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 - ATHEROSCLEROTIC DIS CAROTID

Debug Stats

### Total Build Time: 17 ms 42.957 KB
CONCEPT_NAME gt=1 ms Completed: 1 ms rowSize= 352 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=0 Completed: 0 ms rowSize= 106 bytes
CONCEPT_GENES gt=15 ms Completed: 15 ms rowSize= 41.278 KB
CONCEPT_XREFS gt=0 Completed: 0 ms rowSize= 1.161 KB
CONCEPT_ANCILLARY gt=1 ms Completed: 1 ms rowSize= 14 bytes
Reload Stats

Disease (1)

ATHEROSCLEROTIC DIS CAROTID C0577631

Genes (46)

Species:

human : 46

Page Size

Current 25

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Species	Gene	GeneId	Gene Name	Evidence
Human	NEWENTRY	192343	Record to support submission of GeneRIFs for a gene not in Gene (human; man).	GENERIF, Score=1000, Pubmed Id: 18497465, UMLKSK CUI: C0577631 Decrease in serum salusin-alpha, an anti-atherogenic peptide, may be associated with carotid atherosclerosis in hypertensive patients [salusin-alpha]
Human	PTGES	9536	prostaglandin E synthase	GENERIF, Score=1000, Pubmed Id: 16212965, UMLKSK CUI: C0577631 Patients with carotid atherosclerosis depict an overexpression of COX-2, mPGES-1 and EPs in blood mononuclear cells and plaque of patients with carotid atherosclerosis regulated by nuclear factor-kappaB
Human	PLA2G7	7941	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	GAD, Score=1000, Pubmed Id: 12590019, UMLKSK CUI: C0577631 Title:Association of plasma PAF acetylhydrolase gene polymorphism with IMT of carotid arteries in Japanese type 2 diabetic patients.\|Association:Y\|Conclusion:The results of this study indicate that the missense mutation in plasma PAF acetylhydrolase is associated with development of atherosclerosis in the elderly. GAD, Score=1000, Pubmed Id: 11248283, UMLKSK CUI: C0577631 Title:Evidence for the existence of the PAF acetylhydrolase mutation (Val279Phe) in non-Japanese populations: a preliminary study inTurkey, Azerbaijan, and Kyrgyzstan.\|Association:Not Found\|Conclusion:Contrary to the previous notions, identification of the mutation in Turkey and Kyrgyzstan shows the existence of the mutation in non-Japanese populations as well.
Human	UCP2	7351	uncoupling protein 2 (mitochondrial, proton carrier)	GAD, Score=1000, Pubmed Id: 15604415, UMLKSK CUI: C0577631 Title:Associations of the UCP2 gene locus with asymptomatic carotid atherosclerosis in middle-aged women.\|Association:Y\|Conclusion:Our results suggest a role of UCP2 in atherogenesis as originally proposed from studies in animal and cell culture models.
Human	TP53	7157	tumor protein p53	GENERIF, Score=1000, Pubmed Id: 16973168, UMLKSK CUI: C0577631 study showed the joint effects on the risk of carotid atherosclerosis between the genetic polymorphisms of GSTP1 and p53, and arsenic exposure
Human	TLR4	7099	toll-like receptor 4	GENERIF, Score=1000, Pubmed Id: 15258789, UMLKSK CUI: C0577631 The Asp299Gly TLR4-allele might have a protective role in carotid atherosclerosis, but not in cerebral ischemia
Human	SREBF2	6721	sterol regulatory element binding transcription factor 2	GENERIF, Score=1000, Pubmed Id: 12801623, UMLKSK CUI: C0577631 a common variation in the SREBP-2 gene is related with early-stage carotid atherosclerosis in subjects with a risk of cardiovascular events without detectable change in plasma lipid levels
Human	SOD2	6648	superoxide dismutase 2, mitochondrial	GAD, Score=1000, Pubmed Id: 12732398, UMLKSK CUI: C0577631 Title:The signal sequence polymorphism of the MnSOD gene is associated with the degree of carotid atherosclerosis\|Association:Y\|Conclusion:In conclusion, the signal sequence polymorphism of the MnSOD gene is a minor determinant of carotid IMT pointing out the importance of redox-balance in the atherogenesis.
Human	SELE	6401	selectin E	GENERIF, Score=1000, Pubmed Id: 16554320, UMLKSK CUI: C0577631 in end-stage renal disease, the Leu554Phe polymorphism of E-selectin gene is associated with the severity of carotid atherosclerosis
Human	CCL2	6347	chemokine (C-C motif) ligand 2	GENERIF, Score=1000, Pubmed Id: 16697654, UMLKSK CUI: C0577631 monocyte chemoattractant protein-1 has a role in carotid atherosclerosis in HIV-infected patients with lipodystrophy GENERIF, Score=1000, Pubmed Id: 14620921, UMLKSK CUI: C0577631 MCP-1 genotype was an independent determinant of plasma MCP-1 level; findings indicate plasma MCP-1 associated with carotid atherosclerosis; -2518 SNP is associated with plasma level of MCP-1, but was not directly associated with carotid atherosclerosis
Human	PTGS2	5743	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	GENERIF, Score=1000, Pubmed Id: 16212965, UMLKSK CUI: C0577631 Patients with carotid atherosclerosis depict an overexpression of COX-2, mPGES-1 and EPs in blood mononuclear cells and plaque of patients with carotid atherosclerosis regulated by nuclear factor-kappaB
Human	PTGDS	5730	prostaglandin D2 synthase 21kDa (brain)	GAD, Score=1000, Pubmed Id: 15325247, UMLKSK CUI: C0577631 Title:Identification of gene polymorphism in lipocalin-type prostaglandin D synthase and its association with carotid atherosclerosis in Japanese hypertensive patients.\|Association:Y\|Conclusion:Our results suggested that 4111 A>C polymorphism in the L-PGDS gene contributes to the development of carotid atherosclerosis in Japanese hypertensive patients.
Human	PPARG	5468	peroxisome proliferator-activated receptor gamma	GENERIF, Score=913, Pubmed Id: 15144586, UMLKSK CUI: C0577631 Peroxisome proliferative activated receptor gamma C161-T may play a important role in carotid artery arteriosclerosis GAD, Score=1000, Pubmed Id: 15144586, UMLKSK CUI: C0577631 Title:[Peroxisome proliferator-activated receptor gamma C-161T polymorphism and carotid artery atherosclerosis in metabolic syndrome]\|Association:Not Found\|Conclusion:In MS, CC genotype was prone to lesion of carotid artery, but CT + TT may reduce lesion of carotid artery, which implicates that PPAR gamma C161-T may play a important role in carotid artery arteriosclerosis.
Human	PON1	5444	paraoxonase 1	GAD, Score=1000, Pubmed Id: 12618279, UMLKSK CUI: C0577631 Title:A paraoxonase gene polymorphism, PON 1 (55), as an independent risk factor for increased carotid intima-media thickness in middle-aged women.\|Association:Y\|Conclusion:IY coYclusioY, POY 1 (LL+ML) 55 but Yot POY 1 (Q/R) 192 or POY 2 (S/C) 311, appears to be aY iYdepeYdeYt risk factor for iYcreased carotid IMT iY middle-aged womeY.
Human	PLAUR	5329	plasminogen activator, urokinase receptor	GENERIF, Score=1000, Pubmed Id: 18048089, UMLKSK CUI: C0577631 The carotid atherosclerosis is independently related to uPA/its soluble receptor system in dialysis patients
Human	PLAU	5328	plasminogen activator, urokinase	GENERIF, Score=1000, Pubmed Id: 18048089, UMLKSK CUI: C0577631 The carotid atherosclerosis is independently related to uPA/its soluble receptor system in dialysis patients
Human	PDE4D	5144	phosphodiesterase 4D, cAMP-specific	GENERIF, Score=901, Pubmed Id: 15802632, UMLKSK CUI: C0577631 Lack of association of the PDE4D gene as a major risk factor for ischemic stroke, or early carotid atherosclerosis
Human	NPY	4852	neuropeptide Y	GAD, Score=666, Pubmed Id: 11689216, UMLKSK CUI: C0577631 Title:Leucine7 to proline7 polymorphism in the preproneuropeptide Y is associated with the progression of carotid atherosclerosis blood pressure and serum lipids in Finnish men.\|Association:Y\|Conclusion:This study provides important evidence suggesting that the Pro7 substitution in the prepro-NPY is an important risk factor for accelerated atherosclerotic progression, increased blood pressure and increased serum cholesterol in humans.
Human	NOS3	4846	nitric oxide synthase 3 (endothelial cell)	GENERIF, Score=1000, Pubmed Id: 17586410, UMLKSK CUI: C0577631 In patients on dialysis the risk alleles of G894T and T-786C polymorphisms of the eNOS gene are associated with carotid atherosclerosis GAD, Score=1000, Pubmed Id: 15079780, UMLKSK CUI: C0577631 Title:Influence of eNOS gene polymorphisms on carotid atherosclerosis\|Association:Y\|Conclusion:Our findings suggest that the 4a allele and the eNOS combined genotypes are independent predisposing factors to carotid atherosclerosis. GAD, Score=1000, Pubmed Id: 12666069, UMLKSK CUI: C0577631 Title:Effect of polymorphism of the endothelial nitric oxide synthase and apolipoprotein E genes on carotid atherosclerosis in hemodialysis patients.\|Association:Y\|Conclusion:This cross-sectional study showed a synergistic effect between the intron 4 polymorphism or T(-786)-->C polymorphism of the eNOS gene and the apoE polymorphism with respect to risk for carotid atherosclerosis in nondiabetic hemodialysis patients. GENERIF, Score=901, Pubmed Id: 12605344, UMLKSK CUI: C0577631 ecNOS 4 a/b polymorphism does not interact with the development of early carotid arteriosclerosis in young type-1 diabetic patients, but in these patients it could influence the occurence of diabetic retinopathy
Human	NFKB1	4790	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	GENERIF, Score=1000, Pubmed Id: 16212965, UMLKSK CUI: C0577631 Patients with carotid atherosclerosis depict an overexpression of COX-2, mPGES-1 and EPs in blood mononuclear cells and plaque of patients with carotid atherosclerosis regulated by nuclear factor-kappaB
Human	MTHFR	4524	methylenetetrahydrofolate reductase (NAD(P)H)	GENERIF, Score=1000, Pubmed Id: 17899317, UMLKSK CUI: C0577631 A1298C polymorphism of MTHFR gene appears to be associated with the severity of carotid atherosclerosis and co-occurrence of MTHFR polymorphisms may be a risk factor for cardiovascular disease in patients on hemodialysis GENERIF, Score=840, Pubmed Id: 17228344, UMLKSK CUI: C0577631 MTHFR genotype, plasma folate, vitamin B6 & vitamin B12 & age were significantly correlated to plasma homocysteine; MTHFR 677TT-related carotid atherosclerosis was only identified in healthy elderly subjects with lower level of plasma folate & vitamin B12 GAD, Score=1000, Pubmed Id: 11558898, UMLKSK CUI: C0577631 Title:\|Association:Y\|Conclusion:Not Found
Human	MPO	4353	myeloperoxidase	GENERIF, Score=1000, Pubmed Id: 17161406, UMLKSK CUI: C0577631 myeloperoxidase levels are increased in complicated atherosclerotic plaques and in plasma level of patients with carotid atherosclerosis
Human	MMP9	4318	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	GENERIF, Score=1000, Pubmed Id: 18173548, UMLKSK CUI: C0577631 our results demonstrate associations of MMP-9 genotypes with different stages of carotid atherosclerosis GENERIF, Score=1000, Pubmed Id: 17161406, UMLKSK CUI: C0577631 matrix metalloproteinase 9 (MMP-9)levels are increased in complicated atherosclerotic plaques and in plasma level of patients with carotid atherosclerosis GENERIF, Score=1000, Pubmed Id: 16574900, UMLKSK CUI: C0577631 Number of repeats (> or =22 CA) in microsatellite of MMP-9 promoter, but not MMP-9 plasma levels, is associated to carotid atherosclerosis and particularly to plaques with thin fibrous cap GAD, Score=1000, Pubmed Id: 16159601, UMLKSK CUI: C0577631 Title:\|Association:Not Found\|Conclusion:Not Found
Human	MMP3	4314	matrix metallopeptidase 3 (stromelysin 1, progelatinase)	GENERIF, Score=1000, Pubmed Id: 18801353, UMLKSK CUI: C0577631 Subjects carrying genotypes with 6A allele of MMP3 had significantly higher susceptibility to carotid atherosclerosis GAD, Score=858, Pubmed Id: 11116068, UMLKSK CUI: C0577631 Title:Stromelysin-1 and interleukin-6 gene promoter polymorphisms are determinants of asymptomatic carotid artery atherosclerosis.\|Association:Y\|Conclusion:These data suggest that genetic factors that predispose to reduced matrix remodeling (stromelysin 6A allele) and to increased inflammation (IL-6 G allele) combine to increase susceptibility for intima-media thickening in the carotid bifurcation, a predilection site for atherosclerosis. GAD, Score=1000, Pubmed Id: 11116068, UMLKSK CUI: C0577631 Title:Stromelysin-1 and interleukin-6 gene promoter polymorphisms are determinants of asymptomatic carotid artery atherosclerosis.\|Association:Not Found\|Conclusion:These data suggest that genetic factors that predispose to reduced matrix remodeling (stromelysin 6A allele) and to increased inflammation (IL-6 G allele) combine to increase susceptibility for intima-media thickening in the carotid bifurcation, a predilection site for atherosclerosis.
Human	LIPC	3990	lipase, hepatic	GENERIF, Score=1000, Pubmed Id: 12642787, UMLKSK CUI: C0577631 REVIEW: potential impact of genetic determinants of hepatic lipase activity in modulating both the development of coronary and carotid atherosclerosis will be discussed based on hepatic lipase proposed roles in lipoprotein metabolism

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0577631	ATHEROSCLEROTIC DIS CAROTID	0		self

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