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 - Cystinuria

Debug Stats

### Total Build Time: 45 ms 37.711 KB
CONCEPT_NAME gt=12 ms Completed: 12 ms rowSize= 318 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 466 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=4 ms Completed: 4 ms rowSize= 556 bytes
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=4 ms Completed: 4 ms rowSize= 5.427 KB
CONCEPT_RELATIONSHIPS gt=18 ms Completed: 18 ms rowSize= 13.730 KB
CONCEPT_GENES gt=5 ms Completed: 5 ms rowSize= 15.882 KB
CONCEPT_XREFS gt=2 ms Completed: 2 ms rowSize= 1.145 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Cystinuria C0010691

Definition (1)

An inherited disorder due to defective reabsorption of CYSTINE and other BASIC AMINO ACIDS by the PROXIMAL RENAL TUBULES. This form of aminoaciduria is characterized by the abnormally high urinary levels of cystine; LYSINE; ARGININE; and ORNITHINE. Mutations involve the amino acid transport protein gene SLC3A1.

Semantic Types (1)

Disease or Syndrome (T047)

Parents (1)

C0002534

Ancestral Roots

Relationships (28)

Relation Types:

diso_to_chem : 14

diso_to_diso : 8

diso_to_gene : 4

diso_to_phen : 2

Relationships:

none : 5

gene_associated_with_disease : 4

gene_product_malfunction_associated_with_disease : 2

isa : 3

mapped_to : 1

may_treat : 9

permuted_term_of : 1

related_to : 3

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Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_PHEN	88		genetic aspects C0017399
DISO_to_CHEM	72		Amino Acid Transport Systems, Basic C0949774
DISO_to_PHEN	57		genetic aspects C0017399
DISO_to_CHEM	47		Amino Acid Transport Systems, Basic C0949774
DISO_to_CHEM	33		Amino Acid Transport Systems, Neutral C0969702
DISO_to_CHEM		may_treat	.beta.,.beta.-Dimethylcysteine C0030817
DISO_to_CHEM		may_treat	5,7-Diiod-8-chinolinol C0012341
DISO_to_CHEM		gene_product_malfunction_associated_with_disease	B(0,+)-Type Amino Acid Transporter 1 C2986633
DISO_to_CHEM		may_treat	IODOQUINOL 210 MG ORAL TABLET C0689225
DISO_to_CHEM		may_treat	IODOQUINOL 25GM/BTL PWDR C0977883
DISO_to_CHEM		may_treat	IODOQUINOL 3%/LANOLIN DERIVATIVES SHAMPOO C0977884
DISO_to_CHEM		may_treat	IODOQUINOL 650 MG ORAL TABLET C0689226
DISO_to_CHEM		gene_product_malfunction_associated_with_disease	Neutral and Basic Amino Acid Transport Protein rBAT C2986631
DISO_to_CHEM		may_treat	PENICILLAMINE 125 MG ORAL CAPSULE C0689910
DISO_to_CHEM		may_treat	PENICILLAMINE 250 MG ORAL CAPSULE C0689911
DISO_to_CHEM		may_treat	PENICILLAMINE 250 MG ORAL TABLET, COATED C0689912
DISO_to_DISO		permuted_term_of	CSNU C0010691
DISO_to_DISO		related_to	CYSTINURIA, TYPE A C1857388
DISO_to_DISO		related_to	CYSTINURIA, TYPE A/B C1857390
DISO_to_DISO		related_to	CYSTINURIA, TYPE B C1857389
DISO_to_DISO		mapped_to	Cystinuria type 1 C0268643
DISO_to_DISO		isa	Cystinuria, type 2 C0268644
DISO_to_DISO		isa	Cystinuria, type 3 C0268645
DISO_to_DISO		isa	Hypercystinuria C0268646
DISO_to_GENE		gene_associated_with_disease	SLC3A1 gene C1420191

Genes (5)

Species:

human : 5

Species	Gene	GeneId	Gene Name	Evidence
Human	SLC7A9	11136	solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9	GENERIF, Score=1000, Pubmed Id: 16838140, UMLKSK CUI: C0010691 all carriers of a SLC7A9 mutation manifested cystinuria if their normal allele had non-wild type nucleotides in two or more of the identified polymorphic sites GENERIF, Score=660, Pubmed Id: 16609684, UMLKSK CUI: C0010691 Mutations of SLC7A9 for Japanese cystinuria patients are different from those reported for European and American population GENERIF, Score=660, Pubmed Id: 17701443, UMLKSK CUI: C0010691 a novel splice-acceptor site mutation in the SLC7A9 gene may have a role in cystinuria [case report] GENERIF, Score=1000, Pubmed Id: 14531788, UMLKSK CUI: C0010691 deletions in SLC7A9 in cystinuria GENERIF, Score=1000, Pubmed Id: 12234283, UMLKSK CUI: C0010691 in cystinuria, the detection rate for mutations in SLC7A9 in children was 25% in the SLC7A9 gene for non-type I chromosomes GAD, Score=1000, Pubmed Id: 15635077, UMLKSK CUI: C0010691 Title:New insights into cystinuria: 40 new mutations,genotype-phenotype correlation, and digenic inheritance causing partial phenotype.\|Association:Not Found\|Conclusion:Digenic inheritance is an exception (two of 164 families), with a limited contribution to the aminoaciduria values (partial phenotype) in cystinuria. Further mutational analysis could focus on one of the two genes (SLC3A1 preferentially for type I and SLC7A9 for type non-I probands), while for mixed probands analysis of both genes might be required, with priority given to SLC7A9. GAD, Score=1000, Pubmed Id: 12779097, UMLKSK CUI: C0010691 Title:Genetic variations of the SLC7A9 gene: alleledistribution of 13 polymorphic sites in German cystinuria patients and controls.\|Association:Y\|Conclusion:In summary, our results show that cystinuria is a complex disease which is not only caused by mutations in SLC7A9 and SLC3A1, but also influenced by other modifying factors such as variants in SLC7A9. GAD, Score=1000, Pubmed Id: 12820697, UMLKSK CUI: C0010691 Title:Mutation analysis of SLC7A9 in cystinuria patients in Sweden.\|Association:Not Found\|Conclusion:We conclude that SLC3A1 is still the major disease gene among Swedish cystinuria patients, with only a minor contribution of SLC7A9 mutations as the genetic basis of cystinuria. The absence of SLC3A1 and SLC7A9 mutations in a substantial proportion of the patients implies that mutations in parts of the genes that were not analyzed may be present, as well as large deletions that escape detection by the methods used. However, our results raise the question of whether other, as yet unknown genes, may also be involved in cystinuria. GENERIF, Score=1000, Pubmed Id: 15818803, UMLKSK CUI: C0010691 gene deletion , codon 423 in cystinuria, type non-1 GAD, Score=1000, Pubmed Id: 12239244, UMLKSK CUI: C0010691 Title:Comparison between SLC3A1 and SLC7A9 cystinuria patients and carriers: a need for a newclassification.\|Association:Not Found\|Conclusion:Clinical data show that cystinuria is more severe in males than in females. The two types of cystinuria (A and B) had a similar outcome in this retrospective study, but the effect of the treatment could not be analyzed. Stone events do not correlate with amino acid urinary excretion. Renal function was clearly impaired in 17% of the patients. GAD, Score=1000, Pubmed Id: 14991253, UMLKSK CUI: C0010691 Title:The population-specific distribution and frequencies of genomic variants in the SLC3A1 and SLC7A9 genes and their application in molecular genetic testing of cystinuria\|Association:Not Found\|Conclusion:Generally, we could show that a stepwise analysis directed to the most common mutations in the two cystinuria genes is sufficient to detect variants in more than 75% of patients of European origin. The test consists of nine different PCR-based approaches and therefore represents a low-cost, reliable and timesaving diagnostic tool. OMIM, Score=1000, UMLKSK CUI: C0010691 Cystinuria GENERIF, Score=1000, Pubmed Id: 16138908, UMLKSK CUI: C0010691 SLC3A1 and SLC7A9 mutations may have roles in cystinuria GENERIF, Score=660, Pubmed Id: 12371955, UMLKSK CUI: C0010691 The finding of SLC7A9 mutations in all three subtypes underscores the complex interactions between specific cystinuria genes and other factors influencing cystine excretion
Human	PREPL	9581	prolyl endopeptidase-like	OMIM, Score=1000, UMLKSK CUI: C0010691 Cystinuria, type I (HCS and 2p21del) OMIM, Score=1000, UMLKSK CUI: C0010691 Both contiguous gene syndromes show similar features such as cystinuria, growth impairment, and hypotonia
Human	SLC3A1	6519	solute carrier family 3 (amino acid transporter heavy chain), member 1	Click here to display 16 evidence detail records.
Human	SLC1A5	6510	solute carrier family 1 (neutral amino acid transporter), member 5	GENERIF, Score=694, Pubmed Id: 16435221, UMLKSK CUI: C0010691 analysis of SLC1A5 mutations on 19q13 in cystinuria patients
Human	ARG1	383	arginase 1	OMIM, Score=1000, UMLKSK CUI: C0010691 Diaminoaciduria (arginuria, lysinuria, cystinuria, ornithinuria)

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0010691	Cystinuria	0		self

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