•  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’s 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 (SPHP) 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:SPHP.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 MP term (Not in SDMP)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
Nitric oxide (NO) synthase oxygenase domain	0	DIRECT
SPOC domain-like	0	DIRECT
Flavoproteins	0.002444	INHERITED FROM: increased osteoclast cell number || increased leukocyte cell number
Apolipoprotein A-I	0.008757	INHERITED FROM: increased macrophage derived foam cell number || increased macrophage cell number
L30e-like	0.008757	INHERITED FROM: increased T cell number || increased lymphocyte cell number
E2F-DP heterodimerization region	0.01822	INHERITED FROM: decreased double-positive T cell number
Bcl-2 inhibitors of programmed cell death	0.0215	INHERITED FROM: decreased mature B cell number
Nuclear receptor coactivator interlocking domain	0.02531	INHERITED FROM: increased T cell number
p53-like transcription factors	0.05035	INHERITED FROM: increased leukocyte cell number
Toll/Interleukin receptor TIR domain	0.1017	INHERITED FROM: increased mature B cell number
MHC antigen-recognition domain	0.124	INHERITED FROM: abnormal T cell number || abnormal lymphocyte cell number || absent CD8-positive T cells
TNF receptor-like	0.1388	INHERITED FROM: increased CD4-positive T cell number
C2 domain (Calcium/lipid-binding domain, CaLB)	0.1799	INHERITED FROM: abnormal CD8-positive T cell number
Ferredoxin reductase-like, C-terminal NADP-linked domain	0.2001	INHERITED FROM: increased osteoclast cell number || increased macrophage cell number
Riboflavin synthase domain-like	0.2001	INHERITED FROM: increased osteoclast cell number || increased macrophage cell number
ARID-like	0.3247	INHERITED FROM: increased neutrophil cell number
SMAD/FHA domain	0.3989	INHERITED FROM: decreased plasmacytoid dendritic cell number || abnormal plasmacytoid dendritic cell number
Integrin domains	0.4892	INHERITED FROM: decreased T cell number || decreased CD4-positive T cell number

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

SCOP term	FDR (all)	Annotation (direct or inherited)
Interferons/interleukin-10 (IL-10)	0	DIRECT
RUNT domain	0	DIRECT
Nitric oxide (NO) synthase oxygenase domain	0	DIRECT
Interleukin 17F, IL-17F	0	DIRECT
BAFF receptor-like	0	DIRECT
C1 set domains (antibody constant domain-like)	8.839e-08	DIRECT
Phoshoinositide 3-kinase (PI3K), catalytic domain	0.0001125	DIRECT
Pointed domain	0.001756	INHERITED FROM: decreased leukocyte cell number || decreased lymphocyte cell number || abnormal lymphocyte cell number || decreased thymocyte number
Phoshoinositide 3-kinase (PI3K) helical domain	0.006104	INHERITED FROM: abnormal CD8-positive T cell number || abnormal T cell number || increased granulocyte number || increased neutrophil cell number || abnormal CD4-positive T cell number
E2F dimerization segment	0.006104	INHERITED FROM: abnormal T cell number || decreased double-positive T cell number
Tissue inhibitor of metalloproteinases, TIMP	0.006458	INHERITED FROM: increased granulocyte number || increased neutrophil cell number
Apolipoprotein A-I	0.006458	INHERITED FROM: increased macrophage derived foam cell number || increased macrophage cell number
Cytochrome p450 reductase N-terminal domain-like	0.006458	INHERITED FROM: increased osteoclast cell number || increased macrophage cell number
Interferon regulatory factor	0.009735	INHERITED FROM: decreased plasmacytoid dendritic cell number || abnormal plasmacytoid dendritic cell number || decreased mature B cell number || increased immature B cell number || increased lymphocyte cell number
Bcl-2 inhibitors of programmed cell death	0.01728	INHERITED FROM: decreased mature B cell number
NADPH-cytochrome p450 reductase FAD-binding domain-like	0.01995	INHERITED FROM: increased osteoclast cell number || increased macrophage cell number
NADPH-cytochrome p450 reductase-like	0.01995	INHERITED FROM: increased osteoclast cell number || increased macrophage cell number
Nuclear receptor coactivator interlocking domain	0.01995	INHERITED FROM: increased T cell number
PHD domain	0.03289	INHERITED FROM: decreased pre-B cell number
Cell cycle transcription factor e2f-dp	0.04352	INHERITED FROM: decreased double-positive T cell number
Interferon regulatory factor 3 (IRF3), transactivation domain	0.0685	INHERITED FROM: decreased plasmacytoid dendritic cell number || abnormal plasmacytoid dendritic cell number || decreased mature B cell number || increased B cell number || increased immature B cell number || absent B cells || absent lymphocyte
Toll/Interleukin receptor TIR domain	0.1051	INHERITED FROM: increased mature B cell number
MHC antigen-recognition domain	0.1051	INHERITED FROM: abnormal T cell number || abnormal lymphocyte cell number || absent CD8-positive T cells
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0.1297	INHERITED FROM: abnormal B cell number || decreased osteoclast cell number || increased leukocyte cell number || decreased T cell number
Rel/Dorsal transcription factors, DNA-binding domain	0.1594	INHERITED FROM: abnormal B cell number || decreased osteoclast cell number || increased leukocyte cell number || decreased T cell number
Short-chain cytokines	0.1594	INHERITED FROM: abnormal lymphocyte cell number
DEATH domain, DD	0.1982	INHERITED FROM: increased transitional stage B cell number
TNF receptor-like	0.1982	INHERITED FROM: increased CD4-positive T cell number || increased leukocyte cell number
ARID domain	0.2948	INHERITED FROM: increased neutrophil cell number
Integrin alpha N-terminal domain	0.4294	INHERITED FROM: decreased T cell number
Integrin A (or I) domain	0.4294	INHERITED FROM: abnormal eosinophil cell number
Interleukin-1 (IL-1)	0.444	INHERITED FROM: increased granulocyte number || increased neutrophil cell number
Pleckstrin-homology domain (PH domain)	0.4455	INHERITED FROM: decreased transitional stage B cell number
Integrin domains	0.463	INHERITED FROM: decreased T cell number || decreased CD4-positive T cell number
PLC-like (P variant)	0.463	INHERITED FROM: decreased B-2 B cell number
V set domains (antibody variable domain-like)	0.5195	INHERITED FROM: decreased CD4-positive T cell number
Higher-molecular-weight phosphotyrosine protein phosphatases	0.6408	INHERITED FROM: increased mature B cell number
Myb/SANT domain	0.7329	INHERITED FROM: decreased immature B cell number
C-type lectin domain	0.7909	INHERITED FROM: increased B-1 B cell number

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 MP term (Not in SPMP)
Highlighted in gray are those with FDR>0.001

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Nitric oxide (NO) synthase oxygenase domain	0	DIRECT
SPOC domain-like	0	DIRECT
Flavoproteins	0.001484	INHERITED FROM: increased osteoclast cell number || increased leukocyte cell number
L30e-like	0.005713	INHERITED FROM: abnormal T cell number || increased T cell number || increased lymphocyte cell number
Apolipoprotein A-I	0.005713	INHERITED FROM: increased macrophage derived foam cell number || increased macrophage cell number
E2F-DP heterodimerization region	0.01245	INHERITED FROM: decreased double-positive T cell number
Bcl-2 inhibitors of programmed cell death	0.01494	INHERITED FROM: decreased mature B cell number
Nuclear receptor coactivator interlocking domain	0.01779	INHERITED FROM: increased T cell number
p53-like transcription factors	0.03736	INHERITED FROM: increased leukocyte cell number
Toll/Interleukin receptor TIR domain	0.07995	INHERITED FROM: increased mature B cell number
MHC antigen-recognition domain	0.09932	INHERITED FROM: abnormal T cell number || abnormal lymphocyte cell number || absent CD8-positive T cells
TNF receptor-like	0.1124	INHERITED FROM: increased CD4-positive T cell number
RNI-like	0.123	INHERITED FROM: increased lymphocyte cell number
SET domain	0.1328	INHERITED FROM: decreased B cell number
C2 domain (Calcium/lipid-binding domain, CaLB)	0.1498	INHERITED FROM: abnormal CD8-positive T cell number
Ferredoxin reductase-like, C-terminal NADP-linked domain	0.1682	INHERITED FROM: increased osteoclast cell number || increased macrophage cell number
Riboflavin synthase domain-like	0.1682	INHERITED FROM: increased osteoclast cell number || increased macrophage cell number
ARID-like	0.2847	INHERITED FROM: increased neutrophil cell number
SMAD/FHA domain	0.3567	INHERITED FROM: decreased plasmacytoid dendritic cell number || abnormal plasmacytoid dendritic cell number
(Phosphotyrosine protein) phosphatases II	0.3941	INHERITED FROM: increased mature B cell number
Integrin alpha N-terminal domain	0.415	INHERITED FROM: decreased T cell number
Integrin domains	0.4459	INHERITED FROM: decreased T cell number || decreased CD4-positive T cell number

Supra-domains annotated to this MP term (Not in SPMP)
Highlighted in gray are those with FDR>0.001

Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
55550,55550 55550 - SH2 domain 55550 - SH2 domain	0	DIRECT
54452,48726 54452 - MHC antigen-recognition domain 48726 - Immunoglobulin	1.895e-05	DIRECT
47986,47986 47986 - DEATH domain 47986 - DEATH domain	0.001425	INHERITED FROM: abnormal lymphocyte cell number || abnormal CD4-positive T cell number || increased leukocyte cell number || increased lymphocyte cell number
49562,48371 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 48371 - ARM repeat	0.005298	INHERITED FROM: abnormal CD8-positive T cell number || abnormal T cell number || increased granulocyte number || increased neutrophil cell number || abnormal CD4-positive T cell number
46785,144074 46785 - "Winged helix" DNA-binding domain 144074 - E2F-DP heterodimerization region	0.01245	INHERITED FROM: decreased double-positive T cell number
55550,50044 55550 - SH2 domain 50044 - SH3-domain	0.01245	INHERITED FROM: increased lymphocyte cell number
50729,50044 50729 - PH domain-like 50044 - SH3-domain	0.01245	INHERITED FROM: increased B cell number
50729,56112 50729 - PH domain-like 56112 - Protein kinase-like (PK-like)	0.01245	INHERITED FROM: increased double-negative T cell number || decreased double-positive T cell number || decreased T cell number
48371,56112 48371 - ARM repeat 56112 - Protein kinase-like (PK-like)	0.01245	INHERITED FROM: abnormal CD8-positive T cell number || increased granulocyte number || increased neutrophil cell number || abnormal CD4-positive T cell number
49417,81296 49417 - p53-like transcription factors 81296 - E set domains	0.152	INHERITED FROM: abnormal B cell number || decreased osteoclast cell number || increased leukocyte cell number || decreased T cell number
55550,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.2017	INHERITED FROM: decreased leukocyte cell number
57586,57586 57586 - TNF receptor-like 57586 - TNF receptor-like	0.261	INHERITED FROM: increased CD4-positive T cell number || increased leukocyte cell number || decreased B cell number
50729,50729 50729 - PH domain-like 50729 - PH domain-like	0.2847	INHERITED FROM: increased macrophage cell number
50729,55550 50729 - PH domain-like 55550 - SH2 domain	0.3507	INHERITED FROM: decreased lymphocyte cell number || increased neutrophil cell number || abnormal B cell number || increased leukocyte cell number || increased lymphocyte cell number || decreased B cell number
69318,69179 69318 - Integrin alpha N-terminal domain 69179 - Integrin domains	0.415	INHERITED FROM: decreased T cell number
69179,69179 69179 - Integrin domains 69179 - Integrin domains	0.415	INHERITED FROM: decreased T cell number
48371,48371 48371 - ARM repeat 48371 - ARM repeat	0.432	INHERITED FROM: decreased double-positive T cell number
53300,69318 53300 - vWA-like 69318 - Integrin alpha N-terminal domain	0.432	INHERITED FROM: increased CD8-positive T cell number || increased single-positive T cell number || decreased CD4-positive T cell number
57535,57535 57535 - Complement control module/SCR domain 57535 - Complement control module/SCR domain	0.4802	INHERITED FROM: increased eosinophil cell number

Supra-domains annotated to this MP term (Not in SPMP)
Highlighted in gray are those with FDR>0.001

Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
50729,50044,55550 50729 - PH domain-like 50044 - SH3-domain 55550 - SH2 domain	0	DIRECT
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.00353	INHERITED FROM: decreased leukocyte cell number
49562,48371,56112 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 48371 - ARM repeat 56112 - Protein kinase-like (PK-like)	0.005298	INHERITED FROM: abnormal CD8-positive T cell number || abnormal T cell number || increased granulocyte number || increased neutrophil cell number || abnormal CD4-positive T cell number
50044,55550,56112 50044 - SH3-domain 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.1885	INHERITED FROM: decreased leukocyte cell number || decreased single-positive T cell number
69318,69179,69179 69318 - Integrin alpha N-terminal domain 69179 - Integrin domains 69179 - Integrin domains	0.415	INHERITED FROM: decreased T cell number
55550,56112,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) 56112 - Protein kinase-like (PK-like)	0.432	INHERITED FROM: abnormal B cell number || increased lymphocyte cell number || decreased B cell number
50729,55550,56112 50729 - PH domain-like 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.432	INHERITED FROM: abnormal B cell number || increased lymphocyte cell number || decreased B cell number
53300,69318,69179 53300 - vWA-like 69318 - Integrin alpha N-terminal domain 69179 - Integrin domains	0.432	INHERITED FROM: increased CD8-positive T cell number || increased single-positive T cell number || decreased CD4-positive T cell number

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.