response variant || acetylcholinesterase inhibitor response variant || aldicarb response variant
48431,56968 48431 - Lipovitellin-phosvitin complex, superhelical domain 56968 - Lipovitellin-phosvitin complex; beta-sheet shell regions	0.02756	INHERITED FROM: unfolded protein response variant
81660,56784 81660 - Metal cation-transporting ATPase, ATP-binding domain N 56784 - HAD-like	0.03253	INHERITED FROM: nicotine hypersensitive
46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat	0.05273	INHERITED FROM: drug response variant
50978,50978 50978 - WD40 repeat-like 50978 - WD40 repeat-like	0.05273	INHERITED FROM: odorant chemosensory response variant || positive chemotaxis variant || ivermectin resistant || ivermectin response variant || chemotaxis variant || aqueous positive chemotaxis defective || aqueous chemosensory response variant || positive chemotaxis defective || negative chemotaxis variant || chemosensory behavior variant || drug resistant || aqueous positive chemotaxis variant || osmotic avoidance variant || chemosensory response variant
56784,81665 56784 - HAD-like 81665 - Calcium ATPase, transmembrane domain M	0.05338	INHERITED FROM: nicotine hypersensitive
57889,57889 57889 - Cysteine-rich domain 57889 - Cysteine-rich domain	0.165	INHERITED FROM: drug response variant || drug resistant || aldicarb response variant
48592,54849 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like	0.2105	INHERITED FROM: unfolded protein response variant
54849,52029 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0.2105	INHERITED FROM: unfolded protein response variant
52490,55307 52490 - Tubulin nucleotide-binding domain-like 55307 - Tubulin C-terminal domain-like	0.244	INHERITED FROM: nicotine response variant
90123,52540 90123 - ABC transporter transmembrane region 52540 - P-loop containing nucleoside triphosphate hydrolases	0.6035	INHERITED FROM: colchicine hypersensitive
48065,50729 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like	0.7359	INHERITED FROM: aldicarb response variant
57716,48508 57716 - Glucocorticoid receptor-like (DNA-binding domain) 48508 - Nuclear receptor ligand-binding domain	0.9377	INHERITED FROM: chemical hypersensitive || SDS sensitive dauer

Supra-domains annotated to this WP term (SPWP 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)
74788,75632,46785 74788 - Cullin repeat-like 75632 - Cullin homology domain 46785 - "Winged helix" DNA-binding domain	0	DIRECT
52540,52540,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0.0003767	DIRECT
56968,48431,56968 56968 - Lipovitellin-phosvitin complex; beta-sheet shell regions 48431 - Lipovitellin-phosvitin complex, superhelical domain 56968 - Lipovitellin-phosvitin complex; beta-sheet shell regions	0.02756	INHERITED FROM: unfolded protein response variant
81660,56784,81665 81660 - Metal cation-transporting ATPase, ATP-binding domain N 56784 - HAD-like 81665 - Calcium ATPase, transmembrane domain M	0.05338	INHERITED FROM: nicotine hypersensitive
46966,46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat 46966 - Spectrin repeat	0.1003	INHERITED FROM: drug response variant || drug resistant
48592,54849,52029 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0.2105	INHERITED FROM: unfolded protein response variant

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.