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 - Retinopathy Adverse Event

Debug Stats

### Total Build Time: 34 ms 53.711 KB
CONCEPT_NAME gt=0 Completed: 0 ms rowSize= 348 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
Skipping details on: CONCEPT_DEFINITION gt=NONE 0 Completed: 0 ms rowSize= 0 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= 14 bytes
Skipping details on: CONCEPT_NAMESPACE gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_PARENTS gt=0 Completed: 0 ms rowSize= 7 bytes
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=0 Completed: 0 ms rowSize= 15 bytes
CONCEPT_RELATIONSHIPS gt=17 ms Completed: 17 ms rowSize= 2.155 KB
CONCEPT_GENES gt=15 ms Completed: 15 ms rowSize= 49.986 KB
CONCEPT_XREFS gt=2 ms Completed: 2 ms rowSize= 1.159 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Retinopathy Adverse Event C1962966

Relationships (4)

Relation Types:

diso_to_diso : 4

Relationships:

isa : 4

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_DISO		isa	CTCAE Grade 1 Retinopathy C1557362
DISO_to_DISO		isa	CTCAE Grade 2 Retinopathy C1557363
DISO_to_DISO		isa	CTCAE Grade 3 Retinopathy C1557364
DISO_to_DISO		isa	CTCAE Grade 4 Retinopathy C1557365

Genes (55)

Species:

human : 55

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Species	Gene	GeneId	Gene Name	Evidence
Human	MFSD8	256471	major facilitator superfamily domain containing 8	OMIM, Score=1000, UMLKSK CUI: C1962966 Retinopathy
Human	CPT1C	126129	carnitine palmitoyltransferase 1C	GENERIF, Score=1000, Pubmed Id: 18385088, UMLKSK CUI: C1962966 Accumulation of 3-hydroxylated intermediates of long-chain fatty acids may contribute to the pathogenesis of retinopathy in MTP deficiencies
Human	C1QTNF5	114902	C1q and tumor necrosis factor related protein 5	OMIM, Score=1000, UMLKSK CUI: C1962966 Retinopathy may resemble retinitis pigmentosa
Human	NAA15	80155	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	GENERIF, Score=1000, Pubmed Id: 16518308, UMLKSK CUI: C1962966 Loss of retinal endothelial Tbdn-1 expression may be a contributing factor in retinal blood vessel proliferation in retinopathy of prematurity
Human	ADIPOQ	9370	adiponectin, C1Q and collagen domain containing	GENERIF, Score=1000, Pubmed Id: 15745931, UMLKSK CUI: C1962966 plasma adiponectin concentrations decrease progressively with higher grades of hypertensive retinopathy even after correction for other atherogenic risk factors, suggesting that a critical adiponectin level is needed for the development of retinopathy
Human	PROM1	8842	prominin 1	GENERIF, Score=1000, Pubmed Id: 17605048, UMLKSK CUI: C1962966 phenotypic characteristics of retinopathy caused by nonsense mutations in PROM1
Human	FZD4	8322	frizzled family receptor 4	GAD, Score=1000, Pubmed Id: 15981244, UMLKSK CUI: C1962966 Title:Complexity of the genotype-phenotype correlation in familial exudative vitreoretinopathy with mutations in the LRP5 and/or FZD4 genes.\|Association:Not Found\|Conclusion:Not Found
Human	VEGFA	7422	vascular endothelial growth factor A	GENERIF, Score=827, Pubmed Id: 11642726, UMLKSK CUI: C1962966 upregulated in eye in experimental herpesvirus retinopathy GAD, Score=1000, Pubmed Id: 11978667, UMLKSK CUI: C1962966 Title:A common polymorphism in the 5'-untranslated region of the VEGF gene is associated with diabetic retinopathy in type 2 diabetes\|Association:Y\|Conclusion:These data suggest that the C(-634)G polymorphism in the 5'UTR of the VEGF gene is a novel genetic risk factor for diabetic retinopathy. GAD, Score=1000, Pubmed Id: 15161830, UMLKSK CUI: C1962966 Title:Genetic polymorphisms and retinopathy of prematurity\|Association:Y\|Conclusion:The progression of ROP to threshold ROP in very preterm infants may be influenced by genetic differences in VEGF production. Future efforts at prevention of threshold ROP may be directed toward blocking excess production of VEGF. GENERIF, Score=861, Pubmed Id: 17513698, UMLKSK CUI: C1962966 multiple VEGFA variants are associated with the development of severe retinopathy in type 1 diabetes GAD, Score=1000, Pubmed Id: 15635051, UMLKSK CUI: C1962966 Title:Association of genetic polymorphisms of vascular endothelial growth factor and risk for proliferative retinopathy of prematurity.\|Association:Y\|Conclusion:These findings suggest that the VEGF genotype may be associated with risk for proliferative ROP in VLBW infants. GAD, Score=1000, Pubmed Id: 12090088, UMLKSK CUI: C1962966 Title:Genes and diabetic retinopathy.\|Association:Not Found\|Conclusion:Review article
Human	VCAM1	7412	vascular cell adhesion molecule 1	GENERIF, Score=1000, Pubmed Id: 18791689, UMLKSK CUI: C1962966 correlations found between sVCAM-1, sICAM-1 and sELAM-1 and the presence of retinopathy suggest that cellular adhesion and neovascularization may be linked processes
Human	TNF	7124	tumor necrosis factor	GAD, Score=1000, Pubmed Id: 12724690, UMLKSK CUI: C1962966 Title:Molecular genetics of microvascular disease in diabetic retinopathy.\|Association:Not Found\|Conclusion:Review article GAD, Score=1000, Pubmed Id: 12090088, UMLKSK CUI: C1962966 Title:Genes and diabetic retinopathy.\|Association:Not Found\|Conclusion:Review article GAD, Score=1000, Pubmed Id: 15161830, UMLKSK CUI: C1962966 Title:Genetic polymorphisms and retinopathy of prematurity\|Association:Not Found\|Conclusion:The progression of ROP to threshold ROP in very preterm infants may be influenced by genetic differences in VEGF production. Future efforts at prevention of threshold ROP may be directed toward blocking excess production of VEGF.
Human	TGFB1	7040	transforming growth factor, beta 1	GAD, Score=1000, Pubmed Id: 15161830, UMLKSK CUI: C1962966 Title:Genetic polymorphisms and retinopathy of prematurity\|Association:Not Found\|Conclusion:The progression of ROP to threshold ROP in very preterm infants may be influenced by genetic differences in VEGF production. Future efforts at prevention of threshold ROP may be directed toward blocking excess production of VEGF.
Human	TEAD4	7004	TEA domain family member 4	GENERIF, Score=1000, Pubmed Id: 17652751, UMLKSK CUI: C1962966 Novel RTEF-1 transcripts are present within human ocular vascular endothelial cells and mouse neural retina during normal and retinopathy of prematurity development, and alternatively spliced products are produced under hyperoxic and hypoxic conditions
Human	SELE	6401	selectin E	GENERIF, Score=1000, Pubmed Id: 18791689, UMLKSK CUI: C1962966 correlations found between sVCAM-1, sICAM-1 and sELAM-1 and the presence of retinopathy suggest that cellular adhesion and neovascularization may be linked processes GAD, Score=1000, Pubmed Id: 12027924, UMLKSK CUI: C1962966 Title:Intercellular adhesion molecule-1 (ICAM-1) polymorphism is associated with diabetic retinopathy in Type 2 diabetes mellitus.\|Association:Not Found\|Conclusion:These data suggest that the ICAM-1 469KK genotype could be a genetic risk factor for retinopathy in Type 2 diabetes mellitus.
Human	ATXN1	6310	ataxin 1	GENERIF, Score=694, Pubmed Id: 14985428, UMLKSK CUI: C1962966 We demonstrate that abolishing full-length mutant human ataxin-7 transgene expression did not reverse retinopathy progression in SCA7 mice, raising the possibility that some polyQ-induced pathological events might be irreversible
Human	RAGE	5891		GAD, Score=1000, Pubmed Id: 11375354, UMLKSK CUI: C1962966 Title:Effects of novel polymorphisms in the RAGE gene on transcriptional regulation and their association with diabetic retinopathy.\|Association:Y\|Conclusion:These data suggest that the polymorphisms involved in differences in RAGE gene regulation may influence the pathogenesis of diabetic vascular complications. GAD, Score=1000, Pubmed Id: 12477623, UMLKSK CUI: C1962966 Title:Association of Gly82Ser polymorphism in the RAGE gene with diabetic retinopathy in type II diabetic Asian Indian patients.\|Association:Not Found\|Conclusion:Our result suggests that Ser82 allele in the receptor for AGE gene is a low-risk allele for developing DR in Asian Indian patients who have type II diabetes. GAD, Score=1000, Pubmed Id: 12090088, UMLKSK CUI: C1962966 Title:Genes and diabetic retinopathy.\|Association:Not Found\|Conclusion:Review article
Human	PON2	5445	paraoxonase 2	GENERIF, Score=1000, Pubmed Id: 11918623, UMLKSK CUI: C1962966 diabetic microangiopathy is genetically heterogeneous; PON1 Leu/Leu increases the risk for retinopathy and PON2 Ser/Ser increases the risk for microalbuminuria
Human	PON1	5444	paraoxonase 1	GENERIF, Score=1000, Pubmed Id: 11918623, UMLKSK CUI: C1962966 diabetic microangiopathy is genetically heterogeneous; PON1 Leu/Leu increases the risk for retinopathy and PON2 Ser/Ser increases the risk for microalbuminuria GAD, Score=1000, Pubmed Id: 12724690, UMLKSK CUI: C1962966 Title:Molecular genetics of microvascular disease in diabetic retinopathy.\|Association:Not Found\|Conclusion:Review article
Human	SERPINF1	5176	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1	GENERIF, Score=1000, Pubmed Id: 18455830, UMLKSK CUI: C1962966 PEDF levels are significantly higher in type 1 diabetic patients with retinopathy compared to the patients without it GENERIF, Score=1000, Pubmed Id: 12687338, UMLKSK CUI: C1962966 pigment epithelium-derived factor content in the aqueous humor of diabetic patients strongly predicts who among them will develop progression of retinopathy
Human	PECAM1	5175	platelet/endothelial cell adhesion molecule 1	GAD, Score=1000, Pubmed Id: 12027924, UMLKSK CUI: C1962966 Title:Intercellular adhesion molecule-1 (ICAM-1) polymorphism is associated with diabetic retinopathy in Type 2 diabetes mellitus.\|Association:Not Found\|Conclusion:These data suggest that the ICAM-1 469KK genotype could be a genetic risk factor for retinopathy in Type 2 diabetes mellitus.
Human	SERPINE1	5054	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1	GAD, Score=1000, Pubmed Id: 12724690, UMLKSK CUI: C1962966 Title:Molecular genetics of microvascular disease in diabetic retinopathy.\|Association:Not Found\|Conclusion:Review article GENERIF, Score=1000, Pubmed Id: 18239151, UMLKSK CUI: C1962966 higher PAI-1 plasma level is independently associated with a lower risk of retinopathy but a higher risk of CHD in type 2 diabetes
Human	NPY	4852	neuropeptide Y	GAD, Score=1000, Pubmed Id: 12724690, UMLKSK CUI: C1962966 Title:Molecular genetics of microvascular disease in diabetic retinopathy.\|Association:Not Found\|Conclusion:Review article
Human	NOS3	4846	nitric oxide synthase 3 (endothelial cell)	GAD, Score=1000, Pubmed Id: 11918626, UMLKSK CUI: C1962966 Title:eNOS4 polymorphism of the endothelial nitric oxide synthase predicts risk for severe diabetic retinopathy.\|Association:Y\|Conclusion:We demonstrate in Caucasians with Type 1 diabetes that (i) eNOS4a/a is associated with absent or non-severe DR, and (ii) eNOS4b/b is associated with severe DR. GAD, Score=1000, Pubmed Id: 12724690, UMLKSK CUI: C1962966 Title:Molecular genetics of microvascular disease in diabetic retinopathy.\|Association:Not Found\|Conclusion:Review article GAD, Score=1000, Pubmed Id: 15890549, UMLKSK CUI: C1962966 Title:The T-786C and C774T endothelial nitric oxide synthase gene polymorphisms independently affect the onset pattern of severe diabetic retinopathy.\|Association:Not Found\|Conclusion:These findings, supported by previous associations between eNOS4b/a polymorphism and DR, suggest that T-786C and C774T eNOS polymorphisms affect the onset pattern of severe DR. GAD, Score=1000, Pubmed Id: 12974139, UMLKSK CUI: C1962966 Title:Molecular variation in endothelial nitric oxide synthase gene (eNOS) in western Mediterranean populations.\|Association:Not Found\|Conclusion:The variation found for these polymorphisms indicates that they may be a useful tool for population studies even at microgeographical level.
Human	NOS2	4843	nitric oxide synthase 2, inducible	GAD, Score=1000, Pubmed Id: 12090088, UMLKSK CUI: C1962966 Title:Genes and diabetic retinopathy.\|Association:Not Found\|Conclusion:Review article GAD, Score=1000, Pubmed Id: 12081717, UMLKSK CUI: C1962966 Title:Inducible nitric oxide synthase gene and diabetic retinopathy in Asian Indian patients.\|Association:Y\|Conclusion:In the Asian Indian population, allele 210 bp of the iNOS gene is a high-risk allele for developing retinopathy and alleles 200 and 220 bp protect an individual from developing retinopathy or its complications. GENERIF, Score=1000, Pubmed Id: 12081717, UMLKSK CUI: C1962966 allelic polymorphism of the inducible nitric oxide synthase (iNOS) gene associated with retinopathy in an Asian Indian population GAD, Score=1000, Pubmed Id: 12724690, UMLKSK CUI: C1962966 Title:Molecular genetics of microvascular disease in diabetic retinopathy.\|Association:Not Found\|Conclusion:Review article
Human	NDP	4693	Norrie disease (pseudoglioma)	GAD, Score=1000, Pubmed Id: 16052165, UMLKSK CUI: C1962966 Title:Norrie disease gene sequence variants in an ethnically diverse population with retinopathy of prematurity.\|Association:Not Found\|Conclusion:Of the six sequence alterations found, five were novel nucleotide changes: One in the 5' UTR region of exon 2, and four in the 3' UTR region of exon 3. The extent of NDP polymorphisms in this large, racially diverse group of infants is moderate. NDP polymorphisms may play a role in the pathogenesis of ROP, but do not appear to be a major causative factor. GAD, Score=1000, Pubmed Id: 12145535, UMLKSK CUI: C1962966 Title:A C597-->A polymorphism in the Norrie disease gene is associated with advanced retinopathy of prematurity in premature Kuwaiti infants.\|Association:Y\|Conclusion:The incidence of the AA genotype of the C597A polymorphism was considerably higher in advanced-stage ROP cases (83.3%) compared to spontaneously regressing ROP cases (0%) and the normal controls (10.4%) (p < 0.0001). For the other genotypes, no significant difference was detected between the controls and ROP cases. In the case of the C110G mutation in the ND gene, no significant differences were detected between the controls and ROP cases, and the majority of subjects had a CC genotype in all three groups. GAD, Score=1000, Pubmed Id: 11322656, UMLKSK CUI: C1962966 Title:Insertion and deletion mutations in the dinucleotide repeat region of the Norrie disease gene in patients with advanced retinopathy of prematurity.\|Association:Not Found\|Conclusion:Taking into account the above results, as well as those of other studies, it appears that the ND gene mutations can account for 3% of cases of advanced ROP. Although the ND gene is not frequently involved in advanced ROP, the present large-scale study further supports the hypothesis that genetic influences may play an important role in the development of severe ROP in some premature infants. GENERIF, Score=1000, Pubmed Id: 16052165, UMLKSK CUI: C1962966 NDP polymorphisms may play a role in the pathogenesis of retinopathy of prematurity, but do not appear to be a major causative factor GENERIF, Score=1000, Pubmed Id: 12145535, UMLKSK CUI: C1962966 Data show a strong association between the AA genotype of the C597A Norrie disease gene polymorphism and progression of retinopathy of prematurity GAD, Score=833, Pubmed Id: 12145535, UMLKSK CUI: C1962966 Title:A C597-->A polymorphism in the Norrie disease gene is associated with advanced retinopathy of prematurity in premature Kuwaiti infants.\|Association:Y\|Conclusion:The incidence of the AA genotype of the C597A polymorphism was considerably higher in advanced-stage ROP cases (83.3%) compared to spontaneously regressing ROP cases (0%) and the normal controls (10.4%) (p < 0.0001). For the other genotypes, no significant difference was detected between the controls and ROP cases. In the case of the C110G mutation in the ND gene, no significant differences were detected between the controls and ROP cases, and the majority of subjects had a CC genotype in all three groups. GENERIF, Score=1000, Pubmed Id: 11748312, UMLKSK CUI: C1962966 de novo mutations in the 5' regulatory region in retinopathy of prematurity
Human	MTTP	4547	microsomal triglyceride transfer protein	OMIM, Score=1000, UMLKSK CUI: C1962966 Retinopathy

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C1962966	Retinopathy Adverse Event	0		self

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