GATACA

Credits

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Data

Data - ToppGene Sources

The vast majority of all data in Gataca is from ToppGene so its credits cover data sources that are used within Gataca. The primary reason for utilizing the same sources between these applications is to help ensure consistancy between them. ToppGene, and Gataca, uses data from over 20 sources.

For ToppGene Credits, please visit:

ToppGene Links (Credits)

Data - GUDMAP

GUDMAP

The GUDMAP data within Gataca is only availble within the GUDMAP interface:

Gataca's GUDMAP

Data - UMLSKS

UMLSKS website

Software

Software - Solr

Solr website

Software - PrototypeJS

Prototype JS website

Prototype JavaScript framework, version 1.7
(c) 2005-2010 Sam Stephenson
 
Prototype is freely distributable under the terms of an MIT-style license.
For details, see the Prototype web site: http://www.prototypejs.org/

Software - script.aculo.us

Script.aculo.us website

NOTE: Only the effects.js and dragdrop.js modules from Script.aculo.us are being used.

// script.aculo.us scriptaculous.js v1.9.0, Thu Dec 23 16:54:48 -0500 2010

// Copyright (c) 2005-2010 Thomas Fuchs (http://script.aculo.us, http://mir.aculo.us)
//
// Permission is hereby granted, free of charge, to any person obtaining
// a copy of this software and associated documentation files (the
// "Software"), to deal in the Software without restriction, including
// without limitation the rights to use, copy, modify, merge, publish,
// distribute, sublicense, and/or sell copies of the Software, and to
// permit persons to whom the Software is furnished to do so, subject to
// the following conditions:
//
// The above copyright notice and this permission notice shall be
// included in all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
// EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
// NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
// LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
// OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
// WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
//
// For details, see the script.aculo.us web site: http://script.aculo.us/

Software - canvasXpress

canvasXpress website

CanvasXpress is a javascript library based on the <canvas> tag implemented in HTML5.

This package is currently being used for the Venn Diagram within SetBuilder. Plans are to utilize it in other areas in the generation of other graphs.

Software - Oracle Enterprise Edition

Oracle website

The data within Gataca is being stored in an Oracle 11g database.

Software - Modernizr

modernizr

modernizr provides simple interfacing to check to see what features are available within the client's browser. This is predomantly used to test for HTML 5 features such as canvas or local storage support.

Software - JQTouch

JQTouch website

JQTouch is being used for the mobile edition of Gataca.

Software - jQuery

JQuery website

jQuery is used within JQTouch only.

Software - tablesort

tablesort website

Copyright (c) 2006 Andrew Tetlaw 
http://tetlaw.id.au/view/blog/table-sorting-with-prototype/

Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation
files (the "Software"), to deal in the Software without
restriction, including without limitation the rights to use, copy,
modify, merge, publish, distribute, sublicense, and/or sell copies
of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.

Software - Firebug Light

Firebug Light website

firebugx.js - There is no disclaimer in the original file, but it is an open source project. The main website is http://www.getfirebug.com It is an open source project hosted by Google code.

Link-It Detail - Disease - Wiskott-Aldrich Syndrome

Debug Stats

### Total Build Time: 34 ms 41.423 KB
CONCEPT_NAME gt=3 ms Completed: 3 ms rowSize= 346 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 388 bytes
Skipping details on: CONCEPT_SYNONYM gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
Skipping details on: CONCEPT_TEXT gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_SEMANTIC_TYPE gt=0 Completed: 0 ms rowSize= 188 bytes
Skipping details on: CONCEPT_NAMESPACE gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_PARENTS gt=3 ms Completed: 3 ms rowSize= 2.283 KB
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=2 ms Completed: 2 ms rowSize= 9.330 KB
CONCEPT_RELATIONSHIPS gt=20 ms Completed: 20 ms rowSize= 14.401 KB
CONCEPT_GENES gt=6 ms Completed: 6 ms rowSize= 13.314 KB
CONCEPT_XREFS gt=0 Completed: 0 ms rowSize= 1.158 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Wiskott-Aldrich Syndrome C0043194

Definition (1)

rare x-linked immunodeficiency syndrome of young boys characterized by eczema, thrombocytopenic purpura and recurrent pyogenic infection; IGM levels are low and IGA and IGE levels are elevated; lymphoreticular malignancies are common.

Semantic Types (1)

Disease or Syndrome (T047)

Parents (5)

C0019087

C1138434

C0852077

C0021051

C0024312

Ancestral Roots

Root	Root Plus One	Depth	Parent
Hemic and Lymphatic Diseases C0018981	Hematologic Diseases C0018939	4	Hemorrhagic Disorders C0019087
Congenital, Hereditary, and Neonatal Diseases and Abnormalities C0027612	Genetic Diseases, Inborn C0950123	4	Genetic Diseases, X-Linked C1138434
Hemic and Lymphatic Diseases C0018981	Hematologic Diseases C0018939	5	Blood Coagulation Disorders, Inherited C0852077
Congenital, Hereditary, and Neonatal Diseases and Abnormalities C0027612	Genetic Diseases, Inborn C0950123	4	Blood Coagulation Disorders, Inherited C0852077
Immune System Diseases C0021053	Immunologic Deficiency Syndromes C0021051	3	Immunologic Deficiency Syndromes C0021051
Immune System Diseases C0021053	Immunologic Deficiency Syndromes C0021051	4	Lymphopenia C0024312
Hemic and Lymphatic Diseases C0018981	Hematologic Diseases C0018939	6	Lymphopenia C0024312

Relationships (56)

Relation Types:

diso_to_anat : 3

diso_to_chem : 4

diso_to_diso : 43

diso_to_gene : 2

diso_to_phen : 2

diso_to_phys : 2

Relationships:

none : 15

alias_of : 1

classifies : 1

gene_associated_with_disease : 2

inheritance_type_of : 1

is_finding_of_disease : 1

manifestation_of : 33

mapped_to : 1

may_be_associated_disease_of_disease : 1

Page Size

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Current 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_PHEN	63		genetic aspects C0017399
DISO_to_PHEN	61		genetic aspects C0017399
DISO_to_CHEM	57		Proteins C0033684
DISO_to_CHEM	46		Wiskott-Aldrich Syndrome Protein C0258432
DISO_to_DISO	27		Complication Aspects C1171258
DISO_to_DISO	20		Complication Aspects C1171258
DISO_to_PHYS	19		Mutation C0026882
DISO_to_CHEM	12		Wiskott-Aldrich Syndrome Protein C0258432
DISO_to_DISO	11		Thrombocytopenia C0040034
DISO_to_ANAT	10		In Blood C0005768
DISO_to_ANAT	9		T-Lymphocyte C0039194
DISO_to_DISO	9		Thrombocytopenia C0040034
DISO_to_ANAT	7		In Blood C0005768
DISO_to_CHEM	7		Carrier Protein C0007292
DISO_to_PHYS	7		Mutation C0026882
DISO_to_DISO		manifestation_of	ANAEMIA HAEMOLYTIC C0002878
DISO_to_DISO		manifestation_of	Abnormal delayed hypersensitivity skin test C1833172
DISO_to_DISO		manifestation_of	Abnormal or prolonged bleeding time C0151529
DISO_to_DISO		manifestation_of	Absent microvilli on the surface of peripheral blood lymphocytes C1833173
DISO_to_DISO		manifestation_of	Anemia, Iron-Deficiency C0162316
DISO_to_DISO		manifestation_of	BLOOD SEDIMENTATION INCREASED C0151632
DISO_to_DISO		manifestation_of	Bleeding from mouth C0029163
DISO_to_DISO		manifestation_of	Blood in vomit - symptom C0018926
DISO_to_DISO		classifies	C-50 DISEASES OF THE IMMUNE SYSTEM: GENERAL TERMS C0021053
DISO_to_DISO		manifestation_of	CD43 (sialophorin) defectively expressed on surface of blood cells C1833183

Genes (5)

Species:

human : 5

Species	Gene	GeneId	Gene Name	Evidence
Human	TBX21	30009	T-box 21	GENERIF, Score=673, Pubmed Id: 17082665, UMLKSK CUI: C0043194 A defect in Wiskott Aldrich CD4+ T cells is due to reduction in T-bet mRNA expression and in early nuclear recruitment of NFAT-1
Human	WASF1	8936	WAS protein family, member 1	GENERIF, Score=901, Pubmed Id: 18995840, UMLKSK CUI: C0043194 Dimerization act in hierarchical fashion, enabling WASP/WAVE proteins to integrate different classes of inputs to produce a wide range of cellular actin responses in Wiskoo Aldrich syndrome
Human	WAS	7454	Wiskott-Aldrich syndrome	GENERIF, Score=1000, Pubmed Id: 16002738, UMLKSK CUI: C0043194 Knowledge of the molecular effect of WAS protein mutations provides a logical basis for correlating genotype and clinical phenotype of Wiskott-Aldrich syndrome GENERIF, Score=1000, Pubmed Id: 11793485, UMLKSK CUI: C0043194 mutational analysis in patients with Wiskott-Aldrich syndrome in Argentina GENERIF, Score=1000, Pubmed Id: 12073025, UMLKSK CUI: C0043194 An Alu-mediated deletion at Xp11.23 leading to Wiskott-Aldrich syndrome GENERIF, Score=1000, Pubmed Id: 17400488, UMLKSK CUI: C0043194 study found 28 novel WAS mutations in Wiskott-Aldrich syndrome and X-linked thrombocytopenia (7 missense, 1 nonsense, 1 nonstop change, 5 splice site mutations and 14 deletions or insertions) OMIM, Score=1000, UMLKSK CUI: C0043194 Allelic with Wiskott-Aldrich syndrome ({301000}) and severe congenital X-linked neutropenia ({300299}) GENERIF, Score=1000, Pubmed Id: 12351383, UMLKSK CUI: C0043194 mutated in Wiskott Aldrich syndrome GENERIF, Score=717, Pubmed Id: 17703096, UMLKSK CUI: C0043194 Chinese Wiskott-Aldrich Syndrome (WAS) patients had mutations involving exon 1 of the Wiskott-Aldrich syndrome protein (WASP) gene and none had the X-linked thrombocytopenia phenotype OMIM, Score=1000, UMLKSK CUI: C0043194 Allelic with Wiskott-Aldrich syndrome ({301000}) and X-linked thrombocytopenia ({313900}) GENERIF, Score=694, Pubmed Id: 15728466, UMLKSK CUI: C0043194 The Wiskott-Aldrich WASP protein is an important component for integration of signals leading to nuclear translocation of transcription factors NFAT2 and NF-kappa B RelA during cell-cell contact and natural cytotoxicity receptor NKp46-dependent signaling GENERIF, Score=1000, Pubmed Id: 12969986, UMLKSK CUI: C0043194 WAS protein expression is a useful tool for predicting long-term prognosis for patients with Wiskott-Aldrich syndrome GENERIF, Score=1000, Pubmed Id: 17390083, UMLKSK CUI: C0043194 Two novel mutations of the WASP gene in two Spanish families with patients clinically diagnosed as havingX-linked thrombocytopenia and Wiskott-Aldrich syndrome, were identified GENERIF, Score=1000, Pubmed Id: 12727931, UMLKSK CUI: C0043194 Results describe somatic mosaicism in two brothers affected with Wiskott-Aldrich syndrome (WAS) due to a second-site mutation in the WAS protein (WASP) gene
Human	NFATC2	4773	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	GENERIF, Score=673, Pubmed Id: 17082665, UMLKSK CUI: C0043194 In Wiskott-Aldrich CD8+ T cells, a block in cytokine production correlates with reduced nuclear levels of both NFAT-1 and NFAT-2
Human	IL2	3558	interleukin 2	GENERIF, Score=756, Pubmed Id: 15001467, UMLKSK CUI: C0043194 Treatment with interleukin-2 (IL-2) corrected the functional defects of NK cells by affecting their ability to bind to sensitive target cells and to accumulate F-actin in Wiskott-Aldrich syndrome cells

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0043194	Wiskott-Aldrich Syndrome	0		self

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