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Phenotype Ontology
Like Gene Ontology (GO), phenotypy ontology classifies and organizes gene-mutant/null phenotypic information from the very general at the top to more specific terms in the directed acyclic graph (DAG) by viewing an individual term as a node and its relations to parental terms (allowing for multiple parents) as directed edges. To navigate this hierarchy, we display all parental phenotypic terms to the current phenotypic term of interest ordered by their shortest distances to the current term. Also, only direct children phenotypic terms of the current phenotypic term are listed. Phenotype ontologies we have incorporated are as follows:

• Disease Ontology (DO) Ontology (DO)
  DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI thesaurus, SNOMED and OMIM.
  
• Human Phenotype (HP) Ontology (HP)
  HP captures phenotypic abnormalities that are described in OMIM, along with the corresponding disease-causing genes. It includes three complementary biological concepts: Mode_of_Inheritance (MI), ONset_and_clinical_course (ON), and Phenotypic_Abnormality (PA).
  
• Mouse Phenotype (MP) Ontology (MP)
  MP describes phenotypes of the mouse after a specific gene is genetically disrupted. Using it, Mouse Genome Informatics (MGI) provides high-coverate gene-level phenotypes for the mouse.
  
• Worm Phenotype (WP) Ontology (WP)
  WP classifies and organizes phenotype descriptions for C. elegans and other nematodes. Using it, WormBase provides primary resource for phenotype annotations for C. elegans.
  
• Yeast Phenotype (YP) Ontology (YP)
  Based on YP which is the major contributor to the Ascomycete phenotype ontology, Saccharomyces Genome Database (SGD) provides single mutant phenotypes for every gene in the yeast genome.
  
• Fly Phenotype (FP) Ontology (FP)
  FP refers to FlyBase controlled vocabulary. Specifically, a structured controlled vocabulary is used for the annotation of alleles (for their mutagen etc) in FlyBase.
  
• Fly Anatomy (FA) Ontology (FA)
  FA is a structured controlled vocabulary of the anatomy of Drosophila melanogaster, used for the description of phenotypes and where a gene is expressed.
  
• Zebrafish Anatomy (ZA) Ontology (ZA)
  ZA displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
  
• Xenopus Anatomy (XA) Ontology (XA)
  XA represents the lineage of tissues and the timing of development for frogs (Xenopus laevis and Xenopus tropicalis). It is used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes.
  
• Arabidopsis Plant Ontology (AP) Ontology (AP)
  As a major contributor to Plant Ontology which describes plant anatomical and morphological structures (AN) and growth and developmental stages (DE), the Arabidopsis Information Resource (TAIR) provides arabidopsis plant ontology annotations for the model higher plant Arabidopsis thaliana.
  
• Enzyme Commission (EC) Ontology (EC)
  Each enzyme is allocated a four-digit EC number, the first three digits of which define the reaction catalysed and the fourth of which is a unique identifier (serial number). Each enzyme is also assigned a systematic name that uniquely defines the reaction catalysed.
  
• DrugBank ATC (DB) Ontology (DB)
  In the Anatomical Therapeutic Chemical (ATC) classification system, drugs are classified in groups at five different levels according to the organ or system (1st level, anatomical main group) on which they act and their therapeutic (2nd level, therapeutic subgroup), pharmacological (3rd level, pharmacological subgroup) and chemical properties (4th level, chemical subgroup; 5th level, chemical substance). Only drugs in DrugBank are considered.
  
• UniProtKB KeyWords (KW) Ontology (KW)
  Keywords in UniProtKB are controlled vocabulary, providing a summary of the entry content and are used to index UniProtKB/Swiss-Prot entries based on 10 categories (the category "Technical term" being excluded here). Each keyword is attributed manually to UniProtKB/Swiss-Prot entries and automatically to UniProtKB/TrEMBL entries (according to specific annotation rules).
  
• UniProtKB UniPathway (UP) Ontology (UP)
  UP is a fully manually curated resource for the representation and annotation of metabolic pathways, being used as controlled vocabulary for pathway annotation in UniProtKB.
  

Structural Domain Phenotype Ontology and its Annotations
Structural Classification of Proteins (SCOP) classifies evolutionary-related domains into Superfamily level and Family level. Using the phenotype ontologies above, we have generated the domain-centric phenotype annotations, and further identified those phenotype terms which are the most informative to annotate SCOP domains. Promisingly, domain-centric phenotypic annotations can serve as an alternative starting point to explore genotype-phenotype relationships. We provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

• Structural Domain Disease Ontology (DO) Ontology (SDDO) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DO.txt, and the corresponding ontology:SDDO.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Human Phenotype (HP) Ontology (SDHP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2HP.txt, and the corresponding ontology:SDHP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Mouse Phenotype (MP) Ontology (SDMP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2MP.txt, and the corresponding ontology:SDMP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Worm Phenotype (WP) Ontology (SDWP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2WP.txt, and the corresponding ontology:SDWP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Yeast Phenotype (YP) Ontology (SDYP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2YP.txt, and the corresponding ontology:SDYP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Fly Phenotype (FP) Ontology (SDFP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FP.txt, and the corresponding ontology:SDFP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Fly Anatomy (FA) Ontology (SDFA) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FA.txt, and the corresponding ontology:SDFA.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Zebrafish Anatomy (ZA) Ontology (SDZA) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2ZA.txt, and the corresponding ontology:SDZA.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Xenopus Anatomy (XA) Ontology (SDXA) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2XA.txt, and the corresponding ontology:SDXA.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Arabidopsis Plant Ontology (AP) Ontology (SDAP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2AP.txt, and the corresponding ontology:SDAP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Enzyme Commission (EC) Ontology (SDEC) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2EC.txt, and the corresponding ontology:SDEC.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain DrugBank ATC (DB) Ontology (SDDB) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DB.txt, and the corresponding ontology:SDDB.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain UniProtKB KeyWords (KW) Ontology (SDKW) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2KW.txt, and the corresponding ontology:SDKW.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain UniProtKB UniPathway (UP) Ontology (SDUP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2UP.txt, and the corresponding ontology:SDUP.txt) and mysql tables (Domain2PO.sql.gz).
  

Supra-domain Phenotype Ontology and its Annotations
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are interested in domain combinations. Also, we provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

• Supra-domain Domain Disease Ontology (DO) Ontology (SPDO) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DO.txt, and the corresponding ontology:SPDO.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Human Phenotype (HP) Ontology (SPHO) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2HP.txt, and the corresponding ontology:SPHO.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Mouse Phenotype (MP) Ontology (SPMP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2MP.txt, and the corresponding ontology:SPMP.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Worm Phenotype (WP) Ontology (SPWP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2WP.txt, and the corresponding ontology:SPWP.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Yeast Phenotype (YP) Ontology (SPYP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2YP.txt, and the corresponding ontology:SPYP.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Fly Phenotype (FP) Ontology (SPFP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FP.txt, and the corresponding ontology:SPFP.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Fly Anatomy (FA) Ontology (SPFA) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FA.txt, and the corresponding ontology:SPFA.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Zebrafish Anatomy (ZA) Ontology (SPZA) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2ZA.txt, and the corresponding ontology:SPZA.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Xenopus Anatomy (XA) Ontology (SPXA) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2XA.txt, and the corresponding ontology:SPXA.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Arabidopsis Plant Ontology (AP) Ontology (SPAP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2AP.txt, and the corresponding ontology:SPAP.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Enzyme Commission (EC) Ontology (SPEC) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2EC.txt, and the corresponding ontology:SPEC.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain DrugBank ATC (DB) Ontology (SPDB) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DB.txt, and the corresponding ontology:SPDB.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain UniProtKB KeyWords (KW) Ontology (SPKW) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2KW.txt, and the corresponding ontology:SPKW.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain UniProtKB UniPathway (UP) Ontology (SPUP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2UP.txt, and the corresponding ontology:SPUP.txt) and mysql tables (SP2PO.sql.gz).
  

Superfamily domains annotated to this XA term (SDXA level: Moderately Informative)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
Alanine racemase C-terminal domain-like	0	DIRECT
GINS helical bundle-like	0	DIRECT
PLP-binding barrel	0	DIRECT
PriA/YqbF domain	0	DIRECT
SRF-like	0	DIRECT
Cysteine-rich DNA binding domain, (DM domain)	0	DIRECT
LysM domain	0	DIRECT
Homeodomain-like	0	DIRECT
14-3-3 protein	0	DIRECT
Guanido kinase N-terminal domain	0	DIRECT
Synuclein	0	DIRECT
Hedgehog/DD-peptidase	0	DIRECT
"Winged helix" DNA-binding domain	0.00000000000001853	DIRECT
HLH, helix-loop-helix DNA-binding domain	0.0000000000002456	DIRECT
RNA-binding domain, RBD	0.000000000003278	DIRECT
Cytokine	0.0000003357	DIRECT
Frizzled cysteine-rich domain	0.000001046	DIRECT
HMG-box	0.00004021	DIRECT
Cystine-knot cytokines	0.0001161	DIRECT
Glucocorticoid receptor-like (DNA-binding domain)	0.000188	DIRECT
Sema domain	0.000802	DIRECT
Snake toxin-like	0.002924	INHERITED FROM: involuted dorsal mesoderm || lateral plate mesoderm || ventral mesoderm
p53-like transcription factors	0.003643	INHERITED FROM: lung primordium || lung bud || neurogenic placode || lower blastopore lip || involuted ventral mesoderm || cranial placode || foregut
Orange domain-like	0.004149	INHERITED FROM: chordoneural hinge || presomitic mesoderm || neural tube || lateral plate mesoderm || paraxial mesoderm || cranial placode
GroEL-intermediate domain like	0.004149	INHERITED FROM: anterior dorsal lateral plate region
GroEL equatorial domain-like	0.004149	INHERITED FROM: anterior dorsal lateral plate region
GroEL apical domain-like	0.01323	INHERITED FROM: anterior dorsal lateral plate region
Plexin repeat	0.01399	INHERITED FROM: involuted dorsal mesoderm || presumptive midbrain-hindbrain boundary || otic placode || liver primordium || cranial placode
lambda repressor-like DNA-binding domains	0.02533	INHERITED FROM: neural tube || presumptive midbrain-hindbrain boundary || neurogenic placode || cranial placode
Transducin (alpha subunit), insertion domain	0.09708	INHERITED FROM: dorsal marginal zone
beta-beta-alpha zinc fingers	0.1202	INHERITED FROM: splanchnic layer of lateral plate mesoderm || presumptive rhombomere
TIMP-like	0.1283	INHERITED FROM: prechordal plate || stomodeal-hypophyseal primordium || foregut
Mannose 6-phosphate receptor domain	0.2048	INHERITED FROM: cement gland primordium
Alpha-macroglobulin receptor domain	0.2276	INHERITED FROM: hindgut || midgut || foregut
Globin-like	0.2608	INHERITED FROM: anterior dorsal lateral plate region || hematopoietic stem cell
EGF/Laminin	0.2757	INHERITED FROM: axial mesoderm
FnI-like domain	0.2788	INHERITED FROM: prechordal plate
Kazal-type serine protease inhibitors	0.2909	INHERITED FROM: axial mesoderm
Tropomyosin	0.3893	INHERITED FROM: cardiac mesoderm
DNA-binding domain	0.3912	INHERITED FROM: eye primordium
LDL receptor-like module	0.5617	INHERITED FROM: hindgut
Terpenoid cyclases/Protein prenyltransferases	0.5777	INHERITED FROM: hindgut || midgut

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

SCOP term	FDR (all)	Annotation (direct or inherited)
Guanido kinase catalytic domain	0	DIRECT
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain	0	DIRECT
Hedgehog (development protein), N-terminal signaling domain	0	DIRECT
Ran-binding domain	0	DIRECT
14-3-3 protein	0	DIRECT
Eukaryotic ODC-like	0	DIRECT
Extracellular domain of cell surface receptors	0	DIRECT
Pointed domain	0	DIRECT
Alanine racemase-like, N-terminal domain	0	DIRECT
LysM domain	0	DIRECT
Fibroblast growth factors (FGF)	0	DIRECT
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain	0	DIRECT
Synuclein	0	DIRECT
SRF-like	0	DIRECT
Guanido kinase N-terminal domain	0	DIRECT
Noggin	0	DIRECT
Homeodomain	0	DIRECT
Cysteine-rich DNA binding domain, (DM domain)	0	DIRECT
SH3BGR (SH3-binding, glutamic acid-rich protein-like)	0	DIRECT
Canonical RBD	0.0000000000009336	DIRECT
Forkhead DNA-binding domain	0.000000000001068	DIRECT
HLH, helix-loop-helix DNA-binding domain	0.000000000001192	DIRECT
ets domain	0.00000004918	DIRECT
Transforming growth factor (TGF)-beta	0.0000005824	DIRECT
Frizzled cysteine-rich domain	0.000001428	DIRECT
HMG-box	0.00006502	DIRECT
Sema domain	0.0003888	DIRECT
T-box	0.0004228	DIRECT
POU-specific domain	0.001041	INHERITED FROM: neural tube || presumptive midbrain-hindbrain boundary || neurogenic placode
LIM domain	0.003577	INHERITED FROM: cranial placode
Hairy Orange domain	0.004202	INHERITED FROM: chordoneural hinge || presomitic mesoderm || neural tube || lateral plate mesoderm || paraxial mesoderm || cranial placode
P4 origin-binding domain-like	0.0057	INHERITED FROM: neural tube || otic placode || neurogenic placode || optic vesicle || cranial placode
Group II chaperonin (CCT, TRIC), apical domain	0.01038	INHERITED FROM: anterior dorsal lateral plate region
Group II chaperonin (CCT, TRIC), intermediate domain	0.01543	INHERITED FROM: anterior dorsal lateral plate region
Plexin repeat	0.01673	INHERITED FROM: presumptive midbrain-hindbrain boundary || otic placode || liver primordium || cranial placode
Erythroid transcription factor GATA-1	0.02452	INHERITED FROM: primordium || lateral plate mesoderm || anterior dorsal lateral plate region || hematopoietic stem cell || cardiac mesoderm || cardiac progenitor cell || liver diverticulum
VWC domain	0.03109	INHERITED FROM: prechordal plate || neural tube
Eukaryotic type KH-domain (KH-domain type I)	0.03602	INHERITED FROM: upper blastopore lip
Glutathione peroxidase-like	0.05943	INHERITED FROM: presomitic mesoderm || eye primordium || paraxial mesoderm || presumptive paraxial mesoderm || foregut
Paired domain	0.06086	INHERITED FROM: primordium || anterior neural tube || neural tube || neurogenic placode || posterior neural tube || cranial placode
Tandem AAA-ATPase domain	0.07858	INHERITED FROM: marginal zone || blastopore lip || upper blastopore lip || vegetal yolk mass || blastopore
Transducin (alpha subunit), insertion domain	0.09902	INHERITED FROM: dorsal marginal zone
Classic zinc finger, C2H2	0.1137	INHERITED FROM: splanchnic layer of lateral plate mesoderm || presumptive rhombomere
Class I aldolase	0.1206	INHERITED FROM: primordium
Mannose 6-phosphate receptor domain	0.2044	INHERITED FROM: cement gland primordium
Alpha-macroglobulin receptor domain	0.2253	INHERITED FROM: hindgut || midgut || foregut
Arginine methyltransferase	0.2253	INHERITED FROM: optic vesicle
Tropomyosin	0.2426	INHERITED FROM: cardiac mesoderm
Globins	0.2623	INHERITED FROM: anterior dorsal lateral plate region || hematopoietic stem cell
Complement components	0.3372	INHERITED FROM: hindgut || midgut
LDL receptor-like module	0.5839	INHERITED FROM: hindgut
I set domains	0.7438	INHERITED FROM: optic vesicle

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 XA term (SPXA level: Moderately Informative)
Highlighted in gray are those with FDR>0.001

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
LysM domain	0	DIRECT
SRF-like	0	DIRECT
Cysteine-rich DNA binding domain, (DM domain)	0	DIRECT
Guanido kinase N-terminal domain	0	DIRECT
Synuclein	0	DIRECT
Homeodomain-like	0	DIRECT
Hedgehog/DD-peptidase	0	DIRECT
GINS helical bundle-like	0	DIRECT
14-3-3 protein	0	DIRECT
Alanine racemase C-terminal domain-like	0	DIRECT
PriA/YqbF domain	0	DIRECT
PLP-binding barrel	0	DIRECT
"Winged helix" DNA-binding domain	0.00000000000001282	DIRECT
HLH, helix-loop-helix DNA-binding domain	0.0000000000001702	DIRECT
RNA-binding domain, RBD	0.000000000002278	DIRECT
Cytokine	0.0000002372	DIRECT
Frizzled cysteine-rich domain	0.0000007429	DIRECT
HMG-box	0.00002936	DIRECT
Cystine-knot cytokines	0.00008573	DIRECT
Glucocorticoid receptor-like (DNA-binding domain)	0.0001397	DIRECT
Sema domain	0.0006069	DIRECT
Snake toxin-like	0.002251	INHERITED FROM: ventral mesoderm || lateral plate mesoderm || dorsal lateral plate mesoderm || involuted dorsal mesoderm
p53-like transcription factors	0.002803	INHERITED FROM: involuted ventral mesoderm || foregut || lower blastopore lip || cranial placode || lung bud || neurogenic placode || primordium || lung primordium
GroEL equatorial domain-like	0.003205	INHERITED FROM: anterior dorsal lateral plate region
Orange domain-like	0.003205	INHERITED FROM: presomitic mesoderm || cranial placode || chordoneural hinge || lateral plate mesoderm || neural tube || paraxial mesoderm
GroEL-intermediate domain like	0.003205	INHERITED FROM: anterior dorsal lateral plate region
GroEL apical domain-like	0.01041	INHERITED FROM: anterior dorsal lateral plate region
Plexin repeat	0.01102	INHERITED FROM: otic placode || cranial placode || liver primordium || involuted dorsal mesoderm || presumptive midbrain-hindbrain boundary
lambda repressor-like DNA-binding domains	0.02023	INHERITED FROM: cranial placode || neurogenic placode || neural tube || presumptive midbrain-hindbrain boundary
Transducin (alpha subunit), insertion domain	0.08206	INHERITED FROM: dorsal marginal zone
beta-beta-alpha zinc fingers	0.103	INHERITED FROM: presumptive rhombomere || splanchnic layer of lateral plate mesoderm
TIMP-like	0.1105	INHERITED FROM: foregut || stomodeal-hypophyseal primordium || prechordal plate
F-box domain	0.1423	INHERITED FROM: optic vesicle
Mannose 6-phosphate receptor domain	0.1809	INHERITED FROM: cement gland primordium
Alpha-macroglobulin receptor domain	0.2026	INHERITED FROM: hindgut || foregut || midgut
Globin-like	0.2338	INHERITED FROM: lateral plate mesoderm || hematopoietic stem cell || anterior dorsal lateral plate region
EGF/Laminin	0.2479	INHERITED FROM: axial mesoderm
FnI-like domain	0.2509	INHERITED FROM: neural tube || prechordal plate
Kazal-type serine protease inhibitors	0.2626	INHERITED FROM: axial mesoderm
Tropomyosin	0.3581	INHERITED FROM: cardiac mesoderm
DNA-binding domain	0.36	INHERITED FROM: eye primordium
LDL receptor-like module	0.5252	INHERITED FROM: hindgut
Terpenoid cyclases/Protein prenyltransferases	0.5417	INHERITED FROM: hindgut || midgut

Supra-domains annotated to this XA term (SPXA 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)
103647,103647 103647 - TSP type-3 repeat 103647 - TSP type-3 repeat	0	DIRECT
51419,50621 51419 - PLP-binding barrel 50621 - Alanine racemase C-terminal domain-like	0	DIRECT
52540,53254 52540 - P-loop containing nucleoside triphosphate hydrolases 53254 - Phosphoglycerate mutase-like	0	DIRECT
47095,47095 47095 - HMG-box 47095 - HMG-box	0	DIRECT
53223,51735 53223 - Aminoacid dehydrogenase-like, N-terminal domain 51735 - NAD(P)-binding Rossmann-fold domains	0	DIRECT
48034,55931 48034 - Guanido kinase N-terminal domain 55931 - Glutamine synthetase/guanido kinase	0	DIRECT
54534,54534 54534 - FKBP-like 54534 - FKBP-like	0	DIRECT
63501,50242 63501 - Frizzled cysteine-rich domain 50242 - TIMP-like	0	DIRECT
49899,48726 49899 - Concanavalin A-like lectins/glucanases 48726 - Immunoglobulin	0	DIRECT
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain)	0.0000002828	DIRECT
54928,54928 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD	0.00002837	DIRECT
101912,103575 101912 - Sema domain 103575 - Plexin repeat	0.0006069	DIRECT
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like	0.0006069	DIRECT
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like	0.003205	INHERITED FROM: presomitic mesoderm || cranial placode || chordoneural hinge || lateral plate mesoderm || neural tube || paraxial mesoderm
90209,90209 90209 - Ran binding protein zinc finger-like 90209 - Ran binding protein zinc finger-like	0.01293	INHERITED FROM: vegetal yolk mass || blastopore lip || blastopore || marginal zone || upper blastopore lip
57440,57440 57440 - Kringle-like 57440 - Kringle-like	0.02027	INHERITED FROM: neurogenic placode
103575,48726 103575 - Plexin repeat 48726 - Immunoglobulin	0.02027	INHERITED FROM: cranial placode
47413,46689 47413 - lambda repressor-like DNA-binding domains 46689 - Homeodomain-like	0.02338	INHERITED FROM: cranial placode || neurogenic placode || neural tube || presumptive midbrain-hindbrain boundary
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	0.06126	INHERITED FROM: lateral plate mesoderm || presumptive rhombomere || splanchnic layer of lateral plate mesoderm
55550,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.06563	INHERITED FROM: non-involuting marginal zone
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0.08206	INHERITED FROM: dorsal marginal zone
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.1031	INHERITED FROM: dorsal marginal zone
57850,49599 57850 - RING/U-box 49599 - TRAF domain-like	0.1055	INHERITED FROM: optic vesicle
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.1105	INHERITED FROM: circumblastoporal collar
52540,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0.1764	INHERITED FROM: vegetal yolk mass || blastopore lip || blastopore || upper blastopore lip
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0.4755	INHERITED FROM: presomitic mesoderm || dorsal marginal zone
50044,55550 50044 - SH3-domain 55550 - SH2 domain	0.5013	INHERITED FROM: non-involuting marginal zone

Supra-domains annotated to this XA term (SPXA 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)
49899,48726,49265 49899 - Concanavalin A-like lectins/glucanases 48726 - Immunoglobulin 49265 - Fibronectin type III	0	DIRECT
103647,103647,49899 103647 - TSP type-3 repeat 103647 - TSP type-3 repeat 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
103647,103647,103647 103647 - TSP type-3 repeat 103647 - TSP type-3 repeat 103647 - TSP type-3 repeat	0	DIRECT
47220,47220,47220 47220 - alpha-catenin/vinculin-like 47220 - alpha-catenin/vinculin-like 47220 - alpha-catenin/vinculin-like	0	DIRECT
57603,57603,57603 57603 - FnI-like domain 57603 - FnI-like domain 57603 - FnI-like domain	0.004611	INHERITED FROM: circumblastoporal collar || neural tube
50044,55550,56112 50044 - SH3-domain 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.01041	INHERITED FROM: non-involuting marginal zone
101912,103575,48726 101912 - Sema domain 103575 - Plexin repeat 48726 - Immunoglobulin	0.02027	INHERITED FROM: cranial placode
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin	0.03602	INHERITED FROM: non-neurogenic ectodermal placode
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.05082	INHERITED FROM: presomitic mesoderm || dorsal marginal zone
48371,48371,48371 48371 - ARM repeat 48371 - ARM repeat 48371 - ARM repeat	0.05137	INHERITED FROM: chordoneural hinge
48726,49265,49265 48726 - Immunoglobulin 49265 - Fibronectin type III 49265 - Fibronectin type III	0.1055	INHERITED FROM: optic vesicle
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0.1066	INHERITED FROM: presomitic mesoderm || dorsal marginal zone || paraxial mesoderm
57667,57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	0.9551	INHERITED FROM: splanchnic layer of lateral plate mesoderm

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.