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 V

Debug Stats

### Total Build Time: 29 ms 30.223 KB
CONCEPT_NAME gt=4 ms Completed: 4 ms rowSize= 360 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 268 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=14 ms Completed: 14 ms rowSize= 13.104 KB
CONCEPT_GENES gt=4 ms Completed: 4 ms rowSize= 11.729 KB
CONCEPT_XREFS gt=1 ms Completed: 1 ms rowSize= 1.165 KB
CONCEPT_ANCILLARY gt=1 ms Completed: 1 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Glycogen Storage Disease Type V C0017924

Definition (1)

Glycogenosis due to muscle phosphorylase deficiency. Characterized by painful cramps following sustained exercise.

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 (26)

Relation Types:

diso_to_anat : 1

diso_to_chem : 4

diso_to_diso : 17

diso_to_phen : 2

diso_to_phys : 2

Relationships:

none : 9

associated_with : 3

entry_version_of : 1

manifestation_of : 13

Page Size

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Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_PHEN	53		genetic aspects C0017399
DISO_to_CHEM	40		Glycogen Phosphorylase, Muscle Form C0917783
DISO_to_PHEN	21		genetic aspects C0017399
DISO_to_CHEM	15		Glycogen Phosphorylase, Muscle Form C0917783
DISO_to_ANAT	14		Muscle, Skeletal C0242692
DISO_to_PHYS	12		Missense Mutation C0599155
DISO_to_DISO	11		Complication Aspects C1171258
DISO_to_DISO	10		Complication Aspects C1171258
DISO_to_PHYS	10		Mutation C0026882
DISO_to_CHEM		associated_with	Glycogen C0017911
DISO_to_CHEM		associated_with	Glycogen Phosphorylase, Muscle Form C0917783
DISO_to_DISO		manifestation_of	'Second wind' phenomenon C1856299
DISO_to_DISO		associated_with	270 CONGENITAL DEFICIENCIES C0333006
DISO_to_DISO		manifestation_of	CPK INCREASED C0151576
DISO_to_DISO		manifestation_of	Caused by mutations in the muscle glycogen phosphorylase gene (PYGM, 608455.0001) C1968738
DISO_to_DISO		manifestation_of	Dark urine following exercise C1856292
DISO_to_DISO		manifestation_of	Decreased exercise capacity C0948372
DISO_to_DISO		entry_version_of	Glycogen Storage Disease Type V C0017924
DISO_to_DISO		manifestation_of	Increased ammonia with exercise C1856293
DISO_to_DISO		manifestation_of	Increased uric acid with exercise C1856294
DISO_to_DISO		manifestation_of	Muscle pain and cramps following exercise C1968737
DISO_to_DISO		manifestation_of	Myoglobinuria C0027080
DISO_to_DISO		manifestation_of	Painful cramping following ischemic exercise test C1856300
DISO_to_DISO		manifestation_of	RHABDOMYOLYSIS C0035410
DISO_to_DISO		manifestation_of	Skeletal muscle weakness C1856295

Genes (4)

Species:

human : 4

Species	Gene	GeneId	Gene Name	Evidence
Human	SLC2A4	6517	solute carrier family 2 (facilitated glucose transporter), member 4	GENERIF, Score=734, Pubmed Id: 18067156, UMLKSK CUI: C0017924 McArdle's disease muscle had higher phosphofructokinase protein content and activity as well as glucose transporter 4 (GLUT4) protein content and lower GLUT4 mRNA content than controls
Human	PYGM	5837	phosphorylase, glycogen, muscle	GENERIF, Score=1000, Pubmed Id: 15979037, UMLKSK CUI: C0017924 A new autosomal dominant gene mutation in McArdle disease GENERIF, Score=1000, Pubmed Id: 11749054, UMLKSK CUI: C0017924 McArdle disease may be caused by a R269X nonsense mutation in this gene GENERIF, Score=1000, Pubmed Id: 16154688, UMLKSK CUI: C0017924 We report a Spanish family with muscle glycogen phosphorylase (PYGM) deficiency (McArdle's disease) harbouring a novel compound genotype (A659D/L586P) GAD, Score=1000, Pubmed Id: 9152836, UMLKSK CUI: C0017924 Title:Homozygosity by descent for a rare mutation in the myophosphorylase gene is associated with variable phenotypes in a Druze family with McArdle disease.\|Association:Y\|Conclusion:Not Found GENERIF, Score=1000, Pubmed Id: 12640006, UMLKSK CUI: C0017924 In Mcardle's disease (deficiency of this enzyme) efferent muscle sympathetic nerve activity (MSNA) is attenuated GENERIF, Score=1000, Pubmed Id: 17994553, UMLKSK CUI: C0017924 To investigate if nonsense mediated decay affects the levels of transcripts containing PYGM mutations, 28 Spanish patients with McArdle disease, harboring 17 different mutations with premature termination codons in 77% of their alleles, were studied GENERIF, Score=1000, Pubmed Id: 17324573, UMLKSK CUI: C0017924 findings further demonstrate molecular heterogeneity of myophosphorylase deficiency, absence of genotype-phenotype correlation and expand the already crowded map of mutations within the myophosphorylase gene OMIM, Score=1000, UMLKSK CUI: C0017924 Muscle glycogen phosphorylase deficiency GENERIF, Score=1000, Pubmed Id: 12031624, UMLKSK CUI: C0017924 two new mutations in the myophosphorylase gene in Italian patients with McArdle's disease; both were compound heterozygous, with the common mutation at codon 49 (R49X) on the other allele GENERIF, Score=1000, Pubmed Id: 16786513, UMLKSK CUI: C0017924 19 novel mutations within the PYGM gene are associated with McArdle disease GENERIF, Score=1000, Pubmed Id: 12398832, UMLKSK CUI: C0017924 molecular genetic study of McArdle's disease in Yemenite-Jewish patients expands the already remarkable genetic heterogeneity of McArdle's disease and suggests the existence of ethnic or private mutations within this group
Human	ACE	1636	angiotensin I converting enzyme	GENERIF, Score=1000, Pubmed Id: 17630210, UMLKSK CUI: C0017924 both ACE genotype and gender contribute to how McArdle disease manifests in an individual patient
Human	ACTN3	89	actinin, alpha 3	GENERIF, Score=1000, Pubmed Id: 17560787, UMLKSK CUI: C0017924 In women with McArdle's disease, ACTN3 genotypes might partly explain the large individual variability that exists in the phenotypic manifestation of this disorder

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0017924	Glycogen Storage Disease Type V	0		self

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