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 - Aseptic Necrosis of Bone

Debug Stats

### Total Build Time: 27 ms 37.384 KB
CONCEPT_NAME gt=3 ms Completed: 3 ms rowSize= 346 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 197 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=2 ms Completed: 2 ms rowSize= 106 bytes
CONCEPT_GENES gt=20 ms Completed: 20 ms rowSize= 35.521 KB
CONCEPT_XREFS gt=2 ms Completed: 2 ms rowSize= 1.158 KB
CONCEPT_ANCILLARY gt=0 Completed: 0 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Aseptic Necrosis of Bone C0520474

Definition (1)

bone death due to lack of blood circulation

Genes (23)

Species:

human : 23

Species	Gene	GeneId	Gene Name	Evidence
Human	IL23R	149233	interleukin 23 receptor	GENERIF, Score=1000, Pubmed Id: 18779654, UMLKSK CUI: C0520474 IL23R polymorphisms may play an important role in the development of osteonecrosis of femoral head
Human	KL	9365	klotho	GENERIF, Score=827, Pubmed Id: 15784727, UMLKSK CUI: C0520474 several single nucleotide polymorphisms in bone morphogenic protein 6, annexin A2, and klotho were associated with sickle cell osteonecrosis
Human	VDR	7421	vitamin D (1,25- dihydroxyvitamin D3) receptor	GAD, Score=1000, Pubmed Id: 15459215, UMLKSK CUI: C0520474 Title:Pharmacogenetic risk factors for osteonecrosis of the hip among children with leukemia.\|Association:Y\|Conclusion:Because folate-related and vitamin D-receptor genetic variants have been associated with bone and vasculature morbidity, these pharmacogenetic associations likely reflect the interaction of antileukemic medications with germline sensitivity to drug actions, and might identify ALL patients at highest risk to develop osteonecrosis.
Human	TYMS	7298	thymidylate synthetase	GAD, Score=1000, Pubmed Id: 15459215, UMLKSK CUI: C0520474 Title:Pharmacogenetic risk factors for osteonecrosis of the hip among children with leukemia.\|Association:Not Found\|Conclusion:Because folate-related and vitamin D-receptor genetic variants have been associated with bone and vasculature morbidity, these pharmacogenetic associations likely reflect the interaction of antileukemic medications with germline sensitivity to drug actions, and might identify ALL patients at highest risk to develop osteonecrosis.
Human	TP53	7157	tumor protein p53	GENERIF, Score=861, Pubmed Id: 18979157, UMLKSK CUI: C0520474 Results describe the possible involvement of p53 in the osteocyte apoptosis observed in Idiopathic osteonecrosis of the femoral head
Human	SREBF1	6720	sterol regulatory element binding transcription factor 1	GENERIF, Score=1000, Pubmed Id: 19040658, UMLKSK CUI: C0520474 Polymorphism of the SREBF1 gene is associated with the risk of osteonecrosis of the femoral head in the Korean population
Human	PPARG	5468	peroxisome proliferator-activated receptor gamma	GENERIF, Score=1000, Pubmed Id: 18182855, UMLKSK CUI: C0520474 the examined polymorphisms and haplotypes of the PPARgamma gene are unlikely to be associated with susceptibility to osteonecrosis of the femoral head
Human	PON1	5444	paraoxonase 1	GENERIF, Score=1000, Pubmed Id: 17469180, UMLKSK CUI: C0520474 We conclude that individuals with PON1 192QQ genotype may have increased risk for osteonecrosis of the femoral head and cerebral white matter lesions
Human	ABCB1	5243	ATP-binding cassette, sub-family B (MDR/TAP), member 1	GENERIF, Score=1000, Pubmed Id: 14583680, UMLKSK CUI: C0520474 The ABCB1 variant type showed a lower incidence of osteonecrosis of the femoral head GENERIF, Score=827, Pubmed Id: 18696186, UMLKSK CUI: C0520474 in patients with femoral head osteonecrosis, The synergistic index between the ABCB1 and CBP genes was >1.00 (1.99), revealing the presence of an interaction
Human	SERPINE1	5054	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1	GAD, Score=1000, Pubmed Id: 14742985, UMLKSK CUI: C0520474 Title:Relationship between postrenal transplant osteonecrosis of the femoral head and gene polymorphisms related to the coagulation and fibrinolytic systems in Japanese subjects.\|Association:Not Found\|Conclusion:Genotypes of PAI-1 4G/5G and MTHFR C677T or plasma concentrations of PAI-1 Ag and tHcy had no effect on the incidence of ONFH in Japanese subjects, unlike the results of studies performed in white subjects. The effect of genetic background on the pathologic conditions that developed in patients with postrenal transplant ONFH may differ according to race. GAD, Score=833, Pubmed Id: 12438962, UMLKSK CUI: C0520474 Title:Association of plasminogen activator inhibitor-1 genotype with avascular osteonecrosis in steroid-treated renal allograft recipients\|Association:Not Found\|Conclusion:Hypofibrinolysis conferred by the 4G/4G PAI-1 gene variant is a major predisposing factor for AVN in renal transplant patients. The risk is particularly high in obese subjects or patients with persistent hyperparathyroidism. A prospective intervention study of early anticoagulation after renal transplantation is needed to assess whether glucocorticoid-associated AVN can be prevented. GENERIF, Score=861, Pubmed Id: 12438962, UMLKSK CUI: C0520474 a genetic variant of the plasminogen activator inhibitor-1 (PAI-1) determines the risk of avascular osteonecrosis in glucocorticoid-treated patients GENERIF, Score=1000, Pubmed Id: 18285546, UMLKSK CUI: C0520474 PAI-1 polymorphism (rs6092) was associated with risk of osteonecrosis complicating acute lymphoblastic leukemia
Human	NOS3	4846	nitric oxide synthase 3 (endothelial cell)	GENERIF, Score=861, Pubmed Id: 17974890, UMLKSK CUI: C0520474 The T-786C eNOS polymorphism and resultant reduction of nitric oxide production is associated with, and may contribute to, the pathogenesis of idiopathic osteonecrosis of the femoral head GENERIF, Score=861, Pubmed Id: 18829920, UMLKSK CUI: C0520474 Multifocal and unifocal osteonecrosis are similarly associated with thrombophilia, hypofibrinolysis, and the eNOS T-786C polymorphism GENERIF, Score=812, Pubmed Id: 16779830, UMLKSK CUI: C0520474 carrier state of 4a allele in intron 4 might be a genetic risk factor of nontraumatic femoral head osteonecrosis
Human	MTHFR	4524	methylenetetrahydrofolate reductase (NAD(P)H)	GAD, Score=1000, Pubmed Id: 14742985, UMLKSK CUI: C0520474 Title:Relationship between postrenal transplant osteonecrosis of the femoral head and gene polymorphisms related to the coagulation and fibrinolytic systems in Japanese subjects.\|Association:Not Found\|Conclusion:Genotypes of PAI-1 4G/5G and MTHFR C677T or plasma concentrations of PAI-1 Ag and tHcy had no effect on the incidence of ONFH in Japanese subjects, unlike the results of studies performed in white subjects. The effect of genetic background on the pathologic conditions that developed in patients with postrenal transplant ONFH may differ according to race. GENERIF, Score=861, Pubmed Id: 11801474, UMLKSK CUI: C0520474 The 677C-->T mutation of MTHFR was present in 26.1% of adults with idiopathic osteonecrosis of the femur head and appears to have a role in the complex pathophysiology of the disease GENERIF, Score=1000, Pubmed Id: 16549163, UMLKSK CUI: C0520474 No correlation was determined between factor V Leiden, prothrombin G20210A, and Methylenetetrahydrofolate reductase C677T mutations and osteonecrosis in kidney allograft recipients
Human	IL17A	3605	interleukin 17A	GENERIF, Score=1000, Pubmed Id: 18585926, UMLKSK CUI: C0520474 multiple myeloma patients without osteonecrosis of the jaw and control subjects presented similar values of IL-17 serum levels
Human	HIF1A	3091	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	GENERIF, Score=1000, Pubmed Id: 17292638, UMLKSK CUI: C0520474 variations in HIF1alpha may play an important role in the pathogenesis and risk factor for osteonecrosis of the femoral head
Human	GBA	2629	glucosidase, beta, acid	OMIM, Score=1000, UMLKSK CUI: C0520474 Osteonecrosis
Human	F5	2153	coagulation factor V (proaccelerin, labile factor)	GENERIF, Score=1000, Pubmed Id: 16549163, UMLKSK CUI: C0520474 No correlation was determined between factor V Leiden, prothrombin G20210A, and Methylenetetrahydrofolate reductase C677T mutations and osteonecrosis in renal allograft recipients GENERIF, Score=1000, Pubmed Id: 15723247, UMLKSK CUI: C0520474 The purpose of this study was to examine the association between osteonecrosis of the knee and abnormalities in the thrombotic pathway in the form of factor V Leiden and the prothrombin 20210A gene mutation
Human	CYP2C8	1558	cytochrome P450, family 2, subfamily C, polypeptide 8	GENERIF, Score=861, Pubmed Id: 18594024, UMLKSK CUI: C0520474 Individuals homozygous for the T allele had an increased likelihood of developing osteonecrosis of the jaw (odds ratio 12.75, 95% confidence interval 3.7-43.5)
Human	CTNNB1	1499	catenin (cadherin-associated protein), beta 1, 88kDa	GENERIF, Score=827, Pubmed Id: 18288545, UMLKSK CUI: C0520474 Data suggest the Wnt/beta-catenin signaling pathway may be associated with ethanol-induced osteonecrosis
Human	CREBBP	1387	CREB binding protein	GENERIF, Score=827, Pubmed Id: 18696186, UMLKSK CUI: C0520474 in patients with femoral head osteonecrosis, The synergistic index between the ABCB1 and CBP genes was >1.00 (1.99), revealing the presence of an interaction GENERIF, Score=827, Pubmed Id: 17704997, UMLKSK CUI: C0520474 results indicate that the genetic polymorphism of the CBP, which is one of the essential factors exerting the biological effects of glucocorticoids, may affect susceptibility to steroid-induced osteonecrosis in patients after renal transplantation
Human	BMP6	654	bone morphogenetic protein 6	GENERIF, Score=827, Pubmed Id: 15784727, UMLKSK CUI: C0520474 several single nucleotide polymorphisms in bone morphogenic protein 6, annexin A2, and klotho were associated with sickle cell osteonecrosis
Human	ANXA2	302	annexin A2	GAD, Score=1000, Pubmed Id: 15784727, UMLKSK CUI: C0520474 Title:Association of klotho, bone morphogenic protein 6, and annexin A2 polymorphisms with sickle cell osteonecrosis.\|Association:Not Found\|Conclusion:These genes are important in bone morphology, metabolism and vascular disease. Our results may provide insight into the pathogenesis of osteonecrosis in sickle cell disease, help identify individuals who are at high risk for osteonecrosis, and thus allow earlier and more effective therapeutic intervention. GENERIF, Score=827, Pubmed Id: 15784727, UMLKSK CUI: C0520474 several single nucleotide polymorphisms in bone morphogenic protein 6, annexin A2, and klotho were associated with sickle cell osteonecrosis
Human	ALDH2	217	aldehyde dehydrogenase 2 family (mitochondrial)	GAD, Score=1000, Pubmed Id: 14768474, UMLKSK CUI: C0520474 Title:A case-control study of association between life-style, alcohol dehydrogenase 2 and aldehyde dehydrogenase 2 genotype and idiopathic osteonecrosis of the femoral head.\|Association:Not Found\|Conclusion:The reason for the insignificant multivariate OR of ALDH2(1/1) may be due to the strong confounding of alcohol consumption on the association between ALDH2 genotype and ION. For females, the small sample size made it impossible to produce any meaningful univariate analysis.
Human	ADH1B	125	alcohol dehydrogenase 1B (class I), beta polypeptide	GAD, Score=1000, Pubmed Id: 14768474, UMLKSK CUI: C0520474 Title:A case-control study of association between life-style, alcohol dehydrogenase 2 and aldehyde dehydrogenase 2 genotype and idiopathic osteonecrosis of the femoral head.\|Association:Not Found\|Conclusion:The reason for the insignificant multivariate OR of ALDH2(1/1) may be due to the strong confounding of alcohol consumption on the association between ALDH2 genotype and ION. For females, the small sample size made it impossible to produce any meaningful univariate analysis.

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0520474	Aseptic Necrosis of Bone	0		self

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