Mammalian Phenotype (MP): abnormal leukopoiesis

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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).

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Root: MP Hierarchy (mammalian/mouse phenotype from MGI_4.41)

Shortest distance to current term (+ for parents, - for children) MP term [MP ID] <#Children> (#SF|#FA) #Supra-domain
(Single|Duplex|Triple)

+ + + + + 5: hematopoietic system phenotype [MP:0005397] <2> (72|102) (78|63|30)

+ + + + 4: abnormal hematopoietic system morphology/development [MP:0002396] <5> (58|86) (66|47|21)

+ + + + 4: mammalian phenotype [MP:0000001] <29>

+ + + + 4: abnormal hematopoietic cell morphology [MP:0013656] <9> (49|77) (60|43|18)

+ + + 3: immune system phenotype [MP:0005387] <2> (76|114) (86|66|35)

+ + + 3: abnormal blood cell morphology/development [MP:0002429] <3> (26|35) (28|24|9)

+ + + 3: abnormal blood cell morphology [MP:0013657] <4> (31|49) (37|35|14)

+ + 2: abnormal hemopoiesis [MP:0013693] <2> (25|34) (27|24|9)

+ + 2: abnormal immune system morphology [MP:0000685] <3> (51|76) (60|35|18)

+ 1: abnormal immune system cell morphology [MP:0000716] <5> (38|63) (48|29|16)

+ 1: abnormal definitive hematopoiesis [MP:0002123] <4> (24|34) (26|24|9)

0: abnormal leukopoiesis [MP:0005460] <3> (19|28) (21|18|8)

- 1: abnormal myelopoiesis [MP:0001601] <8> (0|0) (0|0|0)

- 1: abnormal lymphopoiesis [MP:0002401] <3> (19|25) (21|15|6)

- 1: abnormal mononuclear cell differentiation [MP:0002445] <2> (0|0) (0|0|0)

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Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
SPOC domain-like	0	Direct
PsbU/PolX domain-like	0	Direct
SH2 domain	0.0000000000484	Direct
p53-like transcription factors	0.0000009882	Direct
DNA polymerase beta, N-terminal domain-like	0.0001484	Direct
Bcl-2 inhibitors of programmed cell death	0.000637	Direct
E2F-DP heterodimerization region	0.00156	Inherited
BRCT domain	0.005125	Inherited
STAT	0.01046	Inherited
Transcription factor STAT-4 N-domain	0.01046	Inherited
SMAD/FHA domain	0.01425	Inherited
DNA/RNA polymerases	0.01829	Inherited
Nucleotidyltransferase	0.03199	Inherited
Cysteine-rich domain	0.03629	Inherited
SH3-domain	0.08704	Inherited
TNF receptor-like	0.08724	Inherited
SET domain	0.1295	Inherited
DBL homology domain (DH-domain)	0.5313	Inherited
Calponin-homology domain, CH-domain	0.7746	Inherited

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
DNA polymerase beta-like	0	Direct
DNA polymerase beta-like, second domain	0	Direct
SH2 domain	0.00000000003752	Direct
Rel/Dorsal transcription factors, DNA-binding domain	0.0000001044	Direct
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0.0000006529	Direct
PLC-like (P variant)	0.00008721	Direct
DNA polymerase beta, N-terminal domain-like	0.00009282	Direct
E2F dimerization segment	0.0004013	Direct
Bcl-2 inhibitors of programmed cell death	0.0004241	Direct
ets domain	0.00175	Inherited
Cell cycle transcription factor e2f-dp	0.004023	Inherited
DNA polymerase I	0.005692	Inherited
STAT DNA-binding domain	0.007417	Inherited
Transcription factor STAT-4 N-domain	0.007417	Inherited
STAT	0.007417	Inherited
Interferon regulatory factor 3 (IRF3), transactivation domain	0.01047	Inherited
Pointed domain	0.0321	Inherited
Higher-molecular-weight phosphotyrosine protein phosphatases	0.03527	Inherited
Pleckstrin-homology domain (PH domain)	0.03932	Inherited
DEATH domain, DD	0.04342	Inherited
Myb/SANT domain	0.04992	Inherited
MATH domain	0.06571	Inherited
SH3-domain	0.07535	Inherited
FHA domain	0.09504	Inherited
TNF receptor-like	0.11	Inherited
Protein kinase cysteine-rich domain (cys2, phorbol-binding domain)	0.1638	Inherited
DBL homology domain (DH-domain)	0.5042	Inherited
Calponin-homology domain, CH-domain	0.7527	Inherited

Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term

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Supra-domain (including individual superfamily)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
SPOC domain-like	0	Direct
PsbU/PolX domain-like	0	Direct
SH2 domain	0.00000000001762	Direct
p53-like transcription factors	0.0000004025	Direct
DNA polymerase beta, N-terminal domain-like	0.00007406	Direct
Bcl-2 inhibitors of programmed cell death	0.0003399	Direct
E2F-DP heterodimerization region	0.0008748	Direct
BRCT domain	0.003073	Inherited
STAT	0.00655	Inherited
Transcription factor STAT-4 N-domain	0.00655	Inherited
SMAD/FHA domain	0.009136	Inherited
DNA/RNA polymerases	0.01192	Inherited
Nucleotidyltransferase	0.02186	Inherited
Cysteine-rich domain	0.02498	Inherited
beta-beta-alpha zinc fingers	0.05509	Inherited
SH3-domain	0.06481	Inherited
TNF receptor-like	0.06497	Inherited
SET domain	0.1007	Inherited
Acyl-CoA N-acyltransferases (Nat)	0.2831	Inherited
DBL homology domain (DH-domain)	0.4842	Inherited
Calponin-homology domain, CH-domain	0.7379	Inherited

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
47802,81585 47802 - DNA polymerase beta, N-terminal domain-like 81585 - PsbU/PolX domain-like	0	Direct
81585,81301 81585 - PsbU/PolX domain-like 81301 - Nucleotidyltransferase	0	Direct
55550,55550 55550 - SH2 domain 55550 - SH2 domain	0	Direct
47576,48065 47576 - Calponin-homology domain, CH-domain 48065 - DBL homology domain (DH-domain)	0	Direct
49417,81296 49417 - p53-like transcription factors 81296 - E set domains	0.00000006534	Direct
50729,56112 50729 - PH domain-like 56112 - Protein kinase-like (PK-like)	0.000005402	Direct
50729,55550 50729 - PH domain-like 55550 - SH2 domain	0.000008179	Direct
55550,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.0004733	Direct
49562,57889 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 57889 - Cysteine-rich domain	0.0006021	Direct
46785,144074 46785 - "Winged helix" DNA-binding domain 144074 - E2F-DP heterodimerization region	0.0008748	Direct
50044,55550 50044 - SH3-domain 55550 - SH2 domain	0.002843	Inherited
48092,47655 48092 - Transcription factor STAT-4 N-domain 47655 - STAT	0.00655	Inherited
49417,55550 49417 - p53-like transcription factors 55550 - SH2 domain	0.00655	Inherited
47655,49417 47655 - STAT 49417 - p53-like transcription factors	0.00655	Inherited
55550,50044 55550 - SH2 domain 50044 - SH3-domain	0.01395	Inherited
57850,49599 57850 - RING/U-box 49599 - TRAF domain-like	0.01454	Inherited
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	0.02267	Inherited
48065,50729 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like	0.4842	Inherited

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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
47802,81585,81301 47802 - DNA polymerase beta, N-terminal domain-like 81585 - PsbU/PolX domain-like 81301 - Nucleotidyltransferase	0	Direct
55550,56112,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) 56112 - Protein kinase-like (PK-like)	0	Direct
50729,55550,56112 50729 - PH domain-like 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0	Direct
47576,48065,50729 47576 - Calponin-homology domain, CH-domain 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like	0	Direct
49562,57889,57889 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 57889 - Cysteine-rich domain 57889 - Cysteine-rich domain	0.0006021	Direct
48092,47655,49417 48092 - Transcription factor STAT-4 N-domain 47655 - STAT 49417 - p53-like transcription factors	0.00655	Inherited
47655,49417,55550 47655 - STAT 49417 - p53-like transcription factors 55550 - SH2 domain	0.00655	Inherited

Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term

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Mammalian Phenotype (MP): abnormal leukopoiesis

Superfamily

Family

Supra-domain (including individual superfamily)