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 - Glycogen Storage Disease Type I

Debug Stats

### Total Build Time: 47 ms 37.835 KB
CONCEPT_NAME gt=3 ms Completed: 3 ms rowSize= 360 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 535 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=1 ms Completed: 1 ms rowSize= 188 bytes
Skipping details on: CONCEPT_NAMESPACE gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_PARENTS gt=2 ms Completed: 2 ms rowSize= 560 bytes
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=2 ms Completed: 2 ms rowSize= 2.847 KB
CONCEPT_RELATIONSHIPS gt=27 ms Completed: 27 ms rowSize= 13.221 KB
CONCEPT_GENES gt=9 ms Completed: 9 ms rowSize= 18.963 KB
CONCEPT_XREFS gt=3 ms Completed: 3 ms rowSize= 1.165 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Glycogen Storage Disease Type I C0017920

Definition (1)

autosomal recessive disease in which gene expression of glucose-6-phosphatase is absent, resulting in hypoglycemia due to lack of glucose production; accumulation of glycogen in liver and kidney leads to organomegaly, particularly massive hepatomegaly; increased concentrations of lactic acid and hyperlipidemia appear in the plasma; clinical gout often appears in early childhood.

Semantic Types (1)

Disease or Syndrome (T047)

Parents (1)

C0017919

Ancestral Roots

Root	Root Plus One	Depth	Parent
Congenital, Hereditary, and Neonatal Diseases and Abnormalities C0027612	Genetic Diseases, Inborn C0950123	6	Glycogen Storage Disease C0017919
Nutritional and Metabolic Diseases C0028715	Metabolic Diseases C0025517	6	Glycogen Storage Disease C0017919

Relationships (57)

Relation Types:

diso_to_anat : 5

diso_to_chem : 7

diso_to_diso : 41

diso_to_phen : 2

diso_to_phys : 2

Relationships:

none : 21

associated_with : 3

entry_version_of : 1

isa : 1

manifestation_of : 29

mapped_to : 2

Page Size

Current 25

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250

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Prior Page

Current 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_DISO	65		Complication Aspects C1171258
DISO_to_DISO	55		Complication Aspects C1171258
DISO_to_PHEN	48		genetic aspects C0017399
DISO_to_PHEN	35		genetic aspects C0017399
DISO_to_ANAT	22		In Blood C0005768
DISO_to_CHEM	19		GLUCOSE-6-PHOSPHATASE C0017755
DISO_to_DISO	15		Liver Neoplasms C0023903
DISO_to_ANAT	13		In Blood C0005768
DISO_to_CHEM	13		GLUCOSE-6-PHOSPHATASE C0017755
DISO_to_PHYS	11		Mutation C0026882
DISO_to_DISO	10		Adenoma, Liver Cell C0206669
DISO_to_ANAT	9		Liver C0023884
DISO_to_DISO	9		Neutropenia C0027947
DISO_to_ANAT	8		Neutrophils C0027950
DISO_to_CHEM	7		Antiporters C0052088
DISO_to_CHEM	7		Monosaccharide Transport Proteins C0026491
DISO_to_PHYS	7		Mutation C0026882
DISO_to_ANAT	6		Neutrophils C0027950
DISO_to_CHEM	6		GENET VECTORS C0017397
DISO_to_DISO	6		Glycogen Storage Disease Type III C0017922
DISO_to_DISO	6		Hypoglycemia C0020615
DISO_to_CHEM		associated_with	GLUCOSE-6-PHOSPHATASE C0017755
DISO_to_CHEM		associated_with	Glycogen C0017911
DISO_to_DISO		manifestation_of	'Doll-like' facies C1856361
DISO_to_DISO		associated_with	270 CONGENITAL DEFICIENCIES C0333006

Genes (13)

Species:

human : 13

Species	Gene	GeneId	Gene Name	Evidence
Human	G6PC2	57818	glucose-6-phosphatase, catalytic, 2	GENERIF, Score=1000, Pubmed Id: 17607665, UMLKSK CUI: C0017920 missense mutation in exon 4, L173P, found in glycogen storage disease type Ia
Human	UGT1A1	54658	UDP glucuronosyltransferase 1 family, polypeptide A1	GENERIF, Score=1000, Pubmed Id: 18043502, UMLKSK CUI: C0017920 High frequency of UGT1A1 promoter polymorphism, coupled with G-6-PD deficiency, may contribute to the pathogenesis of extreme neonatal hyperbilirubinemia in Nigeria GENERIF, Score=734, Pubmed Id: 12972027, UMLKSK CUI: C0017920 4% of males in the Kuwaiti population have G6PD deficiency coexisting with low activity of the UDPGT1 promoter GAD, Score=1000, Pubmed Id: 11987245, UMLKSK CUI: C0017920 Title:Genotyping by"cold single-strand conformation polymorphism" of the UGT1A1 promoter polymorphism in Mexican mestizos.\|Association:Not Found\|Conclusion:Genotyping by SSCP of the (TA) n polymorphism is an adequate methodological option.
Human	VWF	7450	von Willebrand factor	GENERIF, Score=1000, Pubmed Id: 16435187, UMLKSK CUI: C0017920 analysis of von Willebrand factor antigen (VWF:Ag) in patients with glycogen storage disease type Ia
Human	TNF	7124	tumor necrosis factor	GAD, Score=1000, Pubmed Id: 15718915, UMLKSK CUI: C0017920 Title:Dominance of high-producing interleukin 6 and low-producing interleukin 10 and interferon gamma alleles in glucose-6-phosphate dehydrogenase-deficient trauma patients.\|Association:Not Found\|Conclusion:These investigations indicate a predominant presence of high-producing IL-6 alleles together with low-producing IL-10 and IFN-gamma alleles in individuals with ancestry from malaria-endemic regions. The frequency of low-producing IL-10 genotypes is greater in the G6PD-deficient compared with nondeficient patients. The fact that these genetic differences are preserved in the current African American G6PD-deficient population indicates their potential role in pathophysiological processes in the absence of the selective pressure caused by tropical diseases.
Human	TGFB1	7040	transforming growth factor, beta 1	GAD, Score=1000, Pubmed Id: 15718915, UMLKSK CUI: C0017920 Title:Dominance of high-producing interleukin 6 and low-producing interleukin 10 and interferon gamma alleles in glucose-6-phosphate dehydrogenase-deficient trauma patients.\|Association:Not Found\|Conclusion:These investigations indicate a predominant presence of high-producing IL-6 alleles together with low-producing IL-10 and IFN-gamma alleles in individuals with ancestry from malaria-endemic regions. The frequency of low-producing IL-10 genotypes is greater in the G6PD-deficient compared with nondeficient patients. The fact that these genetic differences are preserved in the current African American G6PD-deficient population indicates their potential role in pathophysiological processes in the absence of the selective pressure caused by tropical diseases.
Human	IL10	3586	interleukin 10	GAD, Score=1000, Pubmed Id: 15718915, UMLKSK CUI: C0017920 Title:Dominance of high-producing interleukin 6 and low-producing interleukin 10 and interferon gamma alleles in glucose-6-phosphate dehydrogenase-deficient trauma patients.\|Association:Not Found\|Conclusion:These investigations indicate a predominant presence of high-producing IL-6 alleles together with low-producing IL-10 and IFN-gamma alleles in individuals with ancestry from malaria-endemic regions. The frequency of low-producing IL-10 genotypes is greater in the G6PD-deficient compared with nondeficient patients. The fact that these genetic differences are preserved in the current African American G6PD-deficient population indicates their potential role in pathophysiological processes in the absence of the selective pressure caused by tropical diseases.
Human	IL8	3576	interleukin 8	GENERIF, Score=1000, Pubmed Id: 18191274, UMLKSK CUI: C0017920 Peripheral neutrophilia and increased serum chemokines (IL-8 and MIP-2) may indicate hepatic injuries in glycogen storage disease type Ia
Human	IL6	3569	interleukin 6 (interferon, beta 2)	GAD, Score=1000, Pubmed Id: 15718915, UMLKSK CUI: C0017920 Title:Dominance of high-producing interleukin 6 and low-producing interleukin 10 and interferon gamma alleles in glucose-6-phosphate dehydrogenase-deficient trauma patients.\|Association:Not Found\|Conclusion:These investigations indicate a predominant presence of high-producing IL-6 alleles together with low-producing IL-10 and IFN-gamma alleles in individuals with ancestry from malaria-endemic regions. The frequency of low-producing IL-10 genotypes is greater in the G6PD-deficient compared with nondeficient patients. The fact that these genetic differences are preserved in the current African American G6PD-deficient population indicates their potential role in pathophysiological processes in the absence of the selective pressure caused by tropical diseases.
Human	IFNG	3458	interferon, gamma	GAD, Score=1000, Pubmed Id: 15718915, UMLKSK CUI: C0017920 Title:Dominance of high-producing interleukin 6 and low-producing interleukin 10 and interferon gamma alleles in glucose-6-phosphate dehydrogenase-deficient trauma patients.\|Association:Not Found\|Conclusion:These investigations indicate a predominant presence of high-producing IL-6 alleles together with low-producing IL-10 and IFN-gamma alleles in individuals with ancestry from malaria-endemic regions. The frequency of low-producing IL-10 genotypes is greater in the G6PD-deficient compared with nondeficient patients. The fact that these genetic differences are preserved in the current African American G6PD-deficient population indicates their potential role in pathophysiological processes in the absence of the selective pressure caused by tropical diseases.
Human	SLC37A4	2542	solute carrier family 37 (glucose-6-phosphate transporter), member 4	GENERIF, Score=1000, Pubmed Id: 16435186, UMLKSK CUI: C0017920 mutational analysis of G6PT1 in type I glycogen storage disease
Human	G6PD	2539	glucose-6-phosphate dehydrogenase	Click here to display 28 evidence detail records.
Human	G6PC	2538	glucose-6-phosphatase, catalytic subunit	GENERIF, Score=723, Pubmed Id: 12373566, UMLKSK CUI: C0017920 homozygosity for one G6PC mutation, G188R, seems to be associated with a glycogen storage disease type I non-a phenotype and homozygosity for the 727G>T mutation may be associated with a milder phenotype but an increased risk for hepatocellular carcinoma GENERIF, Score=1000, Pubmed Id: 18008183, UMLKSK CUI: C0017920 analysis of mutation spectrum of glycogen storage disease type Ia in Tunisia
Human	SCARB1	949	scavenger receptor class B, member 1	GENERIF, Score=780, Pubmed Id: 16777453, UMLKSK CUI: C0017920 The results suggest that the increase in SR-BI -mediated cellular cholesterol efflux and antioxidant capacity in the sera of glycogen storage disease type Ia patients may contribute to protection against premature atherosclerosis

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0017920	Glycogen Storage Disease Type I	0		self

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