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 - Malignant neoplasm of mouth

Debug Stats

### Total Build Time: 40 ms 42.529 KB
CONCEPT_NAME gt=2 ms Completed: 2 ms rowSize= 352 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 1.087 KB
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= 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=30 ms Completed: 30 ms rowSize= 39.764 KB
CONCEPT_XREFS gt=4 ms Completed: 4 ms rowSize= 1.161 KB
CONCEPT_ANCILLARY gt=1 ms Completed: 1 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Malignant neoplasm of mouth C0153381

Definition (1)

Oral cancer can form in any part of the mouth or throat. Most oral cancers begin in the tongue and in the floor of the mouth. Anyone can get oral cancer, but the risk is higher if you are male, over age 40, use tobacco or alcohol or have a history of head or neck cancer. Frequent sun exposure is also a risk for lip cancer.

Symptoms of oral cancer include

White or red patches in your mouth
A mouth sore that won't heal
Bleeding in your mouth
Loose teeth
Problems or pain with swallowing
A lump in your neck
An earache

Oral cancer treatments may include surgery, radiation therapy or chemotherapy. Some patients have a combination of treatments.

NIH: National Cancer Institute

Genes (72)

Species:

human : 72

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Current 1

Species	Gene	GeneId	Gene Name	Evidence
Human	ORAOV1	220064	oral cancer overexpressed 1	GENERIF, Score=734, Pubmed Id: 12172009, UMLKSK CUI: C0153381 High-resolution mapping of the 11q13 amplicon and identification of a gene that is amplified and overexpressed in oral cancer cells
Human	WWOX	51741	WW domain containing oxidoreductase	GENERIF, Score=1000, Pubmed Id: 16152610, UMLKSK CUI: C0153381 WWOX gene is frequently altered in oral squamous cell carcinomas and may contribute to the carcinogenesis processes in oral cancer
Human	POSTN	10631	periostin, osteoblast specific factor	GENERIF, Score=1000, Pubmed Id: 17060937, UMLKSK CUI: C0153381 Periostin is frequently overexpressed and enhances invasion and angiogenesis in oral cancer
Human	XRCC4	7518	X-ray repair complementing defective repair in Chinese hamster cells 4	GENERIF, Score=734, Pubmed Id: 18410587, UMLKSK CUI: C0153381 combined XRCCs 1-4 polymorphisms associated with oral cancer risk GENERIF, Score=1000, Pubmed Id: 18630527, UMLKSK CUI: C0153381 Results provide the first evidence that the heterozygous A allele of the XRCC4 codon 247 may be associated with the development of oral cancer
Human	XRCC3	7517	X-ray repair complementing defective repair in Chinese hamster cells 3	GENERIF, Score=734, Pubmed Id: 18410587, UMLKSK CUI: C0153381 combined XRCCs 1-4 polymorphisms associated with oral cancer risk GAD, Score=1000, Pubmed Id: 16373199, UMLKSK CUI: C0153381 Title:Polymorphism in DNA repair genes and oral squamous cell carcinoma in Thailand\|Association:Not Found\|Conclusion:
Human	XRCC2	7516	X-ray repair complementing defective repair in Chinese hamster cells 2	GENERIF, Score=734, Pubmed Id: 18410587, UMLKSK CUI: C0153381 combined XRCCs 1-4 polymorphisms associated with oral cancer risk
Human	XRCC1	7515	X-ray repair complementing defective repair in Chinese hamster cells 1	GAD, Score=1000, Pubmed Id: 16373199, UMLKSK CUI: C0153381 Title:Polymorphism in DNA repair genes and oral squamous cell carcinoma in Thailand\|Association:Not Found\|Conclusion: GENERIF, Score=734, Pubmed Id: 18410587, UMLKSK CUI: C0153381 combined XRCCs 1-4 polymorphisms associated with oral cancer risk
Human	XPC	7508	xeroderma pigmentosum, complementation group C	GAD, Score=1000, Pubmed Id: 16373199, UMLKSK CUI: C0153381 Title:Polymorphism in DNA repair genes and oral squamous cell carcinoma in Thailand\|Association:Not Found\|Conclusion: GAD, Score=1000, Pubmed Id: 16393248, UMLKSK CUI: C0153381 Title:Gene-environment interaction involved in oral carcinogenesis: molecular epidemiological study formetabolic and DNA repair gene polymorphisms\|Association:Not Found\|Conclusion:
Human	XPA	7507	xeroderma pigmentosum, complementation group A	GAD, Score=1000, Pubmed Id: 16393248, UMLKSK CUI: C0153381 Title:Gene-environment interaction involved in oral carcinogenesis: molecular epidemiological study formetabolic and DNA repair gene polymorphisms\|Association:Not Found\|Conclusion:
Human	VHL	7428	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	GENERIF, Score=1000, Pubmed Id: 12684640, UMLKSK CUI: C0153381 Methylation inactivation of vhl is associated with oral cancer
Human	VEGFA	7422	vascular endothelial growth factor A	GENERIF, Score=1000, Pubmed Id: 15788677, UMLKSK CUI: C0153381 Dual high expression of stromelysin 3 and VEGF is associated with progression from precancerous to cancerous state in oral cancers GAD, Score=1000, Pubmed Id: 15878754, UMLKSK CUI: C0153381 Title:Vascular endothelial growth factor gene-460 C/T polymorphism is a biomarker for oral cancer\|Association:Y\|Conclusion:There is no gender difference in this VEGF gene polymorphism. Therefore, the BstUI polymorphism of the VEGF gene is a suitable genetic marker of oral cancer. GENERIF, Score=913, Pubmed Id: 15826815, UMLKSK CUI: C0153381 High production of VEGF and low production of IL-18 by polymorphonuclear leukocytes of cancer patients may promote neoangiogenesis and may be important for benign tumour cells to acquire metastatic phenotype in the early stage of oral cavity cancer
Human	TP73	7161	tumor protein p73	GENERIF, Score=861, Pubmed Id: 18701437, UMLKSK CUI: C0153381 findings suggest that the combined variants of p53 and p73 significantly increase the risk of HPV16-associated oral cancer, especially among never-smokers
Human	TP53	7157	tumor protein p53	GENERIF, Score=734, Pubmed Id: 17595776, UMLKSK CUI: C0153381 The association of p53 codon 72 and CDKN1A codon 31 polymorphisms with oral cancer risk in a Taiwanese population were investigated GENERIF, Score=913, Pubmed Id: 14719105, UMLKSK CUI: C0153381 p53 mutations are common among oral cavity cancers in the Brazilian population GENERIF, Score=861, Pubmed Id: 18701437, UMLKSK CUI: C0153381 findings suggest that the combined variants of p53 and p73 significantly increase the risk of HPV16-associated oral cancer, especially among never-smokers GAD, Score=1000, Pubmed Id: 14507241, UMLKSK CUI: C0153381 Title:\|Association:Not Found\|Conclusion:Not Found GENERIF, Score=734, Pubmed Id: 17306604, UMLKSK CUI: C0153381 The Pro/Pro genotype of the TP53 codon72 polymorphism increases oral cancer risk in non-smokers and worsens their prognosis GENERIF, Score=734, Pubmed Id: 15941720, UMLKSK CUI: C0153381 in oral cancer cells the Ca(2+)- and cell cycle-dependent p53-S100A2 interaction might modulate proliferation
Human	TNF	7124	tumor necrosis factor	GAD, Score=1000, Pubmed Id: 11808761, UMLKSK CUI: C0153381 Title:Association between genetic polymorphism of tumor necrosis factor-alpha and risk of oral submucous fibrosis a pre-cancerous condition of oral cancer.\|Association:Y\|Conclusion:The finding may imply a multifunctional etiological factor of TNF-alpha in OSF pathogenesis.
Human	SNAI1	6615	snail family zinc finger 1	GENERIF, Score=734, Pubmed Id: 18234959, UMLKSK CUI: C0153381 These data show that Snail functions as a molecular mediator of TGF-beta1-regulated MMP-9 expression by increasing Ets-1 and thereby contributing to oral cancer progression
Human	CXCL12	6387	chemokine (C-X-C motif) ligand 12	GENERIF, Score=1000, Pubmed Id: 18383856, UMLKSK CUI: C0153381 The G801A polymorphism of the SDF-1 gene is associated with advanced stages of oral cancer
Human	SDC1	6382	syndecan 1	GENERIF, Score=734, Pubmed Id: 19020713, UMLKSK CUI: C0153381 syndecan-1 directly contributes to the growth and invasive ability of oral cancer cells
Human	S100A2	6273	S100 calcium binding protein A2	GENERIF, Score=734, Pubmed Id: 15941720, UMLKSK CUI: C0153381 in oral cancer cells the Ca(2+)- and cell cycle-dependent p53-S100A2 interaction might modulate proliferation
Human	PTH1R	5745	parathyroid hormone 1 receptor	GENERIF, Score=1000, Pubmed Id: 18261460, UMLKSK CUI: C0153381 These data indicate that PTHrP contributes to the malignancy of oral cancers downstream of EGFR signaling, and may thus provide a therapeutic target for oral cancer
Human	PTGS2	5743	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	GENERIF, Score=1000, Pubmed Id: 18356024, UMLKSK CUI: C0153381 expression in oral cancer was found to be independent of grade of tumor and stage of disease GENERIF, Score=1000, Pubmed Id: 16822500, UMLKSK CUI: C0153381 Cytoplasmic expression as well as nuclear translocation of PTGS2 increased with progression of oral cancer GENERIF, Score=1000, Pubmed Id: 17354234, UMLKSK CUI: C0153381 Study demonstrates correlation between over expression of NF-kappaB and COX-2 in early precancerous stages of development of oral cancer and sustained elevation down the tumorigenic pathway
Human	PLAU	5328	plasminogen activator, urokinase	GAD, Score=1000, Pubmed Id: 15356878, UMLKSK CUI: C0153381 Title:Urokinase gene 3'-UTR T/C polymorphism is associated with oral cancer\|Association:Y\|Conclusion:Therefore, the urokinase gene 3'-UTR "T" allele is associated with oral cancer and may play a role in oral cancer formation. However, we did not find the relationship between tumor progression and this polymorphism. GENERIF, Score=1000, Pubmed Id: 15356878, UMLKSK CUI: C0153381 The urokinase gene 3'-UTR "T" allele is associated with oral cancer in humans, and may play a role in oral cancer formation
Human	PCBP2	5094	poly(rC) binding protein 2	GENERIF, Score=1000, Pubmed Id: 17219427, UMLKSK CUI: C0153381 Downregulation of HnRNP E2 is associated with oral cancer
Human	OAZ1	4946	ornithine decarboxylase antizyme 1	GENERIF, Score=829, Pubmed Id: 17630775, UMLKSK CUI: C0153381 Ornithine decarboxylase antizyme 1 enhances the ability of UM1 human oral squamous cancer cells to repair DNA double-strand breaks by the nonhomologous end-joining pathway
Human	NFKB1	4790	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	GAD, Score=1000, Pubmed Id: 16387424, UMLKSK CUI: C0153381 Title:\|Association:Not Found\|Conclusion:Not Found GENERIF, Score=1000, Pubmed Id: 16822500, UMLKSK CUI: C0153381 Cytoplasmic expression as well as nuclear translocation of NF-kappaB increased with progression of oral cancer
Human	MYC	4609	v-myc avian myelocytomatosis viral oncogene homolog	GENERIF, Score=734, Pubmed Id: 14672406, UMLKSK CUI: C0153381 Data suggest that cyclin dependent kinase 4 is involved in the development of tobacco-mediated oral carcinogenesis, and that c-myc expression is absent in normal and high in later stages of oral cancer development

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0153381	Malignant neoplasm of mouth	0		self

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